GutPredict Logo GutPredict
HomeGut Health check-upGut microbiome libraryReferenceAbout us
FEEL BETTER, LIVE BETTER - BEGIN WITH YOUR GUT. BECAUSE A HEALTHY GUT IS THE FOUNDATION FOR YOUR WHOLE BODY'S HEALTH
FROM YOUR ENERGY TO YOUR MOOD. WE HELP YOUR GUT'S HIDDEN POWER
More information call us
02 564 7000 EXT.71467
Reference Database

  1. Abrignani, V., Salvo, A., Pacinella, G., & Tuttolomondo, A. (2024). The Mediterranean diet, its microbiome connections, and cardiovascular health: A narrative review. International Journal of Molecular Sciences, 25(9), 4942. https://doi.org/10.3390/ijms25094942
  2. Adams, J. B., Johansen, L. J., Powell, L. D., Quig, D., & Rubin, R. A. (2011). Gastrointestinal flora and gastrointestinal status in children with autism—comparisons to typical children and correlation with autism severity. BMC Gastroenterology, 11, 22. https://doi.org/10.1186/1471-230X-11-22
  3. Akkermansia muciniphila and improved metabolic health during a dietary intervention. (2016). Gut, 65(3), 426–436. Retrieved August 18, 2025, from https://gut.bmj.com/content/65/3/426
  4. Al Bander, Z., Nitert, M. D., Mousa, A., & Naderpoor, N. (2020). The gut microbiota and inflammation: An overview. International Journal of Environmental Research and Public Health, 17(20), 7618. https://doi.org/10.3390/ijerph17207618
  5. Al-Obaide, M. A. I., Singh, R., Datta, P., Rewers-Felkins, K. A., Salguero, M. V., Al-Obaidi, I., Kottapalli, K. R., & Vasylyeva, T. L. (2017). Gut microbiota-dependent trimethylamine-N-oxide and serum biomarkers in patients with T2DM and advanced chronic kidney disease. Journal of Clinical Medicine, 6(9), 86. https://doi.org/10.3390/jcm6090086
  6. Alexander, J. L., Posma, J. M., Scott, A., et al. (2023). Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer. Microbiome, 11, 100. https://doi.org/10.1186/s40168-023-01518-w
  7. Allen-Vercoe, E., Daigneault, M., White, A., Panaccione, R., Duncan, S. H., Flint, H. J., … Lawson, P. A. (2012). Anaerostipes hadrus comb. nov., a dominant species within the human colonic microbiota; reclassification of Eubacterium hadrum Moore et al. 1976. Anaerobe, 18(5), 523–529. https://doi.org/10.1016/j.anaerobe.2012.09.002
  8. Almeida-Santos, A. C., Novais, C., Peixe, L., & Freitas, A. R. (2021). Enterococcus spp. as a producer and target of bacteriocins: A double-edged sword in the antimicrobial resistance crisis context. Antibiotics, 10(10), 1215. https://doi.org/10.3390/antibiotics10101215
  9. Alpha-Ketoglutarate in Low-Protein Diets for Growing Pigs: Effects on Cecal Microbial Communities and Parameters of Microbial Metabolism - Frontiers, accessed July 22, 2025, https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.01057/full
  10. Anania, C., Di Marino, V. P., Olivero, F., De Canditiis, D., Brindisi, G., Iannilli, F., … Duse, M. (2021). Treatment with a probiotic mixture containing Bifidobacterium animalis subsp. lactis BB12 and Enterococcus faecium L3 for the prevention of allergic rhinitis symptoms in children: A randomized controlled trial. Nutrients, 13(4), 1315. https://doi.org/10.3390/nu13041315
  11. Ang, Q. Y., Alexander, M., Newman, J. C., Tian, Y., Cai, J., Upadhyay, V., Turnbaugh, J. A., Verdin, E., Hall, K. D., Leibel, R. L., Ravussin, E., Rosenbaum, M., Patterson, A. D., & Turnbaugh, P. J. (2020). Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells. Cell, 181(6), 1263–1275.e16. https://doi.org/10.1016/j.cell.2020.04.027
  12. Ang, S. C., Lin, C. H., Sung, C. T., & Fang, J. Y. (2014). Antibacterial activities of bacteriocins: Application in foods and pharmaceuticals. Frontiers in Microbiology, 5, 241. https://doi.org/10.3389/fmicb.2014.00241
  13. Arias, N., Arboleya, S., Allison, J., Kaliszewska, A., Higarza, S. G., Gueimonde, M., & Arias, J. L. (2020). The relationship between choline bioavailability from diet, intestinal microbiota composition, and its modulation of human diseases. Nutrients, 12(8), 2340. https://doi.org/10.3390/nu12082340
  14. Arrieta, M. C., Stiemsma, L. T., Amenyogbe, N., Brown, E. M., & Finlay, B. (2014). The intestinal microbiome in early life: health and disease. Frontiers in immunology, 5, 427. https://doi.org/10.3389/fimmu.2014.00427
  15. Ascher, S., & Reinhardt, C. (2018). The gut microbiota: An emerging risk factor for cardiovascular and cerebrovascular disease. European Journal of Immunology, 48(4), 564–575. https://doi.org/10.1002/eji.201646879
  16. Azis, L., Lukman, S., Chareonsirisuthigul, T., & Charoenkiatkul, S. (2021). The correlations between gut microbiota of Muslim Thai lactating women and their dietary intake and gut microbiota of breastfed infants. Malaysian Journal of Nutrition, 27(3), 461–471. https://doi.org/10.31246/mjn-2021-0019
  17. Bäckhed, F., Normark, S., Schweda, E. K., Oscarson, S., & Richter-Dahlfors, A. (2003). Structural requirements for TLR4-mediated LPS signalling: A biological role for LPS modifications. Microbes and Infection, 5(12), 1057–1063. https://doi.org/10.1016/s1286-4579(03)00207-7
  18. Balakrishnan, B., Selvaraju, V., Chen, J., Ayine, P., Yang, L., Ramesh Babu, J., Geetha, T., & Taneja, V. (2021). Ethnic variability associating gut and oral microbiome with obesity in children. Gut Microbes. https://doi.org/10.1080/19490976.2021.1882926
  19. Baños, A., Ariza, J. J., Nuñez, C., Gil-Martínez, L., García-López, J. D., Martínez-Bueno, M., & Valdivia, E. (2019).
  20. Effects of Enterococcus faecalis UGRA10 and the enterocin AS-48 against the fish pathogen Lactococcus garvieae. Studies in vitro and in vivo. Food microbiology, 77, 69–77. https://doi.org/10.1016/j.fm.2018.08.002
  21. Barber, C., Mego, M., Sabater, C., Vallejo, F., Bendezu, R. A., Masihy, M., Guarner, F., Espín, J. C., Margolles, A., & Azpiroz, F. (2021). Differential Effects of Western and Mediterranean-Type Diets on Gut Microbiota: A Metagenomics and Metabolomics Approach. Nutrients, 13(8), 2638. https://doi.org/10.3390/nu13082638
  22. Batta, V. K., Rao, S. C., & Patole, S. K. (2023). Bifidobacterium infantis as a probiotic in preterm infants: A systematic review and meta-analysis. Pediatric Research. https://doi.org/10.1038/s41390-023-02716-w
  23. Bell, H. N., Rebernick, R. J., Goyert, J., Singhal, R., Kuljanin, M., Kerk, S. A., Huang, W., Das, N. K., Andren, A., Solanki, S., Miller, S. L., Todd, P. K., Fearon, E. R., Lyssiotis, C. A., Gygi, S. P., Mancias, J. D., & Shah, Y. M. (2022). Reuterin in the healthy gut microbiome suppresses colorectal cancer growth through altering redox balance. Cancer Cell, 40(2), 185–200.e6. https://doi.org/10.1016/j.ccell.2021.12.001
  24. Beller, A., Kruglov, A., Durek, P., von Goetze, V., Hoffmann, U., Maier, R., Heiking, K., Siegmund, B., Heinz, G. A., Mashreghi, M.-F., Radbruch, A., & Chang, H.-D. (2019). P104 Anaeroplasma, a potential anti-inflammatory probiotic for the treatment of chronic intestinal inflammation [Abstract]. Annals of the Rheumatic Diseases, 78(Suppl 1), A45.2. https://doi.org/10.1136/annrheumdis-2018-EWRR2019.92
  25. Bernbom, N., Licht, T. R., Brogren, C. H., Jelle, B., Johansen, A. H., Badiola, I., … Nørrung, B. (2006). Effects of Lactococcus lactis on composition of intestinal microbiota: Role of nisin. Applied and Environmental Microbiology, 72(1), 239–244. https://doi.org/10.1128/AEM.72.1.239-244.2006
  26. Bessis, S., Amadou, T., Dubourg, G., Raoult, D., & Fournier, P.-E. (2016). “Bariatricus massiliensis” as a new bacterial species from human gut microbiota. New Microbes and New Infections, 12, 54–55. https://doi.org/10.1016/j.nmni.2016.04.003
  27. Bi, D., Zhu, Y., Gao, Y., Li, H., Zhu, X., Wei, R., Xie, R., Cai, C., Wei, Q., & Qin, H. (2022). Profiling Fusobacterium infection at high taxonomic resolution reveals lineage-specific correlations in colorectal cancer. Nature Communications, 13(1), 3336. https://doi.org/10.1038/s41467-022-30957-6
  28. Bifidobacteria and butyrate-producing colon bacteria: Importance and strategies for their stimulation in the human gut. (2016). Frontiers in Microbiology. Retrieved July 22, 2025, from https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2016.00979/full
  29. Binda, C., Lopetuso, L. R., Rizzatti, G., Gibiino, G., Cennamo, V., & Gasbarrini, A. (2018). Actinobacteria: A relevant minority for the maintenance of gut homeostasis.Digestive and Liver Disease: Official Journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver, 50(5), 421–428. https://doi.org/10.1016/j.dld.2018.02.012
  30. Birkeland, E., Gharagozlian, S., Valeur, J., & Aas, A. M. (2023). Short-chain fatty acids as a link between diet and cardiometabolic risk: A narrative review. Lipids in Health and Disease, 22(1), 40. https://doi.org/10.1186/s12944-023-01803-5
  31. Bohn, B., & Mueller, N. T. (2024). Gut check: Sugar, fiber, and infant microbiota. The Journal of Nutrition, 154(1), 7–9. https://doi.org/10.1016/j.tjnut.2023.11.008
  32. Bolte, L. A., Vich Vila, A., Imhann, F., Collij, V., Gacesa, R., Peters, V., … Weersma, R. K. (2021). Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome. Gut, 70(7), 1287–1298. https://doi.org/10.1136/gutjnl-2020-322670
  33. Bordugo, A., Salvetti, E., Rodella, G., Piazza, M., Dianin, A., Amoruso, A., … Felis, G. E. (2021). Assessing gut microbiota in an infant with congenital propionic acidemia before and after probiotic supplementation. Microorganisms, 9(12), 2599. https://doi.org/10.3390/microorganisms9122599
  34. Braga, J. D., Thongngam, M., & Kumrungsee, T. (2024). Gamma-aminobutyric acid as a potential postbiotic mediator in the gut–brain axis. npj Science of Food, 8, 16. https://doi.org/10.1038/s41538-024-00253-2
  35. Brenner, D. M., & Chey, W. D. (2009). Bifidobacterium infantis 35624: A novel probiotic for the treatment of irritable bowel syndrome. Reviews in Gastroenterological Disorders, 9(1), 7–15.
  36. Bui, T. P. N., Mannerås-Holm, L., Puschmann, R., Wu, H., Troise, A. D., Nijsse, B., Boeren, S., Bäckhed, F., Fiedler, D., & de Vos, W. M. (2021). Conversion of dietary inositol into propionate and acetate by commensal Anaerostipes associates with host health. Nature Communications, 12(1), 4798. https://doi.org/10.1038/s41467-021-25081-w
  37. Buret, A. G., Motta, J. P., Allain, T., Ferraz, J., & Wallace, J. L. (2019). Pathobiont release from dysbiotic gut microbiota biofilms in intestinal inflammatory diseases: A role for iron? Journal of Biomedical Science, 26(1), 57. https://doi.org/10.1186/s12929-018-0495-4
  38. Burrichter, A. G., Dörr, S., Bergmann, P., Haiß, S., Keller, A., Fournier, C., Franchini, P., Isono, E., & Schleheck, D. (2021). Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia. BMC Microbiology, 21(1), 340. https://doi.org/10.1186/s12866-021-02386-w
  39. Cai, S., Yang, Y., Kong, Y., Guo, Q., Xu, Y., Xing, P., … Mao, W. (2022). Gut bacteria Erysipelatoclostridium and its related metabolite ptilosteroid A could predict radiation-induced intestinal injury. Frontiers in Public Health, 10, 862598. https://doi.org/10.3389/fpubh.2022.862598
  40. Cai, Y. Y., Huang, F. Q., Lao, X., … Xu, J. (2022). Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis. NPJ Biofilms and Microbiomes, 8, 11. https://doi.org/10.1038/s41522-022-00273-4
  41. Canfora, E. E., Jocken, J. W., & Blaak, E. E. (2015). Short-chain fatty acids in control of body weight and insulin sensitivity. Nature reviews. Endocrinology, 11(10), 577–591. https://doi.org/10.1038/nrendo.2015.128
  42. Chang, C. J., Lin, T. L., Tsai, Y. L., Wu, T. R., Lai, W. F., Lu, C. C., & Lai, H. C. (2019). Next generation probiotics in disease amelioration. Journal of Food and Drug Analysis, 27(3), 615–622. https://doi.org/10.1016/j.jfda.2018.12.011
  43. Chang, S. C., Shen, M. H., Liu, C. Y., Pu, C. M., Hu, J. M., & Huang, C. J. (2020). A gut butyrate-producing bacterium Butyricicoccus pullicaecorum regulates short-chain fatty acid transporter and receptor to reduce the progression of 1,2-dimethylhydrazine-associated colorectal cancer. Oncology Letters, 20(6), 327. https://doi.org/10.3892/ol.2020.12190
  44. Chaput, N., Lepage, P., Coutzac, C., Soularue, E., Le Roux, K., Monot, C., Boselli, L., Routier, E., Cassard, L., Collins, M., Vaysse, T., Marthey, L., Eggermont, A., Asvatourian, V., Lanoy, E., Mateus, C., Robert, C., & Carbonnel, F. (2019). Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab. Annals of Oncology, 30(12), 2012. https://doi.org/10.1093/annonc/mdz224
  45. Charoenthanadhol, T., Wirasorn, K., Sookprasert, A., & Chindaprasert, J. (2025). Alteration of gut microbiota in patients with advanced hepatocellular carcinoma. Journal of Clinical Oncology, 43(4_suppl), Abstract 641. https://doi.org/10.1200/JCO.2025.43.4_suppl.641
  46. Chen, J., & Vitetta, L. (2020). Gut microbiota metabolites in NAFLD pathogenesis and therapeutic implications. International Journal of Molecular Sciences, 21(15), 5214. https://doi.org/10.3390/ijms21155214
  47. Chen, J., Chia, N., Kalari, K. R., Yao, J. Z., Novotna, M., Paz Soldan, M. M., Luckey, D. H., Marietta, E. V., Jeraldo, P. R., Chen, X., Weinshenker, B. G., Rodriguez, M., Kantarci, O. H., Nelson, H., Murray, J. A., & Mangalam, A. K. (2016). Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls. Scientific Reports, 6, 28484. https://doi.org/10.1038/srep28484
  48. Chen, Y.-R., Jing, Q.-L., Chen, F.-L., Zheng, H., Chen, L.-D., & Yang, Z.-C. (2021). Desulfovibrio is not always associated with adverse health effects in the Guangdong Gut Microbiome Project. PeerJ, 9, e12033. https://doi.org/10.7717/peerj.12033
  49. Chen, Y.-R., Zhou, L.-Z., Fang, S.-T., Long, H.-Y., Chen, J.-Y., & Zhang, G.-X. (2019). Isolation of Desulfovibrio spp. from human gut microbiota using a next‐generation sequencing-directed culture method. Letters in Applied Microbiology, 68(6), 553–561. https://doi.org/10.1111/lam.13149
  50. Cheng, J., Hu, J., Geng, F., & Nie, S. (2022). Bacteroides utilization for dietary polysaccharides and their beneficial effects on gut health. Food Science and Human Wellness, 11(3), 735–742. https://doi.org/10.1016/j.fshw.2022.04.002
  51. Cheung, M. K., Yue, G. G. L., Lauw, S., Li, C. S. Y., Yung, M. Y., Ng, S. C., … Lau, C. B. S. (2022). Alterations in gut microbiota of esophageal squamous cell carcinoma patients. Journal of Gastroenterology and Hepatology, 37(10), 1919–1927. https://doi.org/10.1111/jgh.15941
  52. Chia, L. W., Hornung, B. V. H., Aalvink, S., et al. (2018). Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach. Antonie van Leeuwenhoek, 111, 859–873. https://doi.org/10.1007/s10482-018-1040-x
  53. Chichlowski, M., Shah, N., Wampler, J. L., Wu, S. S., & Vanderhoof, J. A. (2020). Bifidobacterium longum subspecies infantis (B. infantis) in pediatric nutrition: Current state of knowledge. Nutrients, 12(6), 1581. https://doi.org/10.3390/nu12061581
  54. Chimplee, K., Chotinantakul, K., Teerapattarakan, N., Chusri, P., & Okada, S. (2024). Gut microbiota in diabetic kidney disease in Northern Thailand: A preliminary study. Journal of Health Science and Alternative Medicine, 6(3), 116–124. https://doi.org/10.14456/jhsam.2024.16
  55. Cho, G.-S., Ritzmann, F., Eckstein, M., Huch, M., Briviba, K., Behsnilian, D., Neve, H., & Franz, C. M. A. P. (2016). Quantification of Slackia and Eggerthella spp. in human feces and adhesion of representative strains to Caco-2 cells. Frontiers in Microbiology, 7, 658. https://doi.org/10.3389/fmicb.2016.00658
  56. Cho, I., & Blaser, M. J. (2012, April). The human microbiome: At the interface of health and disease. Nature Reviews Genetics. https://doi.org/10.1038/nrg3182
  57. Chotelersak, K., Thamacharoensuk, T., Tanasupawat, S., Nantavisai, K., Taweechotipatr, M., & Puttikamonkul, S. (2016). Preliminary studies of lactic acid bacteria isolated from feces of Thai newborns. Chotmaihet Thangphaet [Journal of the Medical Association of Thailand], 99(Suppl 8), S90–S98.
