1932

Abstract

Microbes and animals have a symbiotic relationship that greatly influences nutrient uptake and animal health. This relationship can be studied using selections of microbes termed synthetic communities, or SynComs. SynComs are used in many different animal hosts, including agricultural animals, to investigate microbial interactions with nutrients and how these affect animal health. The most common host focuses for SynComs are currently mouse and human, from basic mechanistic research through to translational disease models and live biotherapeutic products (LBPs) as treatments. We discuss SynComs used in basic research models and findings that relate to human and animal health and nutrition. Translational use cases of SynComs are discussed, followed by LBPs, especially within the context of agriculture. SynComs still face challenges, such as standardization for reproducibility and contamination risks. However, the future of SynComs is hopeful, especially in the areas of genome-guided SynCom design and custom SynCom-based treatments.

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2024-02-15
2024-04-13
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Literature Cited

  1. 1.
    Hooke R. 1665. Micrographia London: Martyn & Allestry
  2. 2.
    van Leeuwenhoek A. 1673. Collected Letters Amsterdam: Swets & Zeitlinger
  3. 3.
    Gest H. 2004. The discovery of microorganisms by Robert Hooke and Antoni Van Leeuwenhoek, fellows of the Royal Society. Notes Rec. R. Soc. Lond. 58:2187–201
    [Google Scholar]
  4. 4.
    Hess M, Paul SS, Puniya AK, van der Giezen M, Shaw C et al. 2020. Anaerobic fungi: past, present, and future. Front. Microbiol. 11:584893
    [Google Scholar]
  5. 5.
    von Strempel A, Weiss AS, Wittmann J, Silva MS, Ring D et al. 2022. Bacteriophages targeting protective commensals impair resistance against Salmonella Typhimurium infection in gnotobiotic mice. bioRxiv. https://doi.org/10.1101/2022.09.28.509654
  6. 6.
    Myer PR, Freetly HC, Wells JE, Smith TPL, Kuehn LA. 2017. Analysis of the gut bacterial communities in beef cattle and their association with feed intake, growth, and efficiency. J. Anim. Sci. 95:73215–24
    [Google Scholar]
  7. 7.
    Schwarzer M, Makki K, Storelli G, Machuca-Gayet I, Srutkova D et al. 2016. Lactobacillus plantarum strain maintains growth of infant mice during chronic undernutrition. Science 351:6275854–57
    [Google Scholar]
  8. 8.
    Nikolopoulos N, Matos RC, Ravaud S, Courtin P, Akherraz H et al. 2023. Structure-function analysis of Lactiplantibacillus plantarum DltE reveals D-alanylated lipoteichoic acids as direct symbiotic cues supporting Drosophila juvenile growth. eLife 12:e84669
    [Google Scholar]
  9. 9.
    Consuegra J, Grenier T, Akherraz H, Rahioui I, Gervais H et al. 2020. Metabolic cooperation among commensal bacteria supports Drosophila juvenile growth under nutritional stress. iScience 23:6101232
    [Google Scholar]
  10. 10.
    Samuel BS, Rowedder H, Braendle C, Félix MA, Ruvkun G. 2016. Caenorhabditis elegans responses to bacteria from its natural habitats. PNAS 113:27E3941–49
    [Google Scholar]
  11. 11.
    Berg G, Rybakova D, Fischer D, Cernava T, Vergès M-CC et al. 2020. Correction to: microbiome definition re-visited: old concepts and new challenges. Microbiome 8:103
    [Google Scholar]
  12. 12.
    Lopes DRG, de Souza Duarte M, La Reau AJ, Chaves IZ, de Oliveira Mendes TA et al. 2021. Assessing the relationship between the rumen microbiota and feed efficiency in Nellore steers. J. Anim. Sci. Biotechnol. 12:79
    [Google Scholar]
  13. 13.
    Suzuki TA, Fitzstevens JL, Schmidt VT, Enav H, Huus KE et al. 2022. Codiversification of gut microbiota with humans. Science 377:66121328–32
    [Google Scholar]
  14. 14.
    Gaskins HR, Collier CT, Anderson DB. 2002. Antibiotics as growth promotants: mode of action. Anim. Biotechnol. 13:129–42
    [Google Scholar]
  15. 15.
