REFERENCES
1. Qin J, Li R, Raes J, et al. MetaHIT Consortium. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59-65.
3. Buford TW. (Dis)Trust your gut: the gut microbiome in age-related inflammation, health, and disease. Microbiome 2017;5:80.
4. Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature 2011;473:174-80.
5. Magne F, Gotteland M, Gauthier L, et al. The firmicutes/Bacteroidetes ratio: a relevant marker of gut dysbiosis in obese patients? Nutrients 2020;12:1474.
6. Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 2021:71.
7. Rinninella E, Raoul P, Cintoni M, et al. What is the healthy gut microbiota composition? Microorganisms 2019;7:14.
9. Enav H, Bäckhed F, Ley RE. The developing infant gut microbiome: a strain-level view. Cell Host Microbe 2022;30:627-38.
10. Forster SC, Kumar N, Anonye BO, et al. A human gut bacterial genome and culture collection for improved metagenomic analyses. Nat Biotechnol 2019;37:186-92.
11. Vonaesch P, Anderson M, Sansonetti PJ. Pathogens, microbiome and the host: emergence of the ecological Koch’s postulates. FEMS Microbiol Rev 2018;42:273-92.
12. Duvallet C, Gibbons SM, Gurry T, Irizarry RA, Alm EJ. Meta-analysis of gut microbiome studies identifies disease-specific and shared responses. Nat Commun 2017;8:1784.
14. Clapp M, Aurora N, Herrera L, Bhatia M, Wilen E, Wakefield S. Gut microbiota’s effect on mental health: The gut-brain axis. Clin Pract 2017;7:987.
15. Usami M, Miyoshi M, Yamashita H. Gut microbiota and host metabolism in liver cirrhosis. World J Gastroenterol 2015;21:11597-608.
16. Gou W, Fu Y, Yue L, et al. Gut microbiota, inflammation, and molecular signatures of host response to infection. J Genet Genomics 2021;48:792-802.
17. Kunasegaran T, Balasubramaniam VRMT, Arasoo VJT, Palanisamy UD, Ramadas A. The modulation of gut microbiota composition in the pathophysiology of gestational diabetes mellitus: a systematic review. Biology 2021;10:1027.
18. Sircana A, Framarin L, Leone N, et al. Altered gut microbiota in type 2 diabetes: just a coincidence? Curr Diab Rep 2018;18:98.
19. Dodd CS, Grueber CE. Functional diversity within gut microbiomes: implications for conserving biodiversity. Conservation 2021;1:311-26.
20. Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature 2012;489:220-30.
21. Scholtens PA, Oozeer R, Martin R, Amor KB, Knol J. The early settlers: intestinal microbiology in early life. Annu Rev Food Sci Technol 2012;3:425-47.
22. Kujawska M, La Rosa SL, Roger LC, et al. Succession of bifidobacterium longum strains in response to a changing early life nutritional environment reveals dietary substrate adaptations. iScience 2020;23:101368.
23. Escalas A, Hale L, Voordeckers JW, et al. Microbial functional diversity: from concepts to applications. Ecol Evol 2019;9:12000-16.
24. Coyte KZ, Rakoff-Nahoum S. Understanding competition and cooperation within the mammalian gut microbiome. Curr Biol 2019;29:R538-44.
25. Saa P, Urrutia A, Silva-Andrade C, Martín AJ, Garrido D. Modeling approaches for probing cross-feeding interactions in the human gut microbiome. Comput Struct Biotechnol J 2022;20:79-89.
26. Goyal A, Wang T, Dubinkina V, Maslov S. Ecology-guided prediction of cross-feeding interactions in the human gut microbiome. Nat Commun 2021;12:1335.
27. Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol 2016;14:20-32.
28. Abu-Ali GS, Mehta RS, Lloyd-Price J, et al. Metatranscriptome of human faecal microbial communities in a cohort of adult men. Nat Microbiol 2018;3:356-66.
29. Faust K, Raes J. Microbial interactions: from networks to models. Nat Rev Microbiol 2012;10:538-50.
30. David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014;505:559-63.
31. Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes 2012;3:289-306.
32. La Rosa SL, Ostrowski MP, Vera-Ponce de León A, et al. Glycan processing in gut microbiomes. Curr Opin Microbiol 2022;67:102143.
33. González-Morelo K J, Vega-Sagardía M, Garrido D. Molecular insights into O-linked glycan utilization by gut microbes. Front Microbiol 2020;11:591568.