  58. Chow, J., Tang, H., & Mazmanian, S. K. (2011). Pathobionts of the gastrointestinal microbiota and inflammatory disease. Current Opinion in Immunology, 23(4), 473–480. https://doi.org/10.1016/j.coi.2011.07.010
  59. Chung, W. S. F., Meijerink, M., Zeuner, B., Holck, J., Louis, P., Meyer, A. S., Wells, J. M., Flint, H. J., & Duncan, S. H. (2017). Prebiotic potential of pectin and pectic oligosaccharides to promote anti-inflammatory commensal bacteria in the human colon. FEMS Microbiology Ecology, 93(11). https://doi.org/10.1093/femsec/fix127
  60. Coello, K., Hansen, T. H., Sørensen, N., Munkholm, K., Kessing, L. V., Pedersen, O., & Vinberg, M. (2019). Gut microbiota composition in patients with newly diagnosed bipolar disorder and their unaffected first-degree relatives. Brain, Behavior, and Immunity, 75, 112–118. https://doi.org/10.1016/j.bbi.2018.09.026
  61. Coletto, E., Latousakis, D., Pontifex, M. G., Crost, E. H., Vaux, L., Perez Santamarina, E., Goldson, A., Brion, A., Hajihosseini, M. K., Vauzour, D., Savva, G. M., & Juge, N. (2022). The role of the mucin-glycan foraging Ruminococcus gnavus in the communication between the gut and the brain. Gut Microbes, 14(1), 2073784. https://doi.org/10.1080/19490976.2022.2073784
  62. Companys, J., Gosalbes, M. J., Pla-Pagà, L., Calderón-Pérez, L., Llauradó, E., Pedret, A., Valls, R. M., Jiménez-Hernández, N., Sandoval-Ramirez, B. A., Del Bas, J. M., Caimari, A., Rubió, L., & Solà, R. (2021). Gut microbiota profile and its association with clinical variables and dietary intake in overweight/obese and lean subjects: A cross-sectional study. Nutrients, 13(6), 2032. https://doi.org/10.3390/nu13062032
  63. Coyne, M. J., Béchon, N., Matano, L. M., … Comstock, L. E. (2019). A family of anti-Bacteroidales peptide toxins wide-spread in the human gut microbiota. Nature Communications, 10, 3460. https://doi.org/10.1038/s41467-019-11494-1
  64. Crost, E. H., Coletto, E., Bell, A., & Juge, N. (2023). Ruminococcus gnavus: Friend or foe for human health. FEMS Microbiology Reviews, 47(2), fuad014. https://doi.org/10.1093/femsre/fuad014
  65. Cui, Y., Zhang, L., Wang, X., Yi, Y., Shan, Y., Liu, B., Zhou, Y., & Lü, X. (2022). Roles of intestinal Parabacteroides in human health and diseases. FEMS Microbiology Letters, 369(1). https://doi.org/10.1093/femsle/fnac072
  66. Dahal, R. H., Kim, S., Kim, Y. K., Kim, E. S., & Kim, J. (2023). Insight into gut dysbiosis of patients with inflammatory bowel disease and ischemic colitis. Frontiers in Microbiology, 14, 1174832. https://doi.org/10.3389/fmicb.2023.1174832
  67. Dahl, W. J., Rivero Mendoza, D., & Lambert, J. M. (2020). Diet, nutrients and the microbiome. Progress in Molecular Biology and Translational Science, 171, 237–263. https://doi.org/10.1016/bs.pmbts.2020.04.006
  68. Dai, A., Hoffman, K., Xu, A. A., Gurwara, S., White, D. L., Kanwal, F., … Jiao, L. (2023). The Association between Caffeine Intake and the Colonic MIBD-Ulcerative diseaseosa-Associated Gut Microbiota in Humans—A Preliminary Investigation. Nutrients, 15(7). https://doi.org/10.3390/nu15071747
  69. David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., … Turnbaugh, P. J. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505, 559–563. https://doi.org/10.1038/nature12820
  70. Davin-Regli, A., Lavigne, J.-P., & Pagès, J.-M. (2019). Enterobacter spp.: Update on taxonomy, clinical aspects, and emerging antimicrobial resistance. Clinical Microbiology Reviews, 32(4). https://doi.org/10.1128/CMR.00002-19
  71. Davis-Richardson, A. G., Ardissone, A. N., Dias, R., Simell, V., Leonard, M. T., Kemppainen, K. M., … Triplett, E. W. (2014). Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes. Frontiers in Microbiology, 5, 678. https://doi.org/10.3389/fmicb.2014.00678
  72. De Angelis, M., Piccolo, M., Vannini, L., Siragusa, S., De Giacomo, A., Serrazzanetti, D. I., Cristofori, F., Guerzoni, M. E., Gobbetti, M., & Francavilla, R. (2013). Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS ONE, 8(10), e76993. https://doi.org/10.1371/journal.pone.0076993
  73. De Filippis, F., Ercolini, D. (2018). Microbiome and Diet. In: Haller, D. (eds) The Gut Microbiome in Health and Disease. Springer, Cham. https://doi.org/10.1007/978-3-319-90545-7_6
  74. de Theije, C. G., Wopereis, H., Ramadan, M., van Eijndthoven, T., Lambert, J., Knol, J., Garssen, J., Kraneveld, A. D., & Oozeer, R. (2014). Altered gut microbiota and activity in a murine model of autism spectrum disorders. Brain, Behavior, and Immunity, 37, 197–206. https://doi.org/10.1016/j.bbi.2013.11.012
  75. De Vadder, F., Kovatcheva-Datchary, P., Zitoun, C., Duchampt, A., Bäckhed, F., & Mithieux, G. (2016). Microbiota-produced succinate improves glucose homeostasis via intestinal gluconeogenesis. Cell Metabolism, 24(1), 151–157. https://doi.org/10.1016/j.cmet.2016.06.013
  76. de Vos, W. M., Tilg, H., Van Hul, M., & Cani, P. D. (2022). Gut microbiome and health: Mechanistic insights. Gut, 71(5), 1020–1032. https://doi.org/10.1136/gutjnl-2021-326789
  77. Deleu, S., Machiels, K., Raes, J., Verbeke, K., & Vermeire, S. (2021). Short chain fatty acids and its producing organisms: An overlooked therapy for inflammatory bowel disease?. EBioMedicine, 66, 103293. https://doi.org/10.1016/j.ebiom.2021.103293
  78. Dempsey, E., & Corr, S. C. (2022). Lactobacillus spp. for gastrointestinal health: Current and future perspectives. Frontiers in Immunology, 13, 840245. https://doi.org/10.3389/fimmu.2022.840245
  79. Deng, M., Wu, X., Duan, X., Xu, J., Yang, X., Sheng, X., Lou, P., Shao, C., Lv, C., & Yu, Z. (2021). Lactobacillus paracasei L9 improves colitis by expanding butyrate-producing bacteria that inhibit the IL-6/STAT3 signaling pathway. Food & Function, 12(21), 10700–10713. https://doi.org/10.1039/d1fo02077c
  80. Dhakan, D. B., Maji, A., Sharma, A. K., Saxena, R., Pulikkan, J., Grace, T., Gomez, A., Scaria, J., Amato, K. R., & Sharma, V. K. (2019). The unique composition of Indian gut microbiome, gene catalogue, and associated fecal metabolome deciphered using multi-omics approaches. GigaScience, 8(3), giz004. https://doi.org/10.1093/gigascience/giz004Diet dictates gut bacteria. (2011). Nature, 477, 134. https://doi.org/10.1038/477134d
  81. Dissayabutra, T., Chuaypen, N., Somnark, P., et al. (2025). Characterization of gut dysbiosis and intestinal barrier dysfunction in patients with metabolic dysfunction-associated steatotic liver disease and chronic kidney disease: A comparative study. Scientific Reports, 15, 15481. https://doi.org/10.1038/s41598-025-00237-6
  82. Dominguez Céspedes, L., & Céspedes Fonseca, Y. M. (2022). Antimicrobial susceptibility of Citrobacter koseri isolated on clinical samples of hospitalized patients. Journal of Microbiology & Experimentation, 10(2), 54–57. https://doi.org/10.15406/jmen.2022.10.00353
  83. Dong, X., Guthrie, B. G. H., Alexander, M., Noecker, C., Ramirez, L., Glasser, N. R., Turnbaugh, P. J., & Balskus, E. P. (2022). Genetic manipulation of the human gut bacterium Eggerthella lenta reveals a widespread family of transcriptional regulators. Nature Communications, 13(1), 7624. https://doi.org/10.1038/s41467-022-33576-3
  84. Duvallet, C., Gibbons, S. M., Gurry, T., Irizarry, R. A., & Alm, E. J. (2017). Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nature Communications, 8(1), 1784. https://doi.org/10.1038/s41467-017-01973-8
  85. El Hage, R., Hernandez-Sanabria, E., Calatayud Arroyo, M., Props, R., & Van de Wiele, T. (2019). Propionate-producing consortium restores antibiotic-induced dysbiosis in a dynamic in vitro model of the human intestinal microbial ecosystem. Frontiers in Microbiology, 10, 1206. https://doi.org/10.3389/fmicb.2019.01206
  86. Engels, C., Ruscheweyh, H. J., Beerenwinkel, N., Lacroix, C., & Schwab, C. (2016). The common gut microbe Eubacterium hallii also contributes to intestinal propionate formation. Frontiers in Microbiology, 7, 713. https://doi.org/10.3389/fmicb.2016.00713
  87. Eribo, O. A., du Plessis, N., & Chegou, N. N. (2022). The intestinal commensal, Bacteroides fragilis, modulates host responses to viral infection and therapy: Lessons for exploration during Mycobacterium tuberculosis infection. Infection and Immunity. American Society for Microbiology. https://doi.org/10.1128/IAI.00321-21
  88. Ezeji, J. C., Sarikonda, D. K., Hopperton, A., Erkkila, H. L., Cohen, D. E., Martinez, S. P., Cominelli, F., Kuwahara, T., Dichosa, A. E. K., Good, C. E., Jacobs, M. R., Khoretonenko, M., Veloo, A., & Rodriguez-Palacios, A. (2021). Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health. Gut Microbes, 13(1), 1922241. https://doi.org/10.1080/19490976.2021.1922241
  89. Fabersani, E., Portune, K., Campillo, I., López-Almela, I., la Paz, S. M., Romaní-Pérez, M., Benítez-Páez, A., & Sanz, Y. (2021). Bacteroides uniformis CECT 7771 alleviates inflammation within the gut-adipose tissue axis involving TLR5 signaling in obese mice. Scientific Reports, 11, 11788. https://doi.org/10.1038/s41598-021-90888-y
  90. Fan, Y., & Pedersen, O. (2021, January 1). Gut microbiota in human metabolic health and disease. Nature Reviews Microbiology. Nature Research. https://doi.org/10.1038/s41579-020-0433-9
  91. Fan, Y., Støving, R. K., Berreira Ibraim, S., Hyötyläinen, T., Thirion, F., Arora, T., Lyu, L., Stankevic, E., Hansen, T. H., Déchelotte, P., & others. (2023). The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice. Nature Microbiology, 8, 787–802. https://doi.org/10.1038/s41564-023-01355-5
  92. Feehley, T., Plunkett, C. H., Bao, R., et al. (2019). Healthy infants harbor intestinal bacteria that protect against food allergy. Nature Medicine, 25, 448–453. https://doi.org/10.1038/s41591-018-0324-xz
  93. Fei, N., & Zhao, L. (2013). An opportunistic pathogen isolated from the gut of an obese human causes obesity in germfree mice. ISME Journal, 7, 880–884. https://doi.org/10.1038/ismej.2012.153
  94. Feng, W., Ao, H., & Peng, C. (2018, November 23). Gut microbiota, short-chain fatty acids, and herbal medicines. Frontiers in Pharmacology. Frontiers Media S.A. https://doi.org/10.3389/fphar.2018.01354
  95. Finegold, S. M., Lawson, P. A., Vaisanen, M.-L., Molitoris, D. R., Song, Y., Liu, C., & Collins, M. D. (2004). Anaerofustis stercorihominis gen. nov., sp. nov., from human feces. Anaerobe, 10(1), 41–45. https://doi.org/10.1016/j.anaerobe.2003.10.002
  96. Flint, H. J., Scott, K. P., Louis, P., & Duncan, S. H. (2012). The role of the gut microbiota in nutrition and health. Nature Reviews Gastroenterology & Hepatology, 9(10), 577–589. https://doi.org/10.1038/nrgastro.2012.156
  97. Foulquier, C., Rivière, A., Heulot, M., et al. (2022). Molecular characterization of the missing electron pathways for butanol synthesis in Clostridium acetobutylicum. Nature Communications, 13, 4691. https://doi.org/10.1038/s41467-022-32269-1
  98. Franconieri, F., Join-Lambert, O., Creveuil, C., Auzou, M., Labombarda, F., Aouba, A., Verdon, R., & de La Blanchardière, A. (2021). Rothia spp. infective endocarditis: A systematic literature review. Infectious Diseases Now, 51(3), 228–235. https://doi.org/10.1016/j.medmal.2020.10.021
  99. Fultz, R., Ticer, T., Ihekweazu, F. D., Horvath, T. D., Haidacher, S. J., Hoch, K. M., … Engevik, M. A. (2021). Unraveling the metabolic requirements of the gut commensal Bacteroides ovatus. Frontiers in Microbiology, 12, 745469. https://doi.org/10.3389/fmicb.2021.745469
  100. Fusco, W., Lorenzo, M. B., Cintoni, M., Porcari, S., Rinninella, E., Kaitsas, F., Lener, E., Mele, M. C., Gasbarrini, A., Collado, M. C., Cammarota, G., & Ianiro, G. (2023). Short-chain fatty-acid-producing bacteria: Key components of the human gut microbiota. Nutrients, 15(9), 2211. https://doi.org/10.3390/nu15092211
  101. Gaastra, W., Kusters, J. G., van Duijkeren, E., & Lipman, L. J. A. (2014). Escherichia fergusonii. Veterinary Microbiology, 172(1–2), 7–12. https://doi.org/10.1016/j.vetmic.2014.04.016
  102. Gao, F., Guo, R., Ma, Q., Li, Y., Wang, W., Fan, Y., Ju, Y., Zhao, B., Gao, Y., Qian, L., et al. (2022). Stressful events induce long-term gut microbiota dysbiosis and associated post-traumatic stress symptoms in healthcare workers fighting against COVID-19. Journal of Affective Disorders, 303, 187–195. https://doi.org/10.1016/j.jad.2022.02.024
  103. Gao, G., Ma, T., Zhang, T., Jin, H., Li, Y., Kwok, L. Y., … Sun, Z. (2021). Adjunctive probiotic Lactobacillus rhamnosus Probio-M9 administration enhances the effect of anti-PD-1 antitumor therapy via restoring antibiotic-disrupted gut microbiota. Frontiers in Immunology, 12, 772532. https://doi.org/10.3389/fimmu.2021.772532
  104. García-Villalba, R., Giménez-Bastida, J. A., Cortés-Martín, A., Ávila-Gálvez, M. Á., Tomás-Barberán, F. A., Selma, M. V., Espín, J. C., & González-Sarrías, A. (2022). Urolithins: a Comprehensive Update on their Metabolism, Bioactivity, and Associated Gut Microbiota. Molecular nutrition & food research, 66(21), e2101019. https://doi.org/10.1002/mnfr.202101019
  105. Gasaly, N., de Vos, P., & Hermoso, M. A. (2021). Impact of bacterial metabolites on gut barrier function and host immunity: A focus on bacterial metabolism and its relevance for intestinal inflammation. Frontiers in Immunology, 12, 658354. https://doi.org/10.3389/fimmu.2021.658354
  106. Geirnaert, A., Calatayud, M., Grootaert, C., et al. (2017). Butyrate-producing bacteria supplemented in vitro to Crohn’s disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity. Scientific Reports, 7, 11450. https://doi.org/10.1038/s41598-017-11734-8
  107. Ghosh, S., Whitley, C. S., Haribabu, B., & Jala, V. R. (2021, January 1). Regulation of intestinal barrier function by microbial metabolites. Cellular and Molecular Gastroenterology and Hepatology (CMGH). Elsevier Inc. https://doi.org/10.1016/j.jcmgh.2021.02.007
  108. Ghosh, T. S., Shanahan, F., & O’Toole, P. W. (2022). The gut microbiome as a modulator of healthy ageing. Nature Reviews Gastroenterology & Hepatology, 19, 565–584. https://doi.org/10.1038/s41575-022-00605-x
  109. Gibiino, G., Lopetuso, L. R., Scaldaferri, F., Rizzatti, G., Binda, C., & Gasbarrini, A. (2018). Exploring Bacteroidetes: Metabolic key points and immunological tricks of our gut commensals. Digestive and Liver Disease, 50(7), 635–639. https://doi.org/10.1016/j.dld.2018.03.016