    Mizrahi I, Wallace RJ, Moraïs S. 2021. The rumen microbiome: balancing food security and environmental impacts. Nat. Rev. Microbiol. 19:9553–66
    [Google Scholar]
  16. 16.
    Weiss AS, Burrichter AG, Durai Raj AC, von Strempel A, Meng C et al. 2022. In vitro interaction network of a synthetic gut bacterial community. ISME J. 16:41095–109
    [Google Scholar]
  17. 17.
    Hitch T, Wylensek D, Harlizius J, Clavel T 2022. The gut microbiota in pigs: ecology and biotherapeutics. Understanding Gut Microbiomes as Targets for Improving Pig Gut Health M Bailey, C Stokes 129–64 Philadelphia: Burleigh Dodds Sci. Publ
    [Google Scholar]
  18. 18.
    Wylensek D, Hitch TCA, Riedel T, Afrizal A, Kumar N et al. 2020. A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. Nat. Commun. 11:6389
    [Google Scholar]
  19. 19.
    Lagkouvardos I, Pukall R, Abt B, Foesel BU, Meier-Kolthoff JP et al. 2016. The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat. Microbiol. 1:16131
    [Google Scholar]
  20. 20.
    van der Lelie D, Oka A, Taghavi S, Umeno J, Fan TJ et al. 2021. Rationally designed bacterial consortia to treat chronic immune-mediated colitis and restore intestinal homeostasis. Nat. Commun. 12:3105
    [Google Scholar]
  21. 21.
    Dsouza M, Menon R, Crossette E, Bhattarai SK, Schneider J et al. 2022. Colonization of the live biotherapeutic product VE303 and modulation of the microbiota and metabolites in healthy volunteers. Cell Host Microbe 30:4583–98.e8
    [Google Scholar]
  22. 22.
    Kurt F, Leventhal GE, Spalinger MR, Anthamatten L, Rogalla von Bieberstein P et al. 2023. Co-cultivation is a powerful approach to produce a robust functionally designed synthetic consortium as a live biotherapeutic product (LBP). Gut Microbes 15:12177486
    [Google Scholar]
  23. 23.
    van Tilburg Bernardes E, Pettersen VK, Gutierrez MW, Laforest-Lapointe I, Jendzjowsky NG et al. 2020. Intestinal fungi are causally implicated in microbiome assembly and immune development in mice. Nat. Commun. 11:2577
    [Google Scholar]
  24. 24.
    Reyes A, Wu M, McNulty NP, Rohwer FL, Gordon JI. 2013. Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut. PNAS 110:5020236–41
    [Google Scholar]
  25. 25.
    Coates M. 1968. The Germ-Free Animal in Research Cambridge, MA: Academic
  26. 26.
    Lysons RJ, Alexander TJ, Wellstead PD, Hobson PN, Mann SO, Stewart CS. 1976. Defined bacterial populations in the rumens of gnotobiotic lambs. J. Gen. Microbiol. 94:2257–69
    [Google Scholar]
  27. 27.
    Wallace RJ, Sasson G, Garnsworthy PC, Tapio I, Gregson E et al. 2019. A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions. Sci. Adv. 5:7eaav8391
    [Google Scholar]
  28. 28.
    Doyle N, Mbandlwa P, Kelly WJ, Attwood G, Li Y et al. 2019. Use of lactic acid bacteria to reduce methane production in ruminants, a critical review. Front. Microbiol. 10:2207
    [Google Scholar]
  29. 29.
    Vasiljevic T, Shah NP. 2008. Probiotics—from Metchnikoff to bioactives. Int. Dairy J. 18:7714–28
    [Google Scholar]
  30. 30.
    Castle WE. 1906. Inbreeding, cross-breeding and sterility in Drosophila. Science 23:578153
    [Google Scholar]
  31. 31.
    Koyle ML, Veloz M, Judd AM, Wong AC-N, Newell PD et al. 2016. Rearing the fruit fly Drosophila melanogaster under axenic and gnotobiotic conditions. J. Vis. Exp.11354219
    [Google Scholar]
  32. 32.