34. Belzer C, Chia LW, Aalvink S, et al. Microbial metabolic networks at the mucus layer lead to diet-independent butyrate and vitamin B(12) production by intestinal symbionts. mBio 2017:8.
35. Koh A, De Vadder F, Kovatcheva-Datchary P, Bäckhed F. From dietary fiber to host physiology: short-chain fatty acids as key bacterial metabolites. Cell 2016;165:1332-45.
36. Makki K, Deehan EC, Walter J, Bäckhed F. The impact of dietary fiber on gut microbiota in host health and disease. Cell Host Microbe 2018;23:705-15.
37. Hirmas B, Gasaly N, Orellana G, et al. Metabolic modeling and bidirectional culturing of two gut microbes reveal cross-feeding interactions and protective effects on intestinal cells. mSystems 2022;7:e0064622.
38. Bourriaud C, Robins RJ, Martin L, et al. Lactate is mainly fermented to butyrate by human intestinal microfloras but inter-individual variation is evident. J Appl Microbiol 2005;99:201-12.
39. Tsukuda N, Yahagi K, Hara T, et al. Key bacterial taxa and metabolic pathways affecting gut short-chain fatty acid profiles in early life. ISME J 2021;15:2574-90.
40. Pokusaeva K, Fitzgerald GF, van Sinderen D. Carbohydrate metabolism in Bifidobacteria. Genes Nutr 2011;6:285-306.
41. Rivière A, Selak M, Lantin D, Leroy F, De Vuyst L. Bifidobacteria and butyrate-producing colon bacteria: importance and strategies for their stimulation in the human gut. Front Microbiol 2016;7:979.
42. Belenguer A, Duncan SH, Calder AG, et al. Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut. Appl Environ Microbiol 2006;72:3593-9.
43. Falony G, Vlachou A, Verbrugghe K, De Vuyst L. Cross-feeding between Bifidobacterium longum BB536 and acetate-converting, butyrate-producing colon bacteria during growth on oligofructose. Appl Environ Microbiol 2006;72:7835-41.
44. Chia LW, Mank M, Blijenberg B, et al. Cross-feeding between Bifidobacterium infantis and Anaerostipes caccae on lactose and human milk oligosaccharides. Benef Microbes 2021;12:69-83.
45. Bunesova V, Lacroix C, Schwab C. Mucin cross-feeding of infant Bifidobacteria and Eubacterium hallii. Microb Ecol 2018;75:228-38.
46. Laursen MF, Sakanaka M, von Burg N, et al. Bifidobacterium species associated with breastfeeding produce aromatic lactic acids in the infant gut. Nat Microbiol 2021;6:1367-82.
47. Parada Venegas D, De la Fuente M K, Landskron G, et al. Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front Immunol 2019;10:277.
48. Corrêa-Oliveira R, Fachi JL, Vieira A, Sato FT, Vinolo MA. Regulation of immune cell function by short-chain fatty acids. Clin Transl Immunol 2016;5:e73.
49. Litvak Y, Byndloss MX, Bäumler AJ. Colonocyte metabolism shapes the gut microbiota. Science 2018;362:eaat9076.
50. Donohoe DR, Garge N, Zhang X, et al. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell Metab 2011;13:517-26.
51. Sun M, Wu W, Liu Z, et al. Microbiota metabolite short chain fatty acids, GPCR, and inflammatory bowel diseases. J Gastroenterol 2017;52:1-8.
52. Gasaly N, de Vos P, Hermoso MA. Impact of bacterial metabolites on gut barrier function and host immunity: a focus on bacterial metabolism and its relevance for intestinal inflammation. Front Immunol 2021;12:658354.
53. Vital M, Howe AC, Tiedje JM. Revealing the bacterial butyrate synthesis pathways by analyzing (meta) genomic data. MBio 2014;5:e00889-14.
54. Clark RL, Connors BM, Stevenson DM, et al. Design of synthetic human gut microbiome assembly and butyrate production. Nat Commun 2021;12:3254.
55. Zmora N, Suez J, Elinav E. You are what you eat: diet, health and the gut microbiota. Nat Rev Gastroenterol Hepatol 2019;16:35-56.
56. Boulangé CL, Neves AL, Chilloux J, Nicholson JK, Dumas ME. Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Med 2016;8:42.
57. Vital M, Penton CR, Wang Q, et al. A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. Microbiome 2013;1:8.
58. Louis P, Flint HJ. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol Lett 2009;294:1-8.
59. O Sheridan P, Martin JC, Lawley TD, et al. Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes. Microb Genom 2016;2:e000043.