  110. Go, J., Chang, D.-H., Ryu, Y.-K., Park, H.-Y., Lee, I.-B., Noh, J.-R., Hwang, D. Y., Kim, B.-C., Kim, K.-S., & Lee, C.-H. (2021). Human gut microbiota Agathobaculum butyriciproducens improves cognitive impairment in LPS-induced and APP/PS1 mouse models of Alzheimer’s disease. Nutrition Research, 86, 96–108. https://doi.org/10.1016/j.nutres.2020.12.010
  111. Gong, H., Zhang, S., Li, Q., Zuo, C., Gao, X., Zheng, B., & Lin, M. (2020). Gut microbiota compositional profile and serum metabolic phenotype in patients with primary open-angle glaucoma. Experimental Eye Research, 191, 107921. https://doi.org/10.1016/j.exer.2020.107921
  112. Goris, T., Cuadrat, R. R. C., & Braune, A. (2021). Flavonoid-modifying capabilities of the human gut microbiome—An in silico study. Nutrients, 13(8), 2688. https://doi.org/10.3390/nu13082688
  113. Gorvitovskaia, A., Holmes, S. P., & Huse, S. M. (2016). Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. Microbiome, 4, 15. https://doi.org/10.1186/s40168-016-0160-7
  114. Gou, Y., Yao, L., Yang, W., et al. (2025). Development of a three-species gut microbiome diagnostic model for acute pancreatitis and its association with systemic inflammation: A prospective cross-sectional study. Scientific Reports, 15, 26034. https://doi.org/10.1038/s41598-025-11042-6
  115. Goubet, A.-G., Wheeler, R., Flibd-Ulcerative Diseasekiger, A., Qu, B., Lemaître, F., Iribarren, K., Mondragón, L., Tidjani Alou, M., Pizzato, E., Durand, S., Derosa, L., Aprahamian, F., Bossut, N., Moya-Nilges, M., Derrien, D., Chen, G., Ledibd-Ulcerative Disease, M., Joseph, A., Pons, N., … Daillère, R. (2021). Multifaceted modes of action of the anticancer probiotic Enterococcus hirae. Cell Death and Differentiation, 28(7), 2276–2295. https://doi.org/10.1038/s41418-021-00753-8
  116. Gough, E. K., Stephens, D. A., Moodie, E. E. M., Prendergast, A. J., Stoltzfus, R. J., Humphrey, J. H., & Manges, A. R. (2016). Erratum to: Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota. Microbiome, 4(1), 5. https://doi.org/10.1186/s40168-016-0149-2
  117. Green, M., Arora, K., & Prakash, S. (2020). Microbial medicine: Prebiotic and probiotic functional foods to target obesity and metabolic syndrome. International Journal of Molecular Sciences, 21(8), 2890. https://doi.org/10.3390/ijms21082890
  118. Greuter, T., Michel, M. C., Thomann, D., Weigmann, H., & Vavricka, S. R. (2020). Randomized, placebo-controlled, double-blind and open-label studies in the treatment and prevention of acute diarrhea with Enterococcus faecium SF68. Frontiers in Medicine, 7, 276. https://doi.org/10.3389/fmed.2020.00276
  119. Gruneck, L., Gentekaki, E., Kespechara, K., Denny, J., Sharpton, T. J., Marriott, L. K., Shannon, J., & Popluechai, S. (2022). The fecal microbiota of Thai school-aged children associated with demographic factors and diet. PeerJ, 10, e13325. https://doi.org/10.7717/peerj.13325
  120. Gruneck, L., Kullawong, N., Kespechara, K., & Popluechai, S. (2020). Gut microbiota of obese and diabetic Thai subjects and interplay with dietary habits and blood profiles. PeerJ, 8, e9622. https://doi.org/10.7717/peerj.9622
  121. Guo, P., Zhang, K., Ma, X., & He, P. (2020). Clostridium species as probiotics: Potentials and challenges. Journal of Animal Science and Biotechnology, 11(1), 24. https://doi.org/10.1186/s40104-019-0402-1
  122. Guo, Z., Zhang, J., Wang, Z., Ang, K. Y., Huang, S., Hou, Q., Su, X., Qiao, J., Zheng, Y., Wang, L., Koh, E., Danliang, H., Xu, J., Lee, Y. K., & Zhang, H. (2016). Intestinal microbiota distinguish gout patients from healthy humans. Scientific Reports, 6(1), 20602. https://doi.org/10.1038/srep20602
  123. Hagihara, M., Ariyoshi, T., Kuroki, Y., & et al. (2021). Clostridium butyricum enhances colonization resistance against Clostridioides difficile by metabolic and immune modulation. Scientific Reports, 11, 15007. https://doi.org/10.1038/s41598-021-94572-z
  124. Hai, N. T., Hongsrichan, N., Intuyod, K., Pinlaor, P., Yingklang, M., Chaidee, A., … Pinlaor, S. (2022). Strongyloides stercoralis infection induces gut dysbiosis in chronic kidney disease patients. PLoS Neglected Tropical Diseases, 16(9), e0010302. https://doi.org/10.1371/journal.pntd.0010302
  125. Hajjar, R., Ambaraghassi, G., Sebajang, H., Schwenter, F., & Su, S.-H. (2020). Raoultella ornithinolytica: Emergence and resistance. Infection and Drug Resistance, 13, 1091–1104. https://doi.org/10.2147/IDR.S191387
  126. Hamilton, A. L., Kamm, M. A., Ng, S. C., & Morrison, M. (2018). Proteus spp. as putative gastrointestinal pathogens. Clinical Microbiology Reviews, 31(3), e00085-17. https://doi.org/10.1128/CMR.00085-17
  127. Han, S. K., Shin, Y. J., Lee, D. Y., et al. (2021). Lactobacillus rhamnosus HDB1258 modulates gut microbiota-mediated immune response in mice with or without lipopolysaccharide-induced systemic inflammation. BMC Microbiology, 21, 146. https://doi.org/10.1186/s12866-021-02192-4
  128. Han, T., Hu, X., Li, K., Zhang, D., Zhang, Y., & Li, J. (2021). Bifidobacterium infantis maintains genome stability in ulcerative colitis via regulating anaphase-promoting complex subunit 7. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.761113
  129. Harnett, J., Davey, G., Patrick, A., & Caddick, C. (2011, December). Lactic acid bacteria | Streptococcus thermophilus. In Encyclopedia of Dairy Sciences (pp. 143–148). Academic Press. https://doi.org/10.1016/B978-0-12-374407-4.00268-5
  130. Harris, S. C., Devendran, S., Méndez-García, C., Mythen, S. M., Wright, C. L., Fields, C. J., Hernandez, A. G., Cann, I., Hylemon, P. B., & Ridlon, J. M. (2018). Bile acid oxidation by Eggerthella lenta strains C592 and DSM 2243T. Gut microbes, 9(6), 523–539. https://doi.org/10.1080/19490976.2018.1458180
  131. He, X., Zhao, S., & Li, Y. (2021). Faecalibacterium prausnitzii: A next-generation probiotic in gut disease improvement. Journal Canadien Des Maladies Infectieuses et de La Microbiologie Medicale [The Canadian Journal of Infectious Diseases & Medical Microbiology], 2021, 1–10. https://doi.org/10.1155/2021/6666114
  132. Hecht, A. L., Harling, L. C., Friedman, E. S., Tanes, C., Lee, J., Firrman, J., Hao, F., Tu, V., Liu, L., Patterson, A. D., Bittinger, K., Goulian, M., & Wu, G. D. (2024). Dietary carbohydrates regulate intestinal colonization and dissemination of Klebsiella pneumoniae. The Journal of Clinical Investigation, 134(9), e174726. https://doi.org/10.1172/JCI174726
  133. Hiippala, K., Barreto, G., Burrello, C., Diaz-Basabe, A., Suutarinen, M., Kainulainen, V., Bowers, J. R., Lemmer, D., Engelthaler, D. M., Eklund, K. K., Facciotti, F., & Satokari, R. (2020). Novel Odoribacter splanchnicus strain and its outer membrane vesicles exert immunoregulatory effects in vitro. Frontiers in Microbiology, 11, 575455. https://doi.org/10.3389/fmicb.2020.575455
  134. Hirmas, B., Gasaly, N., Orellana, G., Vega-Sagardía, M., Saa, P., Gotteland, M., & Garrido, D. (2022). Metabolic modeling and bidirectional culturing of two gut microbes reveal cross-feeding interactions and protective effects on intestinal cells. mSystems, 7(5), e0064622. https://doi.org/10.1128/msystems.00646-22
  135. Honda, S., Eguchi, H., Okino, Y., & Wang, D. S. (2025). The probiotic strain Clostridium butyricum TO-A produces butyrate by utilizing lactate and acetate. International Journal of Molecular Sciences, 26(7), 2951. https://doi.org/10.3390/ijms26072951
  136. Hori, H., Kamikado, K., Aoki, R., et al. (2020). Bifidobacterium animalis subsp. lactis GCL2505 modulates host energy metabolism via the short-chain fatty acid receptor GPR43. Scientific Reports, 10, 4158. https://doi.org/10.1038/s41598-020-60984-6
  137. Hosomi, K., Saito, M., Park, J., Murakami, H., Shibata, N., Ando, M., Nagatake, T., Konishi, K., Ohno, H., Tanisawa, K., Mohsen, A., Chen, Y.-A., Kawashima, H., Natsume-Kitatani, Y., Oka, Y., Shimizu, H., Furuta, M., Tojima, Y., Sawane, K., … Kunisawa, J. (2022). Oral administration of Blautia wexlerae ameliorates obesity and type 2 diabetes via metabolic remodeling of the gut microbiota. Nature Communications, 13(1), 4477. https://doi.org/10.1038/s41467-022-32015-7
  138. Hsiao, E. Y., McBride, S. W., Hsien, S., Sharon, G., Hyde, E. R., McCue, T., Codelli, J. A., Chow, J., Reisman, S. E., Petrosino, J. F., et al. (2013). Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell, 155(7), 1451–1463
  139. Hsieh, Y. Y., Tung, S. Y., Pan, H. Y., Yen, C. W., Xu, H. W., Lin, Y. J., Deng, Y. F., Hsu, W. T., Wu, C. S., & Li, C. (2018). Increased abundance of Clostridium and Fusobacterium in gastric microbiota of patients with gastric cancer in Taiwan. Scientific Reports, 8(1), 158. https://doi.org/10.1038/s41598-017-18596-0
  140. Hu, W., Gao, W., Liu, Z., Fang, Z., Wang, H., Zhao, J., … Chen, W. (2022). Specific Strains of Faecalibacterium prausnitzii Ameliorate Nonalcoholic Fatty Liver Disease in Mice in Association with Gut Microbiota Regulation. Nutrients, 14(14). https://doi.org/10.3390/nu14142945
  141. Huan, N. C., Lai, Y. C., & Khoo, T. S. (2019). Kluyvera ascorbata infections – a case series analysis. Internal Medicine Journal, 49(5), 641–644. https://doi.org/10.1111/imj.13_14300
  142. Huang, R., Wu, F., Zhou, Q., Wei, W., Yue, J., Xiao, B., & Luo, Z. (2022). Lactobacillus and intestinal diseases: Mechanisms of action and clinical applications. Microbiological Research, 260, 127019. https://doi.org/10.1016/j.micres.2022.127019
  143. Huang, Y., Wang, Z., Ma, H., Ji, S., Chen, Z., Cui, Z., Chen, J., & Tang, S. (2021). Dysbiosis and implication of the gut microbiota in diabetic retinopathy. Frontiers in Cellular and Infection Microbiology, 11, 646348. https://doi.org/10.3389/fcimb.2021.646348
  144. Human gut-associated Bifidobacterium species salvage exogenous indole, a uremic toxin precursor, to synthesize indole-3-lactic acid via tryptophan - Taylor & Francis Online, accessed July 22, 2025, https://www.tandfonline.com/doi/full/10.1080/19490976.2024.2347728
  145. Hunthai, S., Usawachintachit, M., Taweevisit, M., et al. (2024). Unraveling the role of gut microbiota by fecal microbiota transplantation in rat model of kidney stone disease. Scientific Reports, 14, 21924. https://doi.org/10.1038/s41598-024-72694-4
  146. Iatcu, C. O., Steen, A., & Covasa, M. (2022). Gut microbiota and complications of type-2 diabetes. Nutrients, 14(1), 166. https://doi.org/10.3390/nu14010166
  147. Ibragimova, S., Ramachandran, R., Ali, F. R., Lipovich, L., & Ho, S. B. (2021). Dietary patterns and associated microbiome changes that promote oncogenesis. Frontiers in Cell and Developmental Biology, 9, 725821. https://doi.org/10.3389/fcell.2021.725821
  148. Ilie, O. D., Ciobica, A., McKenna, J., Doroftei, B., & Mavroudis, I. (2020). Minireview on the relations between gut microflora and Parkinson’s disease: Further biochemical (oxidative stress), inflammatory, and neurological particularities. Oxidative Medicine and Cellular Longevity, 2020, 4518023. https://doi.org/10.1155/2020/4518023
  149. Intarajak, T., Udomchaiprasertkul, W., Khoiri, A. N., Sutheeworapong, S., Kusonmano, K., Kittichotirat, W., Thammarongtham, C., & Cheevadhanarak, S. (2024). Distinct gut microbiomes in Thai patients with colorectal polyps. World Journal of Gastroenterology, 30(27), 3336–3355. https://doi.org/10.3748/wjg.v30.i27.3336
  150. Ioannou, P. (2019). Escherichia hermannii infections in humans: A systematic review. Tropical Medicine and Infectious Disease, 4(1), 17. https://doi.org/10.3390/tropicalmed4010017
  151. Islam, S. M. S., Ryu, H. M., & Sohn, S. (2022). Tetragenococcus halophilus alleviates intestinal inflammation in mice by altering gut microbiota and regulating dendritic cell activation via IBD-Crohn’s disease83. Cells, 11(12), 1903. https://doi.org/10.3390/cells11121903
  152. Jayanama, K., Phuphuakrat, A., Pongchaikul, P., Prombutara, P., Nimitphong, H., Reutrakul, S., & Sungkanuparph, S. (2022). Association between gut microbiota and prediabetes in people living with HIV. Current Research in Microbial Sciences, 3, 100143. https://doi.org/10.1016/j.crmicr.2022.100143
  153. Jeong, H., Kim, S., Hwang, U.-S., Choi, H., & Park, Y.-S. (2023). Immunostimulatory activity of Lactococcus lactis subsp. lactis CAB701 isolated from Jeju cabbage. Microorganisms, 11(7), 1718. https://doi.org/10.3390/microorganisms11071718
  154. Jia, D., Kuang, Z., & Wang, L. (2024). The role of microbial indole metabolites in tumor. Gut Microbes, 16(1), 2409209. https://doi.org/10.1080/19490976.2024.2409209
  155. Jiang, H. Y., Pan, L. Y., Zhang, X., Zhang, Z., Zhou, Y. Y., & Ruan, B. (2020). Altered gut bacterial-fungal interkingdom networks in patients with current depressive episode. Brain and Behavior, 10(10), e01677. https://doi.org/10.1002/brb3.1677
  156. Jiang, L., Shang, M., Yu, S., Liu, Y., Zhang, H., Zhou, Y., Wang, M., Wang, T., Li, H., Liu, Z., & Zhang, X. (2022). A high-fiber diet synergizes with Prevotella copri and exacerbates rheumatoid arthritis. Cellular & Molecular Immunology, 19(12), 1414–1424. https://doi.org/10.1038/s41423-022-00934-6
  157. Jin, D. M., Morton, J. T., & Bonneau, R. (2024). Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases. bioRxiv. https://doi.org/10.1101/2024.02.27.582333
  158. Jinatham, V., Kullawong, N., Kespechara, K., Gentekaki, E., & Popluechai, S. (2018). Comparison of gut microbiota between lean and obese adult Thai individuals. Microbiology and Biotechnology Letters, 46(3), 277–287. https://doi.org/10.4014/mbl.1711.11003
  159. Jinato, T., Chayanupatkul, M., Dissayabutra, T., Chutaputti, A., Tangkijvanich, P., & Chuaypen, N. (2022). Litchi-derived polyphenol alleviates liver steatosis and gut dysbiosis in patients with non-alcoholic fatty liver disease: A randomized double-blinded, placebo-controlled study. Nutrients, 14(14), 2921. https://doi.org/10.3390/nu14142921
  160. Journal of Health Science and Alternative Medicine. (2025). Gut microbiota in diabetic kidney disease in Northern Thailand: A preliminary study. Journal of Health Science and Alternative Medicine. Retrieved August 18, 2025, from https://he01.tci-thaijo.org/index.php/jhealthscialternmed/article/view/275356
  161. Kaczmarczyk, M., Löber, U., Adamek, K., Węgrzyn, D., Skonieczna-Żydecka, K., Malinowski, D., Łoniewski, I., Markó, L., Ulas, T., Forslund, S. K., & Łoniewska, B. (2021). The gut microbiota is associated with the small intestinal paracellular permeability and the development of the immune system in healthy children during the first two years of life. Journal of Translational Medicine, 19(1), 177. https://doi.org/10.1186/s12967-021-02839-w