    Storelli G, Defaye A, Erkosar B, Hols P, Royet J, Leulier F. 2011. Lactobacillus plantarum promotes Drosophila systemic growth by modulating hormonal signals through TOR-dependent nutrient sensing. Cell Metab. 14:3403–14
    [Google Scholar]
  33. 33.
    Almasri H, Liberti J, Brunet J-L, Engel P, Belzunces LP. 2022. Mild chronic exposure to pesticides alters physiological markers of honey bee health without perturbing the core gut microbiota. Sci. Rep. 12:4281
    [Google Scholar]
  34. 34.
    Kešnerová L, Mars RAT, Ellegaard KM, Troilo M, Sauer U, Engel P. 2017. Disentangling metabolic functions of bacteria in the honey bee gut. PLOS Biol. 15:12e2003467
    [Google Scholar]
  35. 35.
    Cabirol A, Schafer J, Neuschwander N, Kesner L, Liberti J. 2023. A defined community of core gut microbiota members promotes cognitive performance in honey bees. bioRxiv. https://doi.org/10.1101/2023.01.03.522593
  36. 36.
    Huang W, Rodrigues J, Bilgo E, Tormo JR, Challenger JD et al. 2023. Delftia tsuruhatensis TC1 symbiont suppresses malaria transmission by anopheline mosquitoes. Science 381:6657533–40
    [Google Scholar]
  37. 37.
    Romoli O, Schönbeck JC, Hapfelmeier S, Gendrin M. 2021. Production of germ-free mosquitoes via transient colonisation allows stage-specific investigation of host-microbiota interactions. Nat. Commun. 12:942
    [Google Scholar]
  38. 38.
    Correa MA, Matusovsky B, Brackney DE, Steven B. 2018. Generation of axenic Aedes aegypti demonstrate live bacteria are not required for mosquito development. Nat. Commun. 9:4464
    [Google Scholar]
  39. 39.
    Corsi AK, Wightman B, Chalfie M. 2015. A transparent window into biology: a primer on Caenorhabditis elegans. Genetics 200:2387–407
    [Google Scholar]
  40. 40.
    Dirksen P, Assié A, Zimmermann J, Zhang F, Tietje AM et al. 2020. CeMbio—the Caenorhabditis elegans microbiome resource. G3 10:93025–39
    [Google Scholar]
  41. 41.
    Choi TY, Choi TI, Lee YR, Choe SK, Kim CH. 2021. Zebrafish as an animal model for biomedical research. Exp. Mol. Med. 53:3310–17
    [Google Scholar]
  42. 42.
    Rendueles O, Ferrières L, Frétaud M, Bégaud E, Herbomel P et al. 2012. A new zebrafish model of oro-intestinal pathogen colonization reveals a key role for adhesion in protection by probiotic bacteria. PLOS Pathog. 8:7e1002815
    [Google Scholar]
  43. 43.
    Aluthge ND, Tom WA, Bartenslager AC, Burkey TE, Miller PS et al. 2020. Differential longitudinal establishment of human fecal bacterial communities in germ-free porcine and murine models. Commun. Biol. 3:760
    [Google Scholar]
  44. 44.
    Laycock G, Sait L, Inman C, Lewis M, Smidt H et al. 2012. A defined intestinal colonization microbiota for gnotobiotic pigs. Vet. Immunol. Immunopathol. 149:3–4216–24
    [Google Scholar]
  45. 45.
    Schaedler RW, Dubos R, Costello R. 1965. The development of the bacterial flora in the gastrointestinal tract of mice. J. Exp. Med. 122:59–66
    [Google Scholar]
  46. 46.
    Stoewsand G, Dymsza H, Ament D, Trexler P. 1968. Lysine requirement of the growing gnotobiotic mouse. Life Sci. 34:278–86
    [Google Scholar]
  47. 47.
    Basic M, Bleich A. 2019. Gnotobiotics: past, present and future. Lab. Anim. 53:3232–43
    [Google Scholar]
  48. 48.
    Clavel T, Lagkouvardos I, Stecher B. 2017. From complex gut communities to minimal microbiomes via cultivation. Curr. Opin. Microbiol. 38:148–55
    [Google Scholar]
  49. 49.