60. Qian Y, Lan F, Venturelli OS. Towards a deeper understanding of microbial communities: integrating experimental data with dynamic models. Curr Opin Microbiol 2021;62:84-92.
61. Petersen C, Round JL. Defining dysbiosis and its influence on host immunity and disease. Cell Microbiol 2014;16:1024-33.
63. Coutzac C, Jouniaux JM, Paci A, et al. Systemic short chain fatty acids limit antitumor effect of CTLA-4 blockade in hosts with cancer. Nat Commun 2020;11:2168.
64. Lupton JR. Microbial degradation products influence colon cancer risk: the butyrate controversy. J Nutr 2004;134:479-82.
65. Honda K, Littman DR. The microbiota in adaptive immune homeostasis and disease. Nature 2016;535:75-84.
66. Dominguez-Bello MG, Godoy-Vitorino F, Knight R, Blaser MJ. Role of the microbiome in human development. Gut 2019;68:1108-14.
67. Takiishi T, Fenero CIM, Câmara NOS. Intestinal barrier and gut microbiota: shaping our immune responses throughout life. Tissue Barriers 2017;5:e1373208.
68. Carding S, Verbeke K, Vipond DT, Corfe BM, Owen LJ. Dysbiosis of the gut microbiota in disease. Microb Ecol Health Dis 2015;26:26191.
69. Nishida A, Inoue R, Inatomi O, Bamba S, Naito Y, Andoh A. Gut microbiota in the pathogenesis of inflammatory bowel disease. Clin J Gastroenterol 2018;11:1-10.
70. Kriss M, Hazleton KZ, Nusbacher NM, Martin CG, Lozupone CA. Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery. Curr Opin Microbiol 2018;44:34-40.
71. Ternes D, Karta J, Tsenkova M, Wilmes P, Haan S, Letellier E. Microbiome in colorectal cancer: how to get from meta-omics to mechanism? Trends Microbiol 2020;28:401-23.
72. Khan I, Bai Y, Zha L, et al. Mechanism of the gut microbiota colonization resistance and enteric pathogen infection. Front Cell Infect Microbiol 2021;11:1273.
73. Diether NE, Willing BP. Microbial fermentation of dietary protein: an important factor in diet-microbe-host interaction. Microorganisms 2019;7:19.
74. Isles NS, Mu A, Kwong JC, Howden BP, Stinear TP. Gut microbiome signatures and host colonization with multidrug-resistant bacteria. Trends Microbiol 2022;30:853-65.
75. Mosca A, Leclerc M, Hugot JP. Gut microbiota diversity and human diseases: should we reintroduce key predators in our ecosystem? Front Microbiol 2016;7:455.
76. Sze MA, Schloss PD. Looking for a signal in the noise: revisiting obesity and the microbiome. MBio 2016;7:e01018-16.
77. Vindigni SM, Zisman TL, Suskind DL, Damman CJ. The intestinal microbiome, barrier function, and immune system in inflammatory bowel disease: a tripartite pathophysiological circuit with implications for new therapeutic directions. Therap Adv Gastroenterol 2016;9:606-25.
78. Shealy NG, Yoo W, Byndloss MX. Colonization resistance: metabolic warfare as a strategy against pathogenic Enterobacteriaceae. Curr Opin Microbiol 2021;64:82-90.
79. Duranti S, Gaiani F, Mancabelli L, et al. Elucidating the gut microbiome of ulcerative colitis: bifidobacteria as novel microbial biomarkers. FEMS Microbiol Ecol 2016;92:fiw191.
80. Li M, Ding J, Stanton C, et al. Bifidobacterium longum subsp. infantis FJSYZ1M3 ameliorates DSS-induced colitis by maintaining the intestinal barrier, regulating inflammatory cytokines, and modifying gut microbiota. Food Funct 2023;14:354-68.
81. Vazquez-Gutierrez P, De Wouters T, Werder J, Chassard C, Lacroix C. High iron-sequestrating bifidobacteria inhibit enteropathogen growth and adhesion to intestinal epithelial cells in vitro. Front Microbiol 2016;7:1480.
82. Vito R, Conte C, Traina G. A multi-strain probiotic formulation improves intestinal barrier function by the modulation of tight and adherent junction proteins. Cells 2022;11:2617.
83. Duranti S, Vivo V, Zini I, et al. Bifidobacterium bifidum PRL2010 alleviates intestinal ischemia/reperfusion injury. PLoS One 2018;13:e0202670.