  162. Kaiyrlykyzy, A., Kozhakhmetov, S., Babenko, D., et al. (2022). Study of gut microbiota alterations in Alzheimer's dementia patients from Kazakhstan. Scientific Reports, 12, 15115. https://doi.org/10.1038/s41598-022-19393-0
  163. Kalkan, A. E., BinMowyna, M. N., Raposo, A., Ahmad, M. F., Ahmed, F., Otayf, A. Y., Carrascosa, C., Saraiva, A., & Karav, S. (2025). Beyond the gut: Unveiling butyrate's global health impact through gut health and dysbiosis-related conditions: A narrative review. Nutrients, 17(8), 1305. https://doi.org/10.3390/nu17081305
  164. Karcher, N., Pasolli, E., Asnicar, F., Huang, K. D., Tett, A., Manara, S., Armanini, F., Bain, D., Duncan, S. H., Louis, P., Zolfo, M., Manghi, P., Valles-Colomer, M., Raffaetà, R., Rota-Stabelli, O., Collado, M. C., Zeller, G., Falush, D., Maixner, F., … Segata, N. (2020). Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. Genome Biology, 21(1), 138. https://doi.org/10.1186/s13059-020-02042-y
  165. Karlsson, F. H., Fåk, F., Nookaew, I., Tremaroli, V., Fagerberg, B., Petranovic, D., Bäckhed, F., & Nielsen, J. (2012). Symptomatic atherosclerosis is associated with an altered gut metagenome. Nature communications, 3, 1245. https://doi.org/10.1038/ncomms2266
  166. Kaur, C. P., Vadivelu, J., & Chandramathi, S. (2018). Impact of Klebsiella pneumoniae in lower gastrointestinal tract diseases. Journal of Digestive Diseases, 19(5), 262–271. https://doi.org/10.1111/1751-2980.12595
  167. Khan, M. A., Ma, C., Knodler, L. A., Valdez, Y., Rosenberger, C. M., Deng, W., Finlay, B. B., & Vallance, B. A. (2006). Toll-like receptor 4 contributes to colitis development but not to host defense during Citrobacter rodentium infection in mice. Infection and Immunity, 74(5), 2522–2536. https://doi.org/10.1128/IAI.74.5.2522-2536.2006
  168. Kim, C. S., Shin, G. E., Cheong, Y., Shin, D. M., & Chun, W. Y. (2022). Experiencing social exclusion changes gut microbiota composition. Translational Psychiatry, 12, 254. https://doi.org/10.1038/s41398-022-02023-8
  169. Kingkaw, A., Raethong, N., Patumcharoenpol, P., Suratannon, N., Nakphaichit, M., Keawsompong, S., Roytrakul, S., & Vongsangnak, W. (2023). Analyzing Predominant Bacterial Species and Potential Short-Chain Fatty Acid-Associated Metabolic Routes in Human Gut Microbiome Using Integrative Metagenomics. Biology, 12(1), 21. https://doi.org/10.3390/biology12010021
  170. Kinross, J. M., Darzi, A. W., & Nicholson, J. K. (2011). Gut microbiome-host interactions in health and disease. Genome Medicine, 3, 14. https://doi.org/10.1186/gm228
  171. Kisuse, J., La-Ongkham, O., Nakphaichit, M., Therdtatha, P., Momoda, R., Tanaka, M., Fukuda, S., Popluechai, S., Kespechara, K., Sonomoto, K., Lee, Y. K., Nitisinprasert, S., & Nakayama, J. (2018). Urban diets linked to gut microbiome and metabolome alterations in children: A comparative cross-sectional study in Thailand. Frontiers in Microbiology, 9, 1345. https://doi.org/10.3389/fmicb.2018.01345
  172. Kivenson, V., & Giovannoni, S. J. (2020). An expanded genetic code enables trimethylamine metabolism in human gut bacteria. mSystems, 5(5), e00413-20. https://doi.org/10.1128/mSystems.00413-20
  173. Klammsteiner, T., Walter, A., Bogataj, T., Heussler, C. D., Stres, B., Steiner, F. M., Schlick-Steiner, B. C., Arthofer, W., & Insam, H. (2020). The core gut microbiome of black soldier fly (Hermetia illucens) larvae raised on low-bioburden diets. Frontiers in Microbiology, 11, 993. https://doi.org/10.3389/fmicb.2020.00993
  174. Kort, R., Schlösser, J., Vazquez, A. R., Atukunda, P., Muhoozi, G. K. M., Wacoo, A. P., Sybesma, W. F. H., Westerberg, A. C., Iversen, P. O., & Schoen, E. D. (2021). Model selection reveals the butyrate-producing gut bacterium Coprococcus eutactus as predictor for language development in 3-year-old rural Ugandan children. Frontiers in Microbiology, 12, 681485. https://doi.org/10.3389/fmicb.2021.681485
  175. Kumar, R., Herold, J. L., Schady, D., Davis, J., Kopetz, S., Martinez-Moczygemba, M., et al. (2017). Streptococcus gallolyticus subsp. gallolyticus promotes colorectal tumor development. PLoS Pathogens, 13(7), e1006440. https://doi.org/10.1371/journal.ppat.1006440
  176. Kumari, M., Singh, P., Nataraj, B. H., Kokkiligadda, A., Naithani, H., Ali, S. A., & Nagpal, R. (2021). Fostering next-generation probiotics in human gut by targeted dietary modulation: An emerging perspective. Food Research International, 150, 110716. https://doi.org/10.1016/j.foodres.2021.110716
  177. Kwong, E. K., & Puri, P. (2021). Gut microbiome changes in nonalcoholic fatty liver disease & alcoholic liver disease. Translational Gastroenterology and Hepatology, 6, 3. https://doi.org/10.21037/tgh.2020.02.18
  178. La Rosa, S. L., Leth, M. L., Michalak, L., Hansen, M. E., Pudlo, N. A., Glowacki, R., Pereira, G., Workman, C. T., Arntzen, M. Ø., Pope, P. B., Martens, E. C., Hachem, M. A., & Westereng, B. (2019). The human gut Firmicute Roseburia intestinalis is a primary degrader of dietary β-mannans. Nature Communications, 10(1), 905. https://doi.org/10.1038/s41467-019-08812-y
  179. La-Ongkham, O., Nakphaichit, M., Leelavatcharamas, V., Keawsompong, S., & Nitisinprasert, S. (2015). Distinct gut microbiota of healthy children from two different geographic regions of Thailand. Archives of Microbiology, 197(4), 561–573. https://doi.org/10.1007/s00203-015-1089-0
  180. La-Ongkham, O., Nakphaichit, M., Nakayama, J., Keawsompong, S., & Nitisinprasert, S. (2020). Age-related changes in the gut microbiota and the core gut microbiome of healthy Thai humans. 3 Biotech, 10(6), 1–14. https://doi.org/10.1007/s13205-020-02265-7
  181. Lai, Y., Masatoshi, H., Ma, Y., Guo, Y., & Zhang, B. (2022). Role of Vitamin K in Intestinal Health. Frontiers in immunology, 12, 791565. https://doi.org/10.3389/fimmu.2021.791565
  182. Latorre-Pérez, A., Hernández, M., Iglesias, J. R., Morán, J., Pascual, J., Porcar, M., Vilanova, C., & Collado, L. (2021). The Spanish gut microbiome reveals links between microorganisms and Mediterranean diet. Scientific Reports, 11(1), 21602. https://doi.org/10.1038/s41598-021-01002-1
  183. Lehner, A., Tall, B. D., Fanning, S., & Srikumar, S. (2018). Cronobacter spp.—opportunistic foodborne pathogens: An update on evolution, osmotic adaptation and pathogenesis. Current Clinical Microbiology Reports, 5(2), 97–105. https://doi.org/10.1007/s40588-018-0089-7
  184. Levy, R., Magis, A. T., Earls, J. C., Manor, O., Wilmanski, T., Lovejoy, J., Gibbons, S. M., Omenn, G. S., Hood, L., & Price, N. D. (2020). Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome. Proceedings of the National Academy of Sciences, 117(24), 13839–13845. https://doi.org/10.1073/pnas.1922498117
  185. Leylabadlo, H. E., Ghotaslou, R., Feizabadi, M. M., Farajnia, S., Moaddab, S. Y., Ganbarov, K., Khodadadi, E., Tanomand, A., Sheykhsaran, E., Yousefi, B., & Kafil, H. S. (2020). The critical role of Faecalibacterium prausnitzii in human health: An overview. Microbial Pathogenesis, 149(104344), 104344. https://doi.org/10.1016/j.micpath.2020.104344
  186. Li, C., Cui, L., Yang, Y., Miao, J., Zhao, X., Zhang, J., Cui, G., & Zhang, Y. (2019). Gut microbiota differs between Parkinson’s disease patients and healthy controls in Northeast China. Frontiers in Molecular Neuroscience, 12, 171. https://doi.org/10.3389/fnmol.2019.00171
  187. Li, J., Yang, G., Zhang, Q., Liu, Z., Jiang, X., & Xin, Y. (2023). Function of Akkermansia muciniphila in type 2 diabetes and related diseases. Frontiers in Microbiology, 14, 1172400. https://doi.org/10.3389/fmicb.2023.1172400
  188. Li, L., Yang, K., Li, C., Zhang, H., Yu, H., Chen, K., … Liu, L. (2022). Metagenomic shotgun sequencing and metabolomic profiling identify specific human gut microbiota associated with diabetic retinopathy in patients with type 2 diabetes. Frontiers in Immunology, 13, 943325. https://doi.org/10.3389/fimmu.2022.943325
  189. Li, N. N., Li, W., Feng, J. X., Zhang, W. W., Zhang, R., Du, S. H., Liu, S. Y., Xue, G. H., Yan, C., Cui, J. H., Zhao, H. Q., Feng, Y. L., Gan, L., Zhang, Q., Chen, C., Liu, D., & Yuan, J. (2021). High alcohol-producing Klebsiella pneumoniae causes fatty liver disease through 2,3-butanediol fermentation pathway in vivo. Gut Microbes, 13(1), 1979883. https://doi.org/10.1080/19490976.2021.1979883
  190. Li, S., Song, J., Ke, P., Kong, L., Lei, B., Zhou, J., et al. (2021). The gut microbiome is associated with brain structure and function in schizophrenia. Scientific Reports, 11, 9743. https://doi.org/10.1038/s41598-021-89166-8
  191. Li, S., Zhuo, M., Huang, X., Huang, Y., Zhou, J., Xiong, D., Li, J., Liu, Y., Pan, Z., Li, H., et al. (2020). Altered gut microbiota associated with symptom severity in schizophrenia. PeerJ, 8, e9574. https://doi.org/10.7717/peerj.9574
  192. Li, X., Ormsby, M. J., Fallata, G., Meikle, L. M., Walker, D., Xu, D., & Wall, D. M. (2023). PF-431396 hydrate inhibition of kinase phosphorylation during adherent-invasive Escherichia coli infection inhibits intra-macrophage replication and inflammatory cytokine release. Microbiology (Reading, England), 169(6), 001337. https://doi.org/10.1099/mic.0.001337
  193. Li, X., Yi, Y., Wu, T., Chen, N., Gu, X., Xiang, L., Jiang, Z., Li, J., & Jin, H. (2023). Integrated microbiome and metabolome analysis reveals the interaction between intestinal flora and serum metabolites as potential biomarkers in hepatocellular carcinoma patients. Frontiers in Cellular and Infection Microbiology, 13, 1170748. https://doi.org/10.3389/fcimb.2023.1170748
  194. Li, Y., Su, X., Gao, Y., Lv, C., Gao, Z., Liu, Y., Wang, Y., Li, S., & Wang, Z. (2020). The potential role of the gut microbiota in modulating renal function in experimental diabetic nephropathy murine models established in same environment. Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, 1866(6), 165764. https://doi.org/10.1016/j.bbadis.2020.165764
  195. Li, Y., Watanabe, E., Kawashima, Y., Plichta, D. R., Wang, Z., Ujike, M., Ang, Q. Y., Wu, R., Furuichi, M., Takeshita, K., Yoshida, K., Nishiyama, K., Kearney, S. M., Suda, W., Hattori, M., Sasajima, S., Matsunaga, T., Zhang, X., Watanabe, K., Fujishiro, J., … Honda, K. (2022). Identification of trypsin-degrading commensals in the large intestine. Nature, 609(7927), 582–589. https://doi.org/10.1038/s41586-022-05181-3
  196. Li, Z., Lai, J., Zhang, P., Ding, J., Jiang, J., Liu, C., Huang, H., Zhen, H., Xi, C., Sun, Y., Wu, L., Wang, L., Gao, X., Li, Y., Fu, Y., Jie, Z., Li, S., Zhang, D., Chen, Y., … Hu, S. (2022). Multi-omics analyses of serum metabolome, gut microbiome and brain function reveal dysregulated microbiota-gut-brain axis in bipolar depression. Molecular Psychiatry, 27(10),
  197. Liao, J., Liu, Y., Pei, Z., Wang, H., Zhu, J., Zhao, J., … Chen, W. (2023). Clostridium butyricum reduces obesity in a butyrate-independent way. Microorganisms, 11(5), 1292. https://doi.org/10.3390/microorganisms11051292
  198. Lin, P., Ding, B., Feng, C., Yin, S., Zhang, T., Qi, X., Lv, H., Guo, X., Dong, K., Zhu, Y., & others. (2017). Prevotella and Klebsiella proportions in fecal microbial communities are potential characteristic parameters for patients with major depressive disorder. Journal of Affective Disorders, 207, 300–304. https://doi.org/10.1016/j.jad.2016.09.051
  199. Liu, L., Liang, L., Liang, H., Wang, M., Lu, B., Xue, M., Deng, J., & Chen, Y. (2019). Fusobacterium nucleatum Aggravates the Progression of Colitis by Regulating M1 Macrophage Polarization via AKT2 Pathway. Frontiers in immunology, 10, 1324. https://doi.org/10.3389/fimmu.2019.01324
  200. Liu, M., Zhang, X., Hao, Y., Ding, J., Shen, J., Xue, Z., … Wang, N. (2019). Protective effects of a novel probiotic strain, Lactococcus lactis ML2018, in colitis: In vivo and in vitro evidence. Food and Function, 10(2), 1132–1145. https://doi.org/10.1039/c8fo02301h
  201. Liu, Q., Mittal, R., Emami, C. N., Iversen, C., Ford, H. R., & Prasadarao, N. V. (2012). Human isolates of Cronobacter sakazakii bind efficiently to intestinal epithelial cells in vitro to induce monolayer permeability and apoptosis. The Journal of Surgical Research, 176(2), 437–447. https://doi.org/10.1016/j.jss.2011.10.030
  202. Liu, S., Li, E., Sun, Z., Fu, D., Duan, G., Jiang, M., Yu, Y., Mei, L., Yang, P., Tang, Y., & Zheng, P. (2019). Altered gut microbiota and short chain fatty acids in Chinese children with autism spectrum disorder. Scientific Reports, 9(1), 287. https://doi.org/10.1038/s41598-018-36430-z
  203. Liu, X., Mao, B., Gu, J., Wu, J., Cui, S., Wang, G., Zhao, J., Zhang, H., & Chen, W. (2021). Blautia-a new functional genus with potential probiotic properties?. Gut microbes, 13(1), 1–21. https://doi.org/10.1080/19490976.2021.1875796
  204. Liu, Y., & Dai, M. (2020). Trimethylamine N-oxide generated by the gut microbiota is associated with vascular inflammation: New insights into atherosclerosis. Mediators of Inflammation, 2020, 4634172. https://doi.org/10.1155/2020/4634172
  205. Lopez-Siles, M., Duncan, S., Garcia-Gil, L., & Martínez-Medina, M. (2017). Faecalibacterium prausnitzii: From microbiology to diagnostics and prognostics. The ISME Journal, 11, 841–852. https://doi.org/10.1038/ismej.2016.176
  206. Lordan, C., Thapa, D., Ross, R. P., & Cotter, P. D. (2020). Potential for enriching next-generation health-promoting gut bacteria through prebiotics and other dietary components. Gut Microbes, 11(1), 1–20. https://doi.org/10.1080/19490976.2019.1613124
  207. Loubinoux, J., Bronowicki, J.-P., Pereira, I. A. C., Mougenel, J.-L., & Faou, A. E. (2002). Sulfate-reducing bacteria in human feces and their association with inflammatory bowel diseases. FEMS Microbiology Ecology, 40(2), 107–112. https://doi.org/10.1111/j.1574-6941.2002.tb00942.x
  208. Louis, P., & Flint, H. J. (2017). Formation of propionate and butyrate by the human colonic microbiota. Environmental microbiology, 19(1), 29–41. https://doi.org/10.1111/1462-2920.13589
  209. Louis, P., Duncan, S. H., Sheridan, P. O., Walker, A. W., & Flint, H. J. (2022). Microbial lactate utilisation and the stability of the gut microbiome. Gut Microbiome, 3, e3. https://doi.org/10.1017/gmb.2022.3
  210. Lu, M., Yuan, B., Yan, X., Sun, Z., Lillehoj, H. S., Lee, Y., Baldwin-Bott, C., & Li, C. (2021). Clostridium perfringens-induced host-pathogen transcriptional changes in the small intestine of broiler chickens. Pathogens, 10(12), 1607. https://doi.org/10.3390/pathogens10121607