    Bolsega S, Bleich A, Basic M. 2021. Synthetic microbiomes on the rise—application in deciphering the role of microbes in host health and disease. Nutrients 13:114173
    [Google Scholar]
  50. 50.
    Dubos RJ, Schaedler RW. 1962. The effect of diet on the fecal bacterial flora of mice and on their resistance to infection. J. Exp. Med. 115:1161–72
    [Google Scholar]
  51. 51.
    Brand MW, Wannemuehler MJ, Phillips GJ, Proctor A, Overstreet AM et al. 2015. The altered Schaedler flora: continued applications of a defined murine microbial community. ILAR J. 56:2169–78
    [Google Scholar]
  52. 52.
    Wells CL, Sugiyama H, Bland SE. 1982. Resistance of mice with limited intestinal flora to enteric colonization by Clostridium botulinum. . J. Infect. Dis. 146:6791–96
    [Google Scholar]
  53. 53.
    Mirsalis JC, Hamm TE, Sherrill JM, Butterworth BE. 1982. Role of gut flora in the genotoxicity of dinitrotoluene. Nature 295:5847322–23
    [Google Scholar]
  54. 54.
    Gomez de Agüero M, Ganal-Vonarburg SC, Fuhrer T, Rupp S, Uchimura Y et al. 2016. The maternal microbiota drives early postnatal innate immune development. Science 351:62791296–302
    [Google Scholar]
  55. 55.
    Brugiroux S, Beutler M, Pfann C, Garzetti D, Ruscheweyh HJ et al. 2016. Genome-guided design of a defined mouse microbiota that confers colonization resistance against Salmonella enterica serovar Typhimurium. Nat. Microbiol. 2:16215
    [Google Scholar]
  56. 56.
    Afrizal A, Jennings SAV, Hitch TCA, Riedel T, Basic M et al. 2022. Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities. Cell Host Microbe 30:111630–45.e25
    [Google Scholar]
  57. 57.
    Darnaud M, De Vadder F, Bogeat P, Boucinha L, Bulteau A et al. 2021. A standardized gnotobiotic mouse model harboring a minimal 15-member mouse gut microbiota recapitulates SOPF/SPF phenotypes. Nat. Commun. 12:6686
    [Google Scholar]
  58. 58.
    Syed SA, Abrams GD, Freter R. 1970. Efficiency of various intestinal bacteria in assuming normal functions of enteric flora after association with germ-free mice. Infect. Immun. 2:4376–86
    [Google Scholar]
  59. 59.
    Becker N, Kunath J, Loh G, Blaut M. 2011. Human intestinal microbiota: characterization of a simplified and stable gnotobiotic rat model. Gut Microbes 2:125–33
    [Google Scholar]
  60. 60.
    Eun CS, Mishima Y, Wohlgemuth S, Liu B, Bower M et al. 2014. Induction of bacterial antigen-specific colitis by a simplified human microbiota consortium in gnotobiotic interleukin-10−/− mice. Infect. Immun. 82:62239–46
    [Google Scholar]
  61. 61.
    Chung H, Pamp SJ, Hill JA, Surana NK, Edelman SM et al. 2012. Gut immune maturation depends on colonization with a host-specific microbiota. Cell 149:71578–93
    [Google Scholar]
  62. 62.
    Seedorf H, Griffin NW, Ridaura VK, Reyes A, Cheng J et al. 2014. Bacteria from diverse habitats colonize and compete in the mouse gut. Cell 159:2253–66
    [Google Scholar]
  63. 63.
    Frese SA, MacKenzie DA, Peterson DA, Schmaltz R, Fangman T et al. 2013. Molecular characterization of host-specific biofilm formation in a vertebrate gut symbiont. PLOS Genet. 9:12e1004057
    [Google Scholar]
  64. 64.
    Cheng AG, Ho P-Y, Aranda-Díaz A, Jain S, Yu FB et al. 2022. Design, construction, and in vivo augmentation of a complex gut microbiome. Cell 185:193617–36.e19
    [Google Scholar]
  65. 65.
    Vital M, Karch A, Pieper DH. 2017. Colonic butyrate-producing communities in humans: an overview using omics data. mSystems 2:6e00130–17
    [Google Scholar]
  66. 66.