84. Koninkx JF, Tooten PC, Malago JJ. Probiotic bacteria induced improvement of the mucosal integrity of enterocyte-like Caco-2 cells after exposure to Salmonella enteritidis 857. J Funct Foods 2010;2:225-34.
85. Kim JY, Bang SJ, Kim JY, et al. The probiotic strain bifidobacterium animalis ssp. lactis HY8002 potentially improves the mucosal integrity of an altered intestinal microbial environment. Front Microbiol 2022;13:1573.
86. Engevik MA, Luk B, Chang-Graham AL, et al. Bifidobacterium dentium fortifies the intestinal mucus layer via autophagy and calcium signaling pathways. MBio 2019;10:e01087-19.
87. Wang X, Fukui H, Ran Y, et al. Probiotic Bifidobacterium bifidum G9-1 has a preventive effect on the acceleration of colonic permeability and M1 macrophage population in maternally separated rats. Biomedicines 2021;9:641.
88. Kurose Y, Minami J, Sen A, et al. Bioactive factors secreted by Bifidobacterium breve B-3 enhance barrier function in human intestinal Caco-2 cells. Benef Microbes 2019;10:89-100.
89. López P, González-Rodríguez I, Sánchez B, et al. Interaction of Bifidobacterium bifidum LMG13195 with HT29 cells influences regulatory-T-cell-associated chemokine receptor expression. Appl Environ Microbiol 2012;78:2850-7.
90. Pacheco AR, Segrè D. A multidimensional perspective on microbial interactions. FEMS Microbiol Lett 2019:366.
91. Klymiuk I, Singer G, Castellani C, Trajanoski S, Obermüller B, Till H. Characterization of the luminal and mucosa-associated microbiome along the gastrointestinal tract: results from surgically treated preterm infants and a murine model. Nutrients 2021;13:1030.
92. Pacheco AR, Moel M, Segrè D. Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems. Nat Commun 2019;10:103.
93. Sung J, Kim S, Cabatbat JJT, et al. Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis. Nat Commun 2017;8:15393.
94. Magnúsdóttir S, Heinken A, Kutt L, et al. Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota. Nat Biotechnol 2017;35:81-9.
95. Wang T, Goyal A, Dubinkina V, Maslov S. Evidence for a multi-level trophic organization of the human gut microbiome. PLoS Comput Biol 2019;15:e1007524.
96. D'Souza G, Shitut S, Preussger D, Yousif G, Waschina S, Kost C. Ecology and evolution of metabolic cross-feeding interactions in bacteria. Nat Prod Rep 2018;35:455-88.
97. Gutiérrez N, Garrido D. Species deletions from microbiome consortia reveal key metabolic interactions between gut microbes. mSystems 2019:4.
98. Egan M, Motherway MO, Kilcoyne M, et al. Cross-feeding by Bifidobacterium breve UCC2003 during co-cultivation with Bifidobacterium bifidum PRL2010 in a mucin-based medium. BMC Microbiol 2014;14:282.
99. Turroni F, Özcan E, Milani C, et al. Glycan cross-feeding activities between bifidobacteria under in vitro conditions. Front Microbiol 2015;6:1030.
100. Kim H, Jeong Y, Kang S, You HJ, Ji GE. Co-culture with Bifidobacterium catenulatum improves the growth, gut colonization, and butyrate production of faecalibacterium prausnitzii: in vitro and in vivo studies. Microorganisms 2020;8:788.
101. Holscher HD. Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut Microbes 2017;8:172-84.
102. Louis P, Flint HJ. Formation of propionate and butyrate by the human colonic microbiota. Environ Microbiol 2017;19:29-41.
103. Stevens EJ, Bates KA, King KC. Host microbiota can facilitate pathogen infection. PLoS Pathog 2021;17:e1009514.
104. Neumann M, Steimle A, Grant ET, et al. Deprivation of dietary fiber in specific-pathogen-free mice promotes susceptibility to the intestinal mucosal pathogen Citrobacter rodentium. Gut Microbes 2021;13:1966263.
105. Ghoul M, Mitri S. The ecology and evolution of microbial competition. Trends Microbiol 2016;24:833-45.
106. Eberl C, Weiss AS, Jochum LM, et al. E. coli enhance colonization resistance against Salmonella Typhimurium by competing for galactitol, a context-dependent limiting carbon source. Cell Host Microbe 2021;29:1680-1692.e7.
107. Litvak Y, Mon KKZ, Nguyen H, et al. Commensal enterobacteriaceae protect against salmonella colonization through oxygen competition. Cell Host Microbe 2019;25:128-139.e5.