  211. Luangphiphat, W., Prombutara, P., Muangsillapasart, V., Sukitpunyaroj, D., Eeckhout, E., & Taweechotipatr, M. (2024). Exploring gut microbiota features in dyslipidemia and chronic coronary syndrome patients undergoing coronary angiography. Frontiers in Microbiology, 15, Article 1384146. https://doi.org/10.3389/fmicb.2024.1384146
  212. Lun, H., Yang, W., Zhao, S., Jiang, M., Xu, M., Liu, F., & Wang, Y. (2019). Altered gut microbiota and microbial biomarkers associated with chronic kidney disease. MicrobiologyOpen, 8(4), e678. https://doi.org/10.1002/mbo3.678
  213. Lunken, G. R., Golding, L., Schick, A., Majdoubi, A., Lavoie, P. M., & Vallance, B. A. (2023). Gut microbiome and dietary fibre intake strongly associate with IgG function and maturation following SARS-CoV-2 mRNA vaccination. Gut, 73(1), 208–210. https://doi.org/10.1136/gutjnl-2022-328556
  214. Luo, M., Sun, M., Wang, T., Zhang, S., Song, X., Liu, X., … Qin, J. (2023). Gut microbiota and type 1 diabetes: A two-sample bidirectional Mendelian randomization study. Frontiers in Cellular and Infection Microbiology, 13, 1163898. https://doi.org/10.3389/fcimb.2023.1163898
  215. Luo, S., Zhao, Y., Zhu, S., Liu, L., Cheng, K., Ye, B., Han, Y., Fan, J., & Xia, M. (2023). Flavonifractor plautii protects against elevated arterial stiffness. Circulation Research, 132(2), 167–181. https://doi.org/10.1161/CIRCRESAHA.122.321975
  216. Ma, L., Shen, Q., Lyu, W., Lv, L., Wang, W., Yu, M., Yang, H., Tao, S., & Xiao, Y. (2022). Clostridium butyricum and its derived extracellular vesicles modulate gut homeostasis and ameliorate acute experimental colitis. Microbiology Spectrum, 10(4), e0136822. https://doi.org/10.1128/spectrum.01368-22
  217. MacCann, R., Li, J., Leon, A. A. G., Negi, R., Alalwan, D., Tinago, W., McGettrick, P., Cotter, A. G., Landay, A., Sabin, C., O'Toole, P. W., Mallon, P. W. G., & Understanding the Pathology of Comorbid Disease in HIV-Infected Individuals (HIV UPBEAT) Study Group (2025). Associations Between the Gut Microbiome, Inflammation, and Cardiovascular Profiles in People With Human Immunodeficiency Virus. The Journal of infectious diseases, 231(4), e781–e791. https://doi.org/10.1093/infdis/jiaf043
  218. Maes, M., Vasupanrajit, A., Jirakran, K., & et al. (2023). Adverse childhood experiences and reoccurrence of illness impact the gut microbiome, which affects suicidal behaviours and the phenome of major depression: Towards enterotypic phenotypes. Acta Neuropsychiatrica, 35(6), 328–345. https://doi.org/10.1017/neu.2023.21
  219. Maioli, T. U., Borras-Nogues, E., Torres, L., Barbosa, S. C., Martins, V. D., Langella, P., Azevedo, V. A., & Chatel, J.-M. (2021). Possible Benefits of Faecalibacterium prausnitzii for Obesity-Associated Gut Disorders. Frontiers in Pharmacology, 12, 740636. https://doi.org/10.3389/fphar.2021.740636
  220. Malan-Muller, S., Valles-Colomer, M., Foxx, C. L., Vieira-Silva, S., van den Heuvel, L. L., Raes, J., Seedat, S., Lowry, C. A., & Hemmings, S. M. J. (2022). Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls. European Neuropsychopharmacology, 56, 24–38. https://doi.org/10.1016/j.euroneuro.2021.11.009
  221. Manchia, M., Fontana, A., Panebianco, C., Paribello, P., Arzedi, C., Cossu, E., Garzilli, M., Montis, M. A., Mura, A., Pisanu, C., & Squassina, A. (2021). Involvement of gut microbiota in schizophrenia and treatment resistance to antipsychotics. Biomedicines, 9(8), 875. https://doi.org/10.3390/biomedicines9080875
  222. Mangifesta, M., Mancabelli, L., Milani, C., Turroni, F., Viappiani, A., Lugli, G. A., Duranti, S., Ferrario, C., Ossiprandi, M. C., van Sinderen, D., Ventura, M., & Turroni, F. (2018). Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer. Scientific Reports, 8, 13974. https://doi.org/10.1038/s41598-018-32413-2
  223. Markowiak-Kopeć, P., & Śliżewska, K. (2020). The effect of probiotics on the production of short-chain fatty acids by human intestinal microbiome. Nutrients, 12(4), 1107. https://doi.org/10.3390/nu12041107
  224. Matsuoka, T., Shimizu, T., Minagawa, T., Hiranuma, W., Takeda, M., Kakuta, R., & Kawamoto, S. (2021). First case of an invasive Bacteroides dorei infection detected in a patient with a mycotic aortic aneurysm—raising a rebellion of major indigenous bacteria in humans: A case report and review. BMC Infectious Diseases, 21(1), 625. https://doi.org/10.1186/s12879-021-06345-8
  225. Matthies, A., Loh, G., Blaut, M., & Braune, A. (2012). Daidzein and genistein are converted to equol and 5-hydroxy-equol by human intestinal Slackia isoflavoniconvertens in gnotobiotic rats. The Journal of Nutrition, 142(1), 40–46. https://doi.org/10.3945/jn.111.148247
  226. McIntyre, R. S., Subramaniapillai, M., Shekotikhina, M., Carmona, N. E., Lee, Y., Mansur, R. B., Brietzke, E., Fus, D., Coles, A. S., Iacobucci, M., et al. (2021). Characterizing the gut microbiota in adults with bipolar disorder: A pilot study. Nutritional Neuroscience, 24, 173–180. https://doi.org/10.1080/1028415X.2019.1612555
  227. Meijnikman, A. S., Davids, M., Herrema, H., et al. (2022). Microbiome-derived ethanol in nonalcoholic fatty liver disease. Nature Medicine, 28(11), 2100–2106. https://doi.org/10.1038/s41591-022-02016-6
  228. Mineharu, Y., Nakamura, Y., Sato, N., et al. (2022). Increased abundance of Ruminococcus gnavus in gut microbiota is associated with moyamoya disease and non-moyamoya intracranial large artery disease. Scientific Reports, 12, 20244. https://doi.org/10.1038/s41598-022-24496-9
  229. Miranda, P. M., Bertolini, F., & Kadarmideen, H. N. (2018). Investigation of gut microbiome association with inflammatory bowel disease and depression: A machine learning approach. F1000Research, 7, 15091. https://doi.org/10.12688/f1000research.15091.2
  230. Mirhakkak, M. H., Schäuble, S., Klassert, T. E., Brunke, S., Brandt, P., Loos, D., Uribe, R. V., Senne de Oliveira Lino, F., Ni, Y., Vylkova, S., Slevogt, H., Hube, B., Weiss, G. J., Sommer, M. O. A., & Panagiotou, G. (2021). Metabolic modeling predicts specific gut bacteria as key determinants for Candida albicans colonization levels. The ISME Journal, 15(5), 1257–1270. https://doi.org/10.1038/s41396-020-00848-z
  231. Mitra, S., Drautz-Moses, D. I., Alhede, M., Maw, M. T., Liu, Y., Purbojati, R. W., Yap, Z. H., Kushwaha, K. K., Gheorghe, A. G., Bjarnsholt, T., Hansen, G. M., Sillesen, H. H., Hougen, H. P., Hansen, P. R., Yang, L., Tolker-Nielsen, T., Schuster, S. C., & Givskov, M. (2015). In silico analyses of metagenomes from human atherosclerotic plaque samples. Microbiome, 3, 38. https://doi.org/10.1186/s40168-015-0100-y
  232. Morales, C., Rojas, G., Rebolledo, C., Rojas-Herrera, M., Arias-Carrasco, R., Cuadros-Orellana, S., Maracaja-Coutinho, V., Saavedra, K., Leal, P., Lanas, F., Salazar, L. A., & Saavedra, N. (2022). Characterization of microbial communities from gut microbiota of hypercholesterolemic and control subjects. Frontiers in Cellular and Infection Microbiology, 12, 943609. https://doi.org/10.3389/fcimb.2022.943609
  233. Mukherjee, A., Lordan, C., Ross, R. P., & Cotter, P. D. (2020). Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health. Gut Microbes. Taylor & Francis. https://doi.org/10.1080/19490976.2020.1802866
  234. Muñiz Pedrogo, D. A., Jensen, M. D., Van Dyke, C. T., Murray, J. A., Woods, J. A., Chen, J., Kashyap, P. C., & Nehra, V. (2018). Gut microbial carbohydrate metabolism hinders weight loss in overweight adults undergoing lifestyle intervention with a volumetric diet. Mayo Clinic Proceedings, 93(8), 1104–1110. https://doi.org/10.1016/j.mayocp.2018.02.019
  235. Murros, K. E., Huynh, V. A., Takala, T. M., & Saris, P. E. J. (2021). Desulfovibrio bacteria are associated with Parkinson's disease. Frontiers in Cellular and Infection Microbiology, 11, 652617. https://doi.org/10.3389/fcimb.2021.652617
  236. Mussa, K. J. (2020). Study on the in vivo and in vitro links between diet and gut microbial community in Thai (Unpublished doctoral thesis). Kyushu University. Retrieved from https://catalog.lib.kyushu-u.ac.jp/opac_download_md/4110571/agr1077.pdf
  237. Mustafa, S. E., Mustafa, S., Ismail, A., Abas, F., Abd Manap, M. Y., Ahmed Hamdi, O. A., Elzen, S., Nahar, L., & Sarker, S. D. (2020). Impact of prebiotics on equol production from soymilk isoflavones by two Bifidobacterium species. Heliyon, 6(10), e05298. https://doi.org/10.1016/j.heliyon.2020.e05298
  238. Nan, X., Zhao, W., Liu, W. H., Li, Y., Li, N., Hong, Y., … Peng, G. (2023). Bifidobacterium animalis subsp. lactis BL-99 ameliorates colitis-related lung injury in mice by modulating short-chain fatty acid production and inflammatory monocytes/macrophages. Food & Function, 14(2), 1099–1112. https://doi.org/10.1039/d2fo03374g
  239. Nath, A. R., & Natarajan, J. (2024). Gut metagenomic analysis of gastric cancer patients reveals Akkermansia, Gammaproteobacteria, and Veillonella microbiota as potential non-invasive biomarkers. Genomics & Informatics, 22(1). https://doi.org/10.1186/s44342-024-00001-8
  240. Ngom, I. I., Hasni, I., Lo, C. I., Traore, S. I., Fontanini, A., Raoult, D., & Fenollar, F. (2020). Taxono-genomics and description of Gordonibacter massiliensis sp. nov., a new bacterium isolated from stool of healthy patient. New Microbes and New Infections, 33(100624), 100624. https://doi.org/10.1016/j.nmni.2019.100624
  241. Nie, K., Ma, K., Luo, W., Shen, Z., Yang, Z., Xiao, M., Tong, T., Yang, Y., & Wang, X. (2021). Roseburia intestinalis: A beneficial gut organism from the discoveries in genus and species. Frontiers in Cellular and Infection Microbiology, 11, 757718. https://doi.org/10.3389/fcimb.2021.757718
  242. Nogal, A., Loa, P., Zhang, X., Wells, P. M., Steves, C. J., Spector, T. D., … Menni, C. (2021). Circulating levels of the short-chain fatty acid acetate mediate the effect of the gut microbiome on visceral fat. Frontiers in Microbiology, 12, 711359. https://doi.org/10.3389/fmicb.2021.711359
  243. Nowak, J. M., Kopczyński, M., Friedman, A., Koziorowski, D., & Figura, M. (2022). Microbiota dysbiosis in Parkinson’s disease—In search of a biomarker. Biomedicines, 10(9), 2057. https://doi.org/10.3390/biomedicines10092057
  244. O’Mahony, L., McCarthy, J., Kelly, P., Hurley, G., Luo, F., Chen, K., O’Sullivan, G. C., Kiely, B., Collins, J. K., Shanahan, F., et al. (2005). Lactobacillus and bifidobacterium in irritable bowel syndrome: Symptom responses and relationship to cytokine profiles. Gastroenterology, 128(3), 541–551. https://doi.org/10.1053/j.gastro.2004.11.050
  245. Oh, B. S., Choi, W. J., Kim, J.-S., Ryu, S. W., Yu, S. Y., Lee, J.-S., Park, S.-H., Kang, S. W., Lee, J., Jung, W. Y., Kim, Y.-M., Jeong, J.-H., & Lee, J. H. (2021). Cell-free supernatant of Odoribacter splanchnicus isolated from human feces exhibits anti-colorectal cancer activity. Frontiers in Microbiology, 12, 736343. https://doi.org/10.3389/fmicb.2021.736343
  246. Oliveira, R. A., Ng, K. M., Correia, M. B., Cabral, V., Shi, H., Sonnenburg, J. L., Huang, K. C., & Xavier, K. B. (2020). Klebsiella michiganensis transmission enhances resistance to Enterobacteriaceae gut invasion by nutrition competition. Nature Microbiology, 5(4), 630–641. https://doi.org/10.1038/s41564-019-0658-4
  247. Olson, C. A., Vuong, H. E., Yano, J. M., Liang, Q. Y., Nusbaum, D. J., & Hsiao, E. Y. (2018). The gut microbiota mediates the anti-seizure effects of the ketogenic diet. Cell, 173(7), 1728–1741.e13. https://doi.org/10.1016/j.cell.2018.04.027
  248. Özcan, E., & Sela, D. A. (2018). Inefficient metabolism of the human milk oligosaccharides Lacto-N-tetraose and Lacto-N-neotetraose shifts Bifidobacterium longum subsp. infantis physiology. Frontiers in Nutrition, 5, 46. https://doi.org/10.3389/fnut.2018.00046
  249. Özcan, E., Sun, J., Rowley, D. C., & Sela, D. A. (2017). A human gut commensal ferments cranberry carbohydrates to produce formate. Applied and Environmental Microbiology, 83(17), e01097-17. https://doi.org/10.1128/AEM.01097-17
  250. Özdirik, B., Müller, T., Wree, A., Tacke, F., & Sigal, M. (2021). The Role of Microbiota in Primary Sclerosing Cholangitis and Related Biliary Malignancies. International journal of molecular sciences, 22(13), 6975. https://doi.org/10.3390/ijms22136975
  251. Parada Venegas, D., De la Fuente, M. K., Landskron, G., González, M. J., Quera, R., Dijkstra, G., Harmsen, H. J. M., Faber, K. N., & Hermoso, M. A. (2019). Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Frontiers in Immunology, 10, 277. https://doi.org/10.3389/fimmu.2019.00277
  252. Parker, B. J., Wearsch, P. A., Veloo, A. C. M., & Rodriguez-Palacios, A. (2020). The genus Alistipes: Gut bacteria with emerging implications to inflammation, cancer, and mental health. Frontiers in Immunology, 11, 906. https://doi.org/10.3389/fimmu.2020.00906
  253. Patterson, A. M., Mulder, I. E., Travis, A. J., Lan, A., Cerf-Bensussan, N., Gaboriau-Routhiau, V., Garden, K., Logan, E., Delday, M. I., Coutts, A. G. P., Monnais, E., Ferraria, V. C., Inoue, R., Grant, G., & Aminov, R. I. (2017). Human gut symbiont Roseburia hominis promotes and regulates innate immunity. Frontiers in Immunology, 8, 1166. https://doi.org/10.3389/fimmu.2017.01166
  254. Perrone, P., & D'Angelo, S. (2025). Gut microbiota modulation through Mediterranean diet foods: Implications for human health. Nutrients, 17(6), 948. https://doi.org/10.3390/nu17060948
  255. Pessoa, R. B. G., de Oliveira, W. F., Correia, M. T. D. S., Fontes, A., & Coelho, L. C. B. B. (2022). Aeromonas and human health disorders: Clinical approaches. Frontiers in Microbiology, 13, 868890. https://doi.org/10.3389/fmicb.2022.868890
  256. Petrov, V. A., Saltykova, I. V., Zhukova, I. A., Alifirova, V. M., Zhukova, N. G., Dorofeeva, Y. B., Tyakht, A. V., Kovarsky, B. A., Alekseev, D. G., Kostryukova, E. S., Mironova, Y. S., Izhboldina, O. P., Nikitina, M. A., Perevozchikova, T. V., Fait, E. A., Babenko, V. V., Vakhitova, M. T., Govorun, V. M., & Sazonov, A. E. (2017). Analysis of gut microbiota in patients with Parkinson’s disease. Bulletin of Experimental Biology and Medicine, 162(6), 734–737. https://doi.org/10.1007/s10517-017-3700-7
  257. Phillips, J. E. (1990). Actinobacillus. In C. L. Carter & J. R. Cole (Eds.), Diagnostic procedure in veterinary bacteriology and mycology (5th ed., pp. 143–149). Academic Press.
  258. Phoonlapark, A., Tangshewinsirikul, C., Phosuwattanakul, J., Kittisakmontri, K., Nitisinprasert, S., Nakayama, J., … Chongviriyaphan, N. (2022). Gut microbiome profiles in Thai healthy pregnant women and its association with types of foods. BMC Pregnancy and Childbirth, 22(1), 395. https://doi.org/10.1186/s12884-022-04397-5
  259. Pi, X., Teng, W., Fei, D., Zhao, G., & Liu, W. (2022). Effects of live combined Bacillus subtilis and Enterococcus faecium on gut microbiota composition in C57BL/6 mice and in humans. Frontiers in Cellular and Infection Microbiology, 12, 821662. https://doi.org/10.3389/fcimb.2022.821662
  260. Pichler, M. J., Yamada, C., Shuoker, B., Alvarez-Silva, C., Gotoh, A., Leth, M. L., Schoof, E., Katoh, T., Sakanaka, M., Katayama, T., Jin, C., Karlsson, N. G., Arumugam, M., Fushinobu, S., & Abou Hachem, M. (2020). Butyrate-producing colonic Clostridiales metabolise human milk oligosaccharides and cross-feed on mucin via conserved pathways. Nature Communications, 11(1), 3285. https://doi.org/10.1038/s41467-020-17075-x
  261. Pierzynowski, S., & Pierzynowska, K. (2022). Alpha-ketoglutarate, a key molecule involved in nitrogen circulation in both animals and plants, in the context of human gut microbiota and protein metabolism. Advances in medical sciences, 67(1), 142–147. https://doi.org/10.1016/j.advms.2022.02.004
  262. Piriyakunthorn, C., Sripusanapan, A., Suntornlekha, N., Suparan, K., Kunasol, C., Leemasawat, K., Suwannasom, P., Chattipakorn, N., & Chattipakorn, S. (2024). Alterations of gut microbiome profiles as potential markers in patients developing acute coronary syndrome. European Heart Journal, 45(Supplement_1), ehae666.1500. https://doi.org/10.1093/eurheartj/ehae666.1500
  263. Pomyen, Y., Chaisaingmongkol, J., Rabibhadana, S., et al. (2023). Gut dysbiosis in Thai intrahepatic cholangiocarcinoma and hepatocellular carcinoma. Scientific Reports, 13, 11406. https://doi.org/10.1038/s41598-023-38307-2
  264. Pötgens, S. A., Brossel, H., Sboarina, M., Catry, E., Cani, P. D., Neyrinck, A. M., Delzenne, N. M., & Bindels, L. B. (2018). Klebsiella oxytoca expands in cancer cachexia and acts as a gut pathobiont contributing to intestinal dysfunction. Scientific Reports, 8(1), 12321. https://doi.org/10.1038/s41598-018-30569-5
  265. Precup, G., & Vodnar, D.-C. (2019). Gut Prevotella as a possible biomarker of diet and its eubiotic versus dysbiotic roles: A comprehensive literature review. The British Journal of Nutrition, 122(2), 131–140. https://doi.org/10.1017/S0007114519000680
  266. Preda, M., Popa, M. I., Mihai, M. M., Oţelea, T. C., & Holban, A. M. (2019). Effects of coffee on intestinal microbiota, immunity, and disease. In Caffeinated and cocoa based beverages: Volume 8. The science of beverages (pp. 391–421). Elsevier. https://doi.org/10.1016/B978-0-12-815864-7.00012-X
  267. Priest, T., Vidal-Melgosa, S., Hehemann, J. H., Amann, R., & Fuchs, B. M. (2023). Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic. ISME Communications, 3(1), 130. https://doi.org/10.1038/s43705-023-00324-7
  268. Priya, S., Burns, M. B., Ward, T., Mars, R. A. T., Adamowicz, B., Lock, E. F., Kashyap, P. C., Knights, D., & Blekhman, R. (2022). Identification of shared and disease-specific host gene–microbiome associations across human diseases using multi-omic integration. Nature Microbiology, 7(6), 780–795. https://doi.org/10.1038/s41564-022-01121-z
  269. Pudlo, N. A., Urs, K., Kumar, S. S., German, J. B., Mills, D. A., & Martens, E. C. (2015). Symbiotic human gut bacteria with variable metabolic priorities for host mucosal glycans. mBio, 6(6), e01282-15. https://doi.org/10.1128/mBio.01282-15
  270. Pujo, J., Petitfils, C., Le Faouder, P., Eeckhaut, V., Payros, G., Maurel, S., Perez-Berezo, T., Van Hul, M., Barreau, F., Blanpied, C., Chavanas, S., Van Immerseel, F., Bertrand-Michel, J., Oswald, E., Knauf, C., Dietrich, G., Cani, P. D., & Cenac, N. (2021). Bacteria-derived long chain fatty acid exhibits anti-inflammatory properties in colitis. Gut, 70(6), 1088–1097. https://doi.org/10.1136/gutjnl-2020-321173
  271. Qi, H., Li, Y., Yun, H., Zhang, T., Huang, Y., Zhou, J., Yan, H., Wei, J., Liu, Y., Zhang, Z., Gao, Y., Che, Y., Su, X., Zhu, D., Zhang, Y., Zhong, J., & Yang, R. (2019). Lactobacillus maintains healthy gut mucosa by producing L-ornithine. Communications Biology, 2, 171. https://doi.org/10.1038/s42003-019-0424-4
  272. Quaglio, A. E. V., Grillo, T. G., De Oliveira, E. C. S., Di Stasi, L. C., & Sassaki, L. Y. (2022). Gut microbiota, inflammatory bowel disease and colorectal cancer. World Journal of Gastroenterology, 28(30), 4053–4060. https://doi.org/10.3748/wjg.v28.i30.4053
  273. Raineri, E., Maaß, S., Wang, M., et al. (2022). Staphylococcus aureus populations from the gut and the blood are not distinguished by virulence traits—a critical role of host barrier integrity. Microbiome, 10, 239. https://doi.org/10.1186/s40168-022-01419-44
  274. Ramireddy, L., Tsen, H. Y., Chiang, Y. C., Hung, C. Y., Chen, F. C., & Yen, H. T. (2021). The gene expression and bioinformatic analysis of choline trimethylamine-lyase (CutC) and its activating enzyme (CutD) for gut microbes and comparison with their TMA production levels. Current Research in Microbial Sciences, 2, 100043. https://doi.org/10.1016/j.crmicr.2021.100043
  275. Ramírez-Carrillo, E., Gaona, O., Nieto, J., Sánchez-Quinto, A., Cerqueda-García, D., Falcón, L. I., Rojas-Ramos, O. A., & González-Santoyo, I. (2020). Disturbance in human gut microbiota networks by parasites and its implications in the incidence of depression. Scientific Reports, 10, 3680. https://doi.org/10.1038/s41598-020-60562-w
  276. Randeni, N., Bordiga, M., & Xu, B. (2024). A comprehensive review of the triangular relationship among diet–gut microbiota–inflammation. International Journal of Molecular Sciences, 25(17), 9366. https://doi.org/10.3390/ijms25179366
  277. Rastogi, S., & Singh, A. (2022). Gut microbiome and human health: Exploring how the probiotic genus Lactobacillus modulate immune responses. Frontiers in Pharmacology, 13, 1042189. https://doi.org/10.3389/fphar.2022.1042189
  278. Ray, K. (2022). Bacterial histamine and abdominal pain in irritable bowel syndrome. Nature Reviews Gastroenterology & Hepatology, 19(10), 623. https://doi.org/10.1038/s41575-022-00681-z
  279. Reichardt, N., Duncan, S. H., Young, P., Belenguer, A., McWilliam Leitch, C., Scott, K. P., Flint, H. J., & Louis, P. (2014). Phylogenetic distribution of three pathways for propionate production within the human gut microbiota. The ISME journal, 8(6), 1323–1335. https://doi.org/10.1038/ismej.2014.14
  280. Repoila, F., Le Bohec, F., Guérin, C., Lacoux, C., Tiwari, S., Jaiswal, A. K., Santana, M. P., Kennedy, S. P., Quinquis, B., Rainteau, D., Juillard, V., Furlan, S., Bouloc, P., Nicolas, P., Miyoshi, A., Azevedo, V., & Serror, P. (2022). Adaptation of the gut pathobiont Enterococcus faecalis to deoxycholate and taurocholate bile acids. Scientific Reports, 12(1), 8485. https://doi.org/10.1038/s41598-022-12552-3
  281. Rey, F. E., Gonzalez, M. D., Cheng, J., Wu, M., Ahern, P. P., & Gordon, J. I. (2013). Metabolic niche of a prominent sulfate-reducing human gut bacterium. Proceedings of the National Academy of Sciences of the United States of America, 110(33), 13582–13587. https://doi.org/10.1073/pnas.1312524110
  282. Ribeiro, T. G., Clermont, D., Branquinho, R., Machado, E., Peixe, L., & Brisse, S. (2017). Citrobacter europaeus sp. nov., isolated from water and human faecal samples. International journal of systematic and evolutionary microbiology, 67(1), 170–173. https://doi.org/10.1099/ijsem.0.001606
  283. Ricanek, P., Lothe, S. M., Frye, S. A., Rydning, A., Vatn, M. H., & Tønjum, T. (2012). Gut bacterial profile in patients newly diagnosed with treatment-naïve Crohn's disease. Clinical and Experimental Gastroenterology, 5, 173–186. https://doi.org/10.2147/CEG.S33858
  284. Richards-Corke, K. C., Jiang, Y., Yeliseyev, V., Zhang, Y., Franzosa, E. A., Wang, Z. A., Yapa Abeywardana, M., Cole, P. A., Huttenhower, C., Bry, L., & Balskus, E. P. (2025). A small-molecule inhibitor of gut bacterial urease protects the host from liver injury. ACS Chemical Biology, 20(1), 48–55. https://doi.org/10.1021/acschembio.3c00556
  285. Rimal, B., Collins, S. L., Tanes, C. E., et al. (2024). Bile salt hydrolase catalyses formation of amine-conjugated bile acids. Nature, 626, 859–863. https://doi.org/10.1038/s41586-023-06990-w
  286. Rinninella, E., Raoul, P., Cintoni, M., Franceschi, F., Miggiano, G. A. D., Gasbarrini, A., & Mele, M. C. (2019). What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms, 7(1), 14. https://doi.org/10.3390/microorganisms7010014
  287. Rivière, A., Selak, M., Lantin, D., Leroy, F., & De Vuyst, L. (2016). Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut. Frontiers in microbiology, 7, 979. https://doi.org/10.3389/fmicb.2016.00979
  288. Rocha, I. M. G. d., Torrinhas, R., Fonseca, D., Lyra, C. d. O., de Sousa Alves Neri, J. L., Balmant, B. D., Callado, L., Charlton, K., Queiroz, N., & Waitzberg, D. L. (2023). Pro-inflammatory diet is correlated with high Veillonella rogosae, gut inflammation and clinical relapse of inflammatory bowel disease. Nutrients, 15(19), 4148. https://doi.org/10.3390/nu15194148
  289. Rodpai, R., Sanpool, O., Janwan, P., Boonroumkaew, P., Sadaow, L., Thanchomnang, T., & Maleewong, W. (2022). Gut microbiota diversity in human strongyloidiasis differs little in two different regions in endemic areas of Thailand. PLOS ONE, 17(12), e0279766. https://doi.org/10.1371/journal.pone.0279766
  290. Rodriguez Jovita, M., Collins, M. D., Sjödén, B., & Falsen, E. (1999). Characterization of a novel Atopobium isolate from the human vagina: Description of Atopobium vaginae sp. nov. International Journal of Systematic Bacteriology, 49(4), 1573–1576. https://doi.org/10.1099/00207713-49-4-1573
  291. Roux, E., Nicolas, A., Valence, F., & al. (2022). The genomic basis of the Streptococcus thermophilus health-promoting properties. BMC Genomics, 23, 210. https://doi.org/10.1186/s12864-022-08459-y
  292. Ruan, W., Engevik, M. A., Spinler, J. K., & Versalovic, J. (2020). Healthy human gastrointestinal microbiome: Composition and function after a decade of exploration. Digestive Diseases and Sciences, 65(3), 695–705. https://doi.org/10.1007/s10620-020-06118-4
  293. Ruengsomwong, S., Korenori, Y., Sakamoto, N., Wannissorn, B., Nakayama, J., & Nitisinprasert, S. (2014). Senior Thai fecal microbiota comparison between vegetarians and non-vegetarians using PCR-DGGE and real-time PCR. Journal of Microbiology and Biotechnology, 24(8), 1026–1033. https://doi.org/10.4014/jmb.1310.10043
  294. Ruengsomwong, S., La-Ongkham, O., Jiang, J., Wannissorn, B., Nakayama, J., & Nitisinprasert, S. (2016). Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk. Journal of microbiology and biotechnology, 26(10), 1723–1735. https://doi.org/10.4014/jmb.1603.03057
  295. Sakaguchi, T., Köhler, H., Gu, X., McCormick, B. A., & Reinecker, H.-C. (2002). Shigella flexneri regulates tight junction-associated proteins in human intestinal epithelial cells. Cellular Microbiology, 4(6), 367–381. https://doi.org/10.1046/j.1462-5822.2002.00197.x
  296. Salazar, N., Binetti, A., Gueimonde, M., Alonso, A., Garrido, P., González del Rey, C., González, C., Ruas-Madiedo, P., & de los Reyes-Gavilán, C. G. (2011). Safety and intestinal microbiota modulation by the exopolysaccharide-producing strains Bifidobacterium animalis IPLA R1 and Bifidobacterium longum IPLA E44 orally administered to Wistar rats. International Journal of Food Microbiology, 144(3), 342–351. https://doi.org/10.1016/j.ijfoodmicro.2010.10.016
  297. Salim, S., Ahmad, F., Banu, A., & Mohammad, F. (2022). Gut microbiome and Parkinson’s disease: Perspective on pathogenesis and treatment. Journal of Advanced Research. https://doi.org/10.1016/j.jare.2022.10.013
  298. Samuthpongtorn, C., Saraya, A. W., Joyjinda, Y., Rodpan, A., & Suwanwela, N. C. (2024). Dysbiosis of gut microbiota in patients with large-artery atherosclerotic stroke: A pilot study. Journal of Microbial & Biochemical Technology, 12(1), 001. https://doi.org/10.4172/2320-3528.12.1.001
  299. Sánchez, C., Fente, C., Regal, P., Lamas, A., & Lorenzo, M. P. (2021). Human milk oligosaccharides (HMOs) and infant microbiota: A scoping review. Foods, 10(6), 1429. https://doi.org/10.3390/foods10061429
  300. Sandler, R. H., Finegold, S. M., Bolte, E. R., Buchanan, C. P., Maxwell, A. P., Väisänen, M. L., Nelson, M. N., & Wexler, H. M. (2000). Short-term benefit from oral vancomycin treatment of regressive-onset autism. Journal of Child Neurology, 15(7), 429–435. https://doi.org/10.1177/088307380001500701
  301. Sanmukh, S., & Paunikar, W. (2012). Unique features of plasmids among different Citrobacter species. Nature Precedings. https://doi.org/10.1038/npre.2012.6836.1
  302. Sarria, J. C., Vidal, A. M., & Kimbrough, R. C. III. (2001). Infections caused by Kluyvera species in humans. Clinical Infectious Diseases, 33(7), E69–E74. https://doi.org/10.1086/322686
  303. Sassone-Corsi, M., Nuccio, S. P., Liu, H., Hernandez, D., Vu, C. T., Takahashi, A. A., Edwards, R. A., & Raffatellu, M. (2016). Microcins mediate competition among Enterobacteriaceae in the inflamed gut. Nature, 540(7632), 280–283. https://doi.org/10.1038/nature20557
  304. Sato, T., Matsuda, T., Tagawa, K., & Segawa, S. (2024). α-ketoglutarate produced by lactic acid bacteria inhibits hyaluronidase activity. Bioscience of Microbiota, Food and Health, 43(4), 391–400. https://doi.org/10.12938/bmfh.2024-017