108. Rogers AWL, Tsolis RM, Bäumler AJ. Salmonella versus the Microbiome. Microbiol Mol Biol Rev 2021:85.
109. Stoffels L, Krehenbrink M, Berks BC, Unden G. Thiosulfate reduction in Salmonella enterica is driven by the proton motive force. J Bacteriol 2012;194:475-85.
110. Winter SE, Thiennimitr P, Winter MG, et al. Gut inflammation provides a respiratory electron acceptor for Salmonella. Nature 2010;467:426-9.
111. Rivera-Chávez F, Zhang LF, Faber F, et al. Depletion of butyrate-producing clostridia from the gut microbiota drives an aerobic luminal expansion of salmonella. Cell Host Microbe 2016;19:443-54.
112. Le Guern R, Stabler S, Gosset P, et al. Colonization resistance against multi-drug-resistant bacteria: a narrative review. J Hosp Infect 2021;118:48-58.
113. Garcia-Gutierrez E, Mayer MJ, Cotter PD, Narbad A. Gut microbiota as a source of novel antimicrobials. Gut Microbes 2019;10:1-21.
114. Hromada S, Qian Y, Jacobson TB, et al. Negative interactions determine Clostridioides difficile growth in synthetic human gut communities. Mol Syst Biol 2021;17:e10355.
115. Smith DR, Temime L, Opatowski L. Microbiome-pathogen interactions drive epidemiological dynamics of antibiotic resistance: a modeling study applied to nosocomial pathogen control. Elife 2021:10.
116. Martinez FA, Balciunas EM, Converti A, Cotter PD, de Souza Oliveira RP. Bacteriocin production by Bifidobacterium spp. A review. Biotechnol Adv 2013;31:482-8.
117. Liu G, Ren G, Zhao L, Cheng L, Wang C, Sun B. Antibacterial activity and mechanism of bifidocin A against Listeria monocytogenes. Food Control 2017;73:854-61.
118. Mahdi LH, Laftah AR, Yaseen KH, Auda IG, Essa RH. Establishing novel roles of bifidocin LHA, antibacterial, antibiofilm and immunomodulator against Pseudomonas aeruginosa corneal infection model. Int J Biol Macromol 2021;186:433-44.
119. Fukuda S, Toh H, Hase K, et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 2011;469:543-7.
120. Walker AW, Duncan SH, McWilliam Leitch EC, Child MW, Flint HJ. pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon. Appl Environ Microbiol 2005;71:3692-700.
121. Park SY, Rao C, Coyte KZ, et al. Strain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite. Cell 2022;185:513-529.e21.
122. Shelton CD, Yoo W, Shealy NG, et al. Salmonella enterica serovar Typhimurium uses anaerobic respiration to overcome propionate-mediated colonization resistance. Cell Rep 2022;38:110180.
123. Jacobson A, Lam L, Rajendram M, et al. A gut commensal-produced metabolite mediates colonization resistance to salmonella infection. Cell Host Microbe 2018;24:296-307.e7.
124. Becattini S, Littmann ER, Carter RA, et al. Commensal microbes provide first line defense against Listeria monocytogenes infection. J Exp Med 2017;214:1973-89.
125. Caballero S, Kim S, Carter RA, et al. Cooperating commensals restore colonization resistance to vancomycin-resistant enterococcus faecium. Cell Host Microbe 2017;21:592-602.e4.
126. Kim SG, Becattini S, Moody TU, et al. Microbiota-derived lantibiotic restores resistance against vancomycin-resistant Enterococcus. Nature 2019;572:665-9.
127. Aires J. First 1000 days of life: consequences of antibiotics on gut microbiota. Front Microbiol 2021;12:681427.
128. Ramirez J, Guarner F, Bustos Fernandez L, et al. Antibiotics as major disruptors of gut microbiota. Front Cell Infect Microbiol 2020;10:572912.
129. Bokulich NA, Chung J, Battaglia T, et al. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med 2016;8:343ra82.
130. Martín R, Langella P. Emerging health concepts in the probiotics field: streamlining the definitions. Front Microbiol 2019;10:1047.
131. Hill C, Guarner F, Reid G, et al. Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 2014;11:506-14.
132. Sanders ME, Merenstein D, Merrifield CA, Hutkins R. Probiotics for human use. Nutr Bull 2018;43:212-25.
133. Han S, Lu Y, Xie J, et al. Probiotic gastrointestinal transit and colonization after oral administration: a long journey. Front Cell Infect Microbiol 2021;11:609722.