  305. Satthawiwat, N., Jinato, T., Sutheeworapong, S., Tanpowpong, N., Chuaypen, N., & Tangkijvanich, P. (2024). Distinct gut microbial signature and host genetic variants in association with liver fibrosis severity in patients with MASLD. Nutrients, 16(12), 1800. https://doi.org/10.3390/nu16121800
  306. Sayavedra, L., Li, T., Bueno Batista, M., Seah, B. K. B., Booth, C., Zhai, Q., Chen, W., & Narbad, A. (2022). Desulfovibrio diazotrophicus sp. nov., a sulfate-reducing bacterium from the human gut capable of nitrogen fixation. Environmental Microbiology, 24(10), 4971–4986. https://doi.org/10.1111/1462-2920.16239
  307. Schoefer, L., Mohan, R., Schwiertz, A., Braune, A., & Blaut, M. (2003). Anaerobic degradation of flavonoids by Clostridium orbiscindens. Applied and Environmental Microbiology, 69(10), 5849–5854. https://doi.org/10.1128/AEM.69.10.5849-5854.2003
  308. Schwab, C., Ruscheweyh, H.-J., Bunesova, V., Pham, V. T., Beerenwinkel, N., & Lacroix, C. (2017). Trophic interactions of infant Bifidobacteria and Eubacterium hallii during L-fucose and fucosyllactose degradation. Frontiers in Microbiology, 8, 95. https://doi.org/10.3389/fmicb.2017.00095
  309. Sehgal, K., & Khanna, S. (2021). Gut microbiome and Clostridioides difficile infection: a closer look at the microscopic interface. Therapeutic advances in gastroenterology, 14, 1756284821994736. https://doi.org/10.1177/1756284821994736
  310. Senavonge, A., Nakphaichit, M., Vongsangnak, W., Roytrakul, S., Patumcharoenpol, P., Kingkaw, A., Wongoutong, C., Weerapakorn, W., Pornputtapong, N., La-Ongkham, O., Poovorawan, Y., Wanlapakorn, N., Kittipongpattana, P., Nitisinprasert, S., Chatchatee, P., & Suratannon, N. (2025). Dysbiosis involving methionine and PPAR-γ pathways is associated with early onset atopic dermatitis and food allergy. Asian Pacific journal of allergy and immunology, 10.12932/AP-131223-1749. Advance online publication. https://doi.org/10.12932/AP-131223-1749
  311. Senthilkumar, H., & Arumugam, M. (2025). Gut microbiota: a hidden player in polycystic ovary syndrome. Journal of translational medicine, 23(1), 443. https://doi.org/10.1186/s12967-025-06315-7
  312. Shock, T., Badang, L., Ferguson, B., & Martinez-Guryn, K. (2021). The interplay between diet, gut microbes, and host epigenetics in health and disease. Journal of Nutritional Biochemistry, 94, 108631. https://doi.org/10.1016/j.jnutbio.2021.108631
  313. Siddiqui, R., Makhlouf, Z., Alharbi, A. M., Alfahemi, H., & Khan, N. A. (2022, November 1). The gut microbiome and female health. Biology. MDPI. https://doi.org/10.3390/biology11111683
  314. Singh, R. K., Chang, H. W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., Abrouk, M., Farahnik, B., Nakamura, M., Zhu, T. H., Bhutani, T., & Liao, W. (2017). Influence of diet on the gut microbiome and implications for human health. Journal of Translational Medicine, 15, 73. https://doi.org/10.1186/s12967-017-1175-y
  315. Singh, S. B., Carroll-Portillo, A., & Lin, H. C. (2023). Desulfovibrio in the gut: The enemy within? Microorganisms, 11(7), 1772. https://doi.org/10.3390/microorganisms11071772
  316. Singh, V., Lee, G., Son, H., Koh, H., Kim, E. S., Unno, T., & Shin, J. H. (2023). Butyrate producers, The Sentinel of Gut: Their intestinal significance with and beyond butyrate, and prospective use as microbial therapeutics. Frontiers in microbiology, 13, 1103836. https://doi.org/10.3389/fmicb.2022.1103836
  317. Sinsuebchuea, J., Paenkaew, P., Wutthiin, M., Nantanaranon, T., Laeman, K., Kittichotirat, W., Wattanachaisaereekul, S., Dulsawat, S., Nopharatana, M., Vorapreeda, N., Bhumiratana, S., Cheevadhanarak, S., & Sutheeworapong, S. (2023). Characterization of the gut microbiota in urban Thai individuals reveals enterotype-specific signature. Microorganisms, 11(1), 136. https://doi.org/10.3390/microorganisms11010136
  318. Smajdor, J., Jedlińska, K., Porada, R., et al. (2023). The impact of gut bacteria producing long chain homologs of vitamin K2 on colorectal carcinogenesis. Cancer Cell International, 23, 268. https://doi.org/10.1186/s12935-023-03114-2
  319. Sobhonslidsuk, A., Chanprasertyothin, S., Pongrujikorn, T., Kaewduang, P., Promson, K., Petraksa, S., & Ongphiphadhanakul, B. (2018). The association of gut microbiota with nonalcoholic steatohepatitis in Thais. BioMed Research International, 2018, 9340316. https://doi.org/10.1155/2018/9340316
  320. Soldan, M., Argalasova, L., Hadvinova, L., et al. (2024). The effect of dietary types on gut microbiota composition and development of non-communicable diseases: A narrative review. Nutrients, 16(18), 3134. https://doi.org/10.3390/nu16183134
  321. Song, L., Huang, Y., Liu, G., Li, X., Xiao, Y., Liu, C., Zhang, Y., Li, J., Xu, J., Lu, S., & Ren, Z. (2022). A novel immunobiotics Bacteroides dorei ameliorates influenza virus infection in mice. Frontiers in Immunology, 12, 828887. https://doi.org/10.3389/fimmu.2021.828887
  322. Spiegelhauer, M. R., Andersen, P. F., Frandsen, T. H., Nordestgaard, R. L. M., & Andersen, L. P. (2019). Leclercia adecarboxylata: A case report and literature review of 74 cases demonstrating its pathogenicity in immunocompromised patients. Infectious Diseases, 51(3), 179–188. https://doi.org/10.1080/23744235.2018.1536830
  323. Steed, A. L., Christophi, G. P., Kaiko, G. E., Sun, L., Goodwin, V. M., Jain, U., Esaulova, E., Artyomov, M. N., Morales, D. J., Holtzman, M. J., Boon, A. C. M., Lenschow, D. J., & Stappenbeck, T. S. (2017). The microbial metabolite desaminotyrosine protects from influenza through type I interferon. Science, 357(6350), 498–502. https://doi.org/10.1126/science.aam5336
  324. Steinberg, J.P., & Burd, E.M. (2015). Other gram-negative and gram-variable bacilli. Mandell, Douglas, and Bennett's Principles and Practice of Infectious Diseases, 3023, 2667-2683.
  325. Stephens, M., & von der Weid, P. Y. (2020). Lipopolysaccharides modulate intestinal epithelial permeability and inflammation in a species-specific manner. Gut Microbes, 11(3), 421–432. https://doi.org/10.1080/19490976.2019.1629235
  326. Stracke, K., Adisakwattana, P., Phuanukoonnon, S., Yoonuan, T., Poodeepiyasawat, A., Dekumyoy, P., … Jex, A. R. (2021). Field evaluation of the gut microbiome composition of pre-school and school-aged children in Tha Song Yang, Thailand, following oral MDA for STH infections. PLoS Neglected Tropical Diseases, 15(7), e0009597. https://doi.org/10.1371/journal.pntd.0009597
  327. Strati, F., Cavalieri, D., Albanese, D., De Felice, C., Donati, C., Hayek, J., … De Filippo, C. (2017). New evidences on the altered gut microbiota in autism spectrum disorders. Microbiome, 5(1). https://doi.org/10.1186/s40168-017-0242-1
  328. Sudo, N., Chida, Y., Aiba, Y., Sonoda, J., Oyama, N., Yu, X. N., Kubo, C., & Koga, Y. (2004). Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice. The Journal of Physiology, 558(Pt 1), 263–275. https://doi.org/10.1113/jphysiol.2004.063388
  329. Sun, F., Zhang, Q., Zhao, J., Zhang, H., Zhai, Q., & Chen, W. (2019). A potential species of next-generation probiotics? The dark and light sides of Bacteroides fragilis in health. Food Research International, 126, 108590. https://doi.org/10.1016/j.foodres.2019.108590
  330. Suryavanshi, M. V., Bhute, S. S., Gune, R. P., & Shouche, Y. S. (2018). Functional eubacteria species along with trans-domain gut inhabitants favour dysgenic diversity in oxalate stone disease. Scientific Reports, 8(1), 16598. https://doi.org/10.1038/s41598-018-33773-5
  331. Suskun, C., Kilic, O., Yilmaz Ciftdogan, D., et al. (2022). Intestinal microbiota composition of children with infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and multisystem inflammatory syndrome (MIS-C). European Journal of Pediatrics, 181(8), 3175–3191. https://doi.org/10.1007/s00431-022-04494-9
  332. Szczyrek, M., Bitkowska, P., Chunowski, P., Czuchryta, P., Krawczyk, P., & Milanowski, J. (2021). Diet, microbiome, and cancer immunotherapy: A comprehensive review. Nutrients, 13(7), 2217. https://doi.org/10.3390/nu13072217
  333. Tan, H., Zhao, J., Zhang, H., … Chen, W. (2019). Novel strains of Bacteroides fragilis and Bacteroides ovatus alleviate the LPS-induced IBD-ulcerative disease inflammation in mice. Applied Microbiology and Biotechnology, 103(6), 2353–2365. https://doi.org/10.1007/s00253-019-09617-1
  334. Therdtatha, P., Song, Y., Tanaka, M., Mariyatun, M., Almunifah, M., Manurung, N. E. P., … Nakayama, J. (2021). Gut microbiome of Indonesian adults associated with obesity and type 2 diabetes: A cross-sectional study in an Asian city, Yogyakarta. Microorganisms, 9(5), 897. https://doi.org/10.3390/microorganisms9050897
  335. Tomazetto, G., Hahnke, S., Wibberg, D., Pühler, A., Klocke, M., & Schlüter, A. (2018). Proteiniphilum saccharofermentans str. M3/6T isolated from a laboratory biogas reactor is versatile in polysaccharide and oligopeptide utilization as deduced from genome-based metabolic reconstructions. Biotechnology Reports (Amsterdam, Netherlands), 18, e00254. https://doi.org/10.1016/j.btre.2018.e00254
  336. Tomova, A., Bukovsky, I., Rembert, E., Yonas, W., Alwarith, J., Barnard, N. D., & Kahleova, H. (2019). The Effects of Vegetarian and Vegan Diets on Gut Microbiota. Frontiers in nutrition, 6, 47. https://doi.org/10.3389/fnut.2019.00047
  337. Torres, M. D. T., Brooks, E., Cesaro, A., Sberro, H., Nicolaou, C., Bhatt, A. S., & de la Fuente-Nunez, C. (2023). Human gut metagenomic mining reveals an untapped source of peptide antibiotics [Preprint]. bioRxiv. https://doi.org/10.1101/2023.08.31.555711
  338. Ubeda, C., Bucci, V., Caballero, S., Djukovic, A., Toussaint, N. C., Equinda, M., Lipuma, L., Ling, L., Gobourne, A., No, D., Taur, Y., Jenq, R. R., van den Brink, M. R., Xavier, J. B., & Pamer, E. G. (2013). Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization. Infection and Immunity, 81(3), 965–973. https://doi.org/10.1128/IAI.01197-12
  339. Uriot, O., Keboibd-Ulcerative Diseasehi, M., Lorson, E., Galia, W., Denis, S., Chalancon, S., Hafeez, Z., Roux, E., Genay, M., Blanquet-Diot, S., & Dary-Mourot, A. (2021). Identification of Streptococcus thermophilus genes specifically expressed under simulated human digestive conditions using R-IVET technology. Microorganisms, 9(6), 1113. https://doi.org/10.3390/microorganisms9061113
  340. Vacca, M., Celano, G., Calabrese, F. M., Portincasa, P., Gobbetti, M., & De Angelis, M. (2020). The controversial role of human gut Lachnospiraceae. Microorganisms, 8(4), 573. https://doi.org/10.3390/microorganisms8040573
  341. Valles-Colomer, M., Falony, G., Darzi, Y., Tigchelaar, E. F., Wang, J., Tito, R. Y., Schiweck, C., Kurilshikov, A., Joossens, M., Wijmenga, C., … Raes, J. (2019). The neuroactive potential of the human gut microbiota in quality of life and depression. Nature Microbiology, 4, 623–632. https://doi.org/10.1038/s41564-018-0337-x
  342. vBag, S., Ghosh, T. S., & Das, B. (2017). Complete genome sequence of Collinsella aerofaciens isolated from the gut of a healthy Indian subject. Genome Announcements, 5(47). https://doi.org/10.1128/genomeA.01361-17
  343. Verma, R., Morrad, S., & Wirtz, J. J. (2017). Peptoniphilus asaccharolyticus-associated septic arthritis and osteomyelitis in a woman with osteoarthritis and diabetes mellitus. BMJ Case Reports, 2017, bcr2017219969. https://doi.org/10.1136/bcr-2017-219969
  344. Vernocchi, P., Del Chierico, F., & Putignani, L. (2016). Gut microbiota profiling: Metabolomics based approach to unravel compounds affecting human health. Frontiers in Microbiology, 7, 1144. https://doi.org/10.3389/fmicb.2016.01144
  345. Visuthranukul, C., SriswAutism Spectrum Disorderi, S., Tepaamorndech, S., Joyjinda, Y., Saengpanit, P., Kwanbunbumpen, T., … Chomtho, S. (2022). Association of human intestinal microbiota with lifestyle activity, adiposity, and metabolic profiles in Thai children with obesity. Journal of Nutrition and Metabolism, 2022. https://doi.org/10.1155/2022/3029582
  346. Vital, M., Howe, A. C., & Tiedje, J. M. (2014). Revealing the bacterial butyrate synthesis pathways by analyzing (meta)genomic data. mBio, 5(2), e00889. https://doi.org/10.1128/mBio.00889-14
  347. Walters, S. S., Quiros, A., Rolston, M., Grishina, I., Li, J., Fenton, A., DeSantis, T. Z., Thai, A., Andersen, G. L., Papathakis, P., Nieves, R., Prindiville, T., & Dandekar, S. (2014). Analysis of gut microbiome and diet modification in patients with Crohn's disease. SOJ Microbiology & Infectious Diseases, 2(3), 1–13. https://doi.org/10.15226/sojmid/2/3/00122
  348. Wanapaisan, P., Chuansangeam, M., Nopnipa, S., Mathuranyanon, R., Nonthabenjawan, N., Ngamsombat, C., Thientunyakit, T., & Muangpaisan, W. (2022). Association between gut microbiota with mild cognitive impairment and Alzheimer's disease in a Thai population. Neuro-degenerative Diseases, 22(2), 43–54. https://doi.org/10.1159/000526947
  349. Wang, C., Zhao, J., Zhang, H., Lee, Y.-K., Zhai, Q., & Chen, W. (2020). Roles of intestinal Bacteroides in human health and diseases. Critical Reviews in Food Science and Nutrition. https://doi.org/10.1080/10408398.2020.1802695
  350. Wang, H., Ainiwaer, A., Song, Y., Qin, L., Peng, A., Bao, H., & Qin, H. (2023). Perturbed gut microbiome and fecal and serum metabolomes are associated with chronic kidney disease severity. Microbiome, 11(1), 14. https://doi.org/10.1186/s40168-022-01443-4
  351. Wang, L. J., Li, S. C., Li, S. W., Kuo, H. C., Lee, S. Y., Huang, L. H., Chin, C. Y., & Yang, C. Y. (2022). Gut microbiota and plasma cytokine levels in patients with attention-deficit/hyperactivity disorder. Translational Psychiatry, 12(76). https://doi.org/10.1038/s41398-022-01844-x
  352. Wang, L., Christophersen, C. T., Sorich, M. J., Gerber, J. P., Angley, M. T., & Conlon, M. A. (2011). Low relative abundances of the mucolytic bacterium Akkermansia muciniphila and Bifidobacterium spp. in feces of children with autism. Applied and Environmental Microbiology, 77(18), 6718–6721. https://doi.org/10.1128/AEM.05212-11
  353. Wang, M., Wang, Z., Lessing, D. J., Guo, M., & Chu, W. (2023). Fusobacterium nucleatum and its metabolite hydrogen sulfide alter gut microbiota composition and autophagy process and promote colorectal cancer progression. Microbiology spectrum, 11(6), e0229223. https://doi.org/10.1128/spectrum.02292-23
  354. Wang, X., Qi, Y., & Zheng, H. (2022). Dietary polyphenol, gut microbiota, and health benefits. Antioxidants, 11(6), 1212. https://doi.org/10.3390/antiox11061212
  355. Wang, X., Xu, X., & Xia, Y. (2017). Further analysis reveals new gut microbiome markers of type 2 diabetes mellitus. Antonie van Leeuwenhoek, 110(3), 445–453. https://doi.org/10.1007/s10482-016-0805-3
  356. Wang, Y. C., Ku, W. C., Liu, C. Y., Cheng, Y. C., Chien, C. C., Chang, K. W., & Huang, C. J. (2021). Supplementation of probiotic Butyricicoccus pullicaecorum mediates anticancer effect on bladder urothelial cells by regulating butyrate-responsive molecular signatures. Diagnostics, 11(12), 2270. https://doi.org/10.3390/diagnostics11122270
  357. Wang, Y., Ouyang, M., Gao, X., Wang, S., Fu, C., Zeng, J., & He, X. (2020). Pseudoflavonifractor and Lactobacillus intestinalis: Three potential biomarkers of gut microbiota that affect progression and complications of obesity-induced type 2 diabetes mellitus. Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy, 13, 835–850. https://doi.org/10.2147/DMSO.S240728
  358. Wang, Y., Wan, X., Wu, X., Zhang, C., Liu, J., & Hou, S. (2021). Eubacterium rectale contributes to colorectal cancer initiation via promoting colitis. Gut Pathogens, 13(1), 2. https://doi.org/10.1186/s13099-020-00396-z
  359. Wang, Y., Wu, J., Lv, M., Shao, Z., Hungwe, M., Wang, J., Bai, X., Xie, J., Wang, Y., & Geng, W. (2021). Metabolism characteristics of lactic acid bacteria and the expanding applications in food industry. Frontiers in Bioengineering and Biotechnology, 9, 612285. https://doi.org/10.3389/fbioe.2021.612285
  360. Waters, J. L., & Ley, R. E. (2019). The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health. BMC Biology, 17(1), 83. https://doi.org/10.1186/s12915-019-0699-4
  361. Wei, M., Gu, E., Luo, J., Zhang, Z., Xu, D., Tao, X., Shah, N. P., & Wei, H. (2020). Enterococcus hirae WEHI01 isolated from a healthy Chinese infant ameliorates the symptoms of type 2 diabetes by elevating the abundance of Lactobacillales in rats. Journal of Dairy Science, 103(4), 2969–2981. https://doi.org/10.3168/jds.2019-17185
  362. Wei, Y., Li, Y., Yan, L., Sun, C., Miao, Q., Wang, Q., Xiao, X., Lian, M., Li, B., Chen, Y., Zhang, J., Li, Y., Huang, B., Li, Y., Cao, Q., Fan, Z., Chen, X., Fang, J. Y., Gershwin, M. E., Tang, R., … Ma, X. (2020). Alterations of gut microbiome in autoimmune hepatitis. Gut, 69(3), 569–577. https://doi.org/10.1136/gutjnl-2018-317836
  363. Wilck, N., Matus, M. G., Kearney, S. M., Olesen, S. W., Forslund, K., Bartolomaeus, H., Haase, S., Mähler, A., Balogh, A., Markó, L., Vvedenskaya, O., Kleiner, F. H., Tsvetkov, D., Klug, L., Costea, P. I., Sunagawa, S., Maier, L., Rakova, N., Schatz, V., Neubert, P., … Müller, D. N. (2017). Salt-responsive gut commensal modulates TH17 axis and disease. Nature, 551(7682), 585–589. https://doi.org/10.1038/nature24628
  364. Williams, A., Porter, J., Kingsley, K., & Howard, K. M. (2024). Higher prevalence of the periodontal pathogen Selenomonas noxia among pediatric and adult patients may be associated with overweight and obesity. Pathogens, 13(4), 338. https://doi.org/10.3390/pathogens13040338
  365. Wolter, M., Grant, E. T., Boudaud, M., Steimle, A., Pereira, G. V., Martens, E. C., & Desai, M. S. (2021, December 1). Leveraging diet to engineer the gut microbiome. Nature Reviews Gastroenterology & Hepatology. https://doi.org/10.1038/s41575-021-00512-7
  366. Won, E. J., Jang, H. H., Park, H., & Kim, S. J. (2022). A potential predictive role of the scalp microbiome profiling in patients with alopecia areata: Staphylococcus caprae, Corynebacterium, and Cutibacterium species. Microorganisms, 10(5), 864. https://doi.org/10.3390/microorganisms10050864
  367. Wu, Q. L., Fang, X. T., Wan, X. X., Ding, Q. Y., Zhang, Y. J., Ji, L., Lou, Y. L., & Li, X. (2024). Fusobacterium nucleatum-induced imbalance in microbiome-derived butyric acid levels promotes the occurrence and development of colorectal cancer. World journal of gastroenterology, 30(14), 2018–2037. https://doi.org/10.3748/wjg.v30.i14.2019
  368. Wu, Y. T., Shen, S. J., Liao, K. F., & Huang, C. Y. (2022). Dietary plant and animal protein sources oppositely modulate fecal Bilophila and Lachnoclostridium in vegetarians and omnivores. Microbiology Spectrum, 10(2), e0204721. https://doi.org/10.1128/spectrum.02047-21
  369. Wutthi-in, M., Cheevadhanarak, S., Yasom, S., Kerdphoo, S., Thiennimitr, P., Phrommintikul, A., … Chattipakorn, S. (2020). Gut microbiota profiles of treated metabolic syndrome patients and their relationship with metabolic health. Scientific Reports, 10, 10085. https://doi.org/10.1038/s41598-020-67078-3
  370. Xing, J., Niu, T., Yu, T., Zou, B., Fan, S., Wang, C., Shi, C., Zhang, D., Wang, N., Jiang, Y., Huang, H., Cao, X., Zeng, Y., Wang, J., Zhang, D., Yang, G., & Yang, W. (2025). Gut microbiota-derived isovaleric acid ameliorates influenza virus infection via gut-lung axis. NPJ Biofilms and Microbiomes, 11(1), 116. https://doi.org/10.1038/s41522-025-00753-3
  371. Xiong, R. G., Li, J., Cheng, J., Zhou, D. D., Wu, S. X., Huang, S. Y., Saimaiti, A., Yang, Z. J., Gan, R. Y., & Li, H. B. (2023). The role of gut microbiota in anxiety, depression, and other mental disorders as well as the protective effects of dietary components. Nutrients, 15(14), 3258. https://doi.org/10.3390/nu15143258
  372. Xu, H., Liu, M., Cao, J., Li, X., Fan, D., Xia, Y., Lu, X., Li, J., Ju, D., & Zhao, H. (2019). The dynamic interplay between the gut microbiota and autoimmune diseases. Journal of Immunology Research, 2019, 7546047. https://doi.org/10.1155/2019/7546047
  373. Yang, G., Hong, S., Yang, P., Sun, Y., Wang, Y., Zhang, P., Jiang, W., & Gu, Y. (2021). Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria. Nature Communications, 12(1), 790. https://doi.org/10.1038/s41467-021-20974-2
  374. Yang, S. C., Lin, C. H., Sung, C. T., & Fang, J. Y. (2014). Antibacterial activities of bacteriocins: Application in foods and pharmaceuticals. Frontiers in Microbiology, 5, 241. https://doi.org/10.3389/fmicb.2014.00241
  375. Yao, S., Zhao, Y., Chen, H., Sun, R., Chen, L., Huang, J., Yu, Z., & Chen, S. (2023). Exploring the plasticity of diet on gut microbiota and its correlation with gut health. Nutrients, 15(15), 3460. https://doi.org/10.3390/nu151534600
  376. Yarahmadi, A., Afkhami, H., Javadi, A., & Kashfi, M. (2024). Understanding the complex function of gut microbiota: Its impact on the pathogenesis of obesity and beyond: A comprehensive review. Diabetology & Metabolic Syndrome, 16(1), 308. https://doi.org/10.1186/s13098-024-01561-z
  377. Yeh, T.-K., Lin, H.-J., Liu, P.-Y., Wang, J.-H., & Hsueh, P.-R. (2022). Antibiotic resistance in Enterobacter hormaechei. International Journal of Antimicrobial Agents, 60(4), 106650. https://doi.org/10.1016/j.ijantimicag.2022.106650
  378. Yincharoen, P., Mordmuang, A., Techarang, T., et al. (2025). Microbiome and biofilm insights from normal vs tumor tissues in Thai colorectal cancer patients. NPJ Precision Oncology, 9, 98. https://doi.org/10.1038/s41698-025-00873-1
  379. Yong, C. C., Sakurai, T., Kaneko, H., Horigome, A., Mitsuyama, E., Nakajima, A., … Katayama, T. (2024). Human gut-associated Bifidobacterium species salvage exogenous indole, a uremic toxin precursor, to synthesize indole-3-lactic acid via tryptophan. Gut Microbes, 16(1). https://doi.org/10.1080/19490976.2024.2347728
  380. Yoshida, N., Emoto, T., Yamashita, T., Watanabe, H., Hayashi, T., Tabata, T., Hoshi, N., Hatano, N., Ozawa, G., Sasaki, N., Mizoguchi, T., Amin, H. Z., Hirota, Y., Ogawa, W., Yamada, T., & Hirata, K. I. (2018). Bacteroides vulgatus and Bacteroides dorei gut microbial lipopolysaccharide production and inhibit atherosclerosis. Circulation, 138(22), 2486–2498. https://doi.org/10.1161/CIRCULATIONAHA.118.033714
  381. Yoshii, K., Hosomi, K., Sawane, K., & Kunisawa, J. (2019). Metabolism of dietary and microbial vitamin B family in the regulation of host immunity. Frontiers in Nutrition, 6, 48. https://doi.org/10.3389/fnut.2019.00048
  382. Zafar, H., & Saier, M. H. Jr. (2021). Gut Bacteroides species in health and disease. Gut Microbes, 13(1), 1–20. https://doi.org/10.1080/19490976.2020.1848158 PMC7872030.
  383. Ze, X., Duncan, S., Louis, P., & Flint, H. J. (2012). Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. The ISME Journal, 6(7), 1535–1543. https://doi.org/10.1038/ismej.2012.4
  384. Zhang, L., Liu, J., Deng, M., & others. (2023). Enterococcus faecalis promotes the progression of colorectal cancer via its metabolite: Biliverdin. Journal of Translational Medicine, 21, 72. https://doi.org/10.1186/s12967-023-03929-7
  385. Zhang, L., Qing, P., Yang, H., Wu, Y., Liu, Y., & Luo, Y. (2021). Gut microbiome and metabolites in systemic lupus erythematosus: Link, mechanisms and intervention. Frontiers in Immunology, 12, 686501. https://doi.org/10.3389/fimmu.2021.686501
  386. Zhang, M., Sun, K., Wu, Y., Yang, Y., Tso, P., & Wu, Z. (2017). Interactions between intestinal microbiota and host immune response in inflammatory bowel disease. Frontiers in Immunology, 8, 942. https://doi.org/10.3389/fimmu.2017.00942
  387. Zhang, Q., Guo, W. L., Chen, G. M., Qian, M., Han, J. Z., Lv, X. C., … Ni, L. (2022). Pediococcus acidilactici FZU106 alleviates high-fat diet-induced lipid metabolism disorder in association with the modulation of intestinal microbiota in hyperlipidemic rats. Current Research in Food Science, 5, 775–788. https://doi.org/10.1016/j.crfs.2022.04.009
  388. Zhang, Q., Wu, Y., Wang, J., Wu, G., Long, W., Xue, Z., Wang, L., Zhang, X., Pang, X., Zhao, Y., Zhao, L., & Zhang, C. (2016). Accelerated dysbiosis of gut microbiota during aggravation of DSS-induced colitis by a butyrate-producing bacterium. Scientific Reports, 6, 27572. https://doi.org/10.1038/srep27572
  389. Zhang, Q., Zou, R., Guo, M., Duan, M., Li, Q., & Zheng, H. (2021). Comparison of gut microbiota between adults with autism spectrum disorder and obese adults. PeerJ, 9, e10946. https://doi.org/10.7717/peerj.10946
  390. Zhang, S., Lu, J., Jin, Z., Xu, H., Zhang, D., Chen, J., & Wang, J. (2024). Gut microbiota metabolites: Potential therapeutic targets for Alzheimer's disease? Frontiers in Pharmacology, 15, 1459655. https://doi.org/10.3389/fphar.2024.1459655
  391. Zhang, Y., Ma, J., Jing, N., Zhang, H., Xie, Y., Liu, H., Shan, X., Ren, J., & Jin, J. (2023). Bifidobacterium animalis A12 and Lactobacillus salivarius M18-6 alleviate alcohol injury by Keap1-Nrf2 pathway and thioredoxin system. Foods, 12(3), 439. https://doi.org/10.3390/foods12030439
  392. Zhao, H., Yang, C. E., Liu, T., Zhang, M. X., Niu, Y., Wang, M., & Yu, J. (2023). The roles of gut microbiota and its metabolites in diabetic nephropathy. Frontiers in Microbiology, 14, 1207132. https://doi.org/10.3389/fmicb.2023.1207132
  393. Zhao, L., Huang, Y., Lu, L., … et al. (2018). Saturated long-chain fatty acid-producing bacteria contribute to enhanced colonic motility in rats. Microbiome, 6, 107. https://doi.org/10.1186/s40168-018-0492-6
  394. Zheng, D., Liwinski, T., & Elinav, E. (2020). Interaction between microbiota and immunity in health and disease. Cell Research, 30(6), 492–506. https://doi.org/10.1038/s41422-020-0332-7
  395. Zheng, J., Hoffman, K. L., Chen, J.-S., Shivappa, N., Sood, A., Browman, G. J., Dirba, D. D., Hanash, S., Wei, P., Hebert, J. R., Petrosino, J. F., Schembre, S. M., & Daniel, C. R. (2020). Dietary inflammatory potential in relation to the gut microbiome: Results from a cross-sectional study. The British Journal of Nutrition, 124(9), 931–942. https://doi.org/10.1017/S0007114520001853
  396. Zhou, Y., Zhang, X., Pan, L., Zhang, W., Chen, F., Hu, S., & Jiang, H. (2022). Fecal microbiota in pediatric depression and its relation to bowel habits. Journal of Psychiatric Research, 150, 113–121. https://doi.org/10.1016/j.jpsychires.2022.03.037
  397. Zhou, Z., Sun, B., Yu, D., & Zhu, C. (2022). Gut microbiota: An important player in type 2 diabetes mellitus. Frontiers in Cellular and Infection Microbiology, 12, 834485. https://doi.org/10.3389/fcimb.2022.834485
  398. Zhu, C., Zheng, M., Ali, U., Xia, Q., Wang, Z., Yao, C., Yao, L., Chen, Y., Yan, J., Wang, K., … & Zhang, X. (2021). Association between abundance of Haemophilus in the gut microbiota and negative symptoms of schizophrenia. Frontiers in Psychiatry, 12, 685910. https://doi.org/10.3389/fpsyt.2021.685910
  399. Zhu, S., Jiang, Y., Xu, K., Cui, M., Ye, W., Zhao, G., & Chen, X. (2020). The progress of gut microbiome research related to brain disorders. Journal of Neuroinflammation, 17(1), 25. https://doi.org/10.1186/s12974-020-1705-z
  400. Zhuang, Z., Yang, R., Wang, W., et al. (2020). Associations between gut microbiota and Alzheimer’s disease, major depressive disorder, and schizophrenia. Journal of Neuroinflammation, 17, 288. https://doi.org/10.1186/s12974-020-01961-8