    Li Y, Watanabe E, Kawashima Y, Plichta DR, Wang Z et al. 2022. Identification of trypsin-degrading commensals in the large intestine. Nature 609:7927582–89
    [Google Scholar]
  67. 67.
    Yoon H, Schaubeck M, Lagkouvardos I, Blesl A, Heinzlmeir S et al. 2018. Increased pancreatic protease activity in response to antibiotics impairs gut barrier and triggers colitis. Cell. Mol. Gastroenterol. Hepatol. 6:3370–388.e3
    [Google Scholar]
  68. 68.
    Clark RL, Connors BM, Stevenson DM, Hromada SE, Hamilton JJ et al. 2021. Design of synthetic human gut microbiome assembly and butyrate production. Nat. Commun. 12:3254
    [Google Scholar]
  69. 69.
    Lubin J-B, Green J, Maddux S, Denu L, Duranova T et al. 2023. Arresting microbiome development limits immune system maturation and resistance to infection in mice. Cell Host Microbe 31:4554–70.e7
    [Google Scholar]
  70. 70.
    Lyte JM, Proctor A, Phillips GJ, Lyte M, Wannemuehler M. 2019. Altered Schaedler flora mice: a defined microbiota animal model to study the microbiota-gut-brain axis. Behav. Brain Res. 356:221–26
    [Google Scholar]
  71. 71.
    Lengfelder I, Sava IG, Hansen JJ, Kleigrewe K, Herzog J et al. 2019. Complex bacterial consortia reprogram the colitogenic activity of Enterococcus faecalis in a gnotobiotic mouse model of chronic, immune-mediated colitis. Front. Immunol. 10:1420
    [Google Scholar]
  72. 72.
    Bolsega S, Basic M, Smoczek A, Buettner M, Eberl C et al. 2019. Composition of the intestinal microbiota determines the outcome of virus-triggered colitis in mice. Front. Immunol. 10:1708
    [Google Scholar]
  73. 73.
    Feng T, Wang L, Schoeb TR, Elson CO, Cong Y. 2010. Microbiota innate stimulation is a prerequisite for T cell spontaneous proliferation and induction of experimental colitis. J. Exp. Med. 207:61321–32
    [Google Scholar]
  74. 74.
    Bayer F, Ascher S, Kiouptsi K, Kittner JM, Stauber RH, Reinhardt C. 2021. Colonization with altered Schaedler flora impacts leukocyte adhesion in mesenteric ischemia-reperfusion injury. Microorganisms 9:81601
    [Google Scholar]
  75. 75.
    Nowosad CR, Mesin L, Castro TBR, Wichmann C, Donaldson GP et al. 2020. Tunable dynamics of B cell selection in gut germinal centres. Nature 588:7837321–26
    [Google Scholar]
  76. 76.
    Woting A, Pfeiffer N, Loh G, Klaus S, Blaut M. 2014. Clostridium ramosum promotes high-fat diet-induced obesity in gnotobiotic mouse models. mBio 5:5 https://doi.org/10.1128/mbio.01530-14
    [Google Scholar]
  77. 77.
    Pereira FC, Wasmund K, Cobankovic I, Jehmlich N, Herbold CW et al. 2020. Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridioides difficile colonization. Nat. Commun. 11:5104
    [Google Scholar]
  78. 78.
    Cordaillat-Simmons M, Rouanet A, Pot B. 2020. Live biotherapeutic products: the importance of a defined regulatory framework. Exp. Mol. Med. 52:91397–406
    [Google Scholar]
  79. 79.
    Metchnikoff É. 1908. The Prolongation of Life: Optimistic Studies New York: Knickerbocker
  80. 80.
    Fuller R. 1989. Probiotics in man and animals. J. Appl. Bacteriol. 66:5365–78
    [Google Scholar]
  81. 81.
    Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ et al. 2014. 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. 11:8506–14
    [Google Scholar]
  82. 82.
    Cani PD, Depommier C, Derrien M, Everard A, de Vos WM. 2022. Akkermansia muciniphila: paradigm for next-generation beneficial microorganisms. Nat. Rev. Gastroenterol. Hepatol. 19:10625–37
    [Google Scholar]
  83. 83.
    Derrien M, Vaughan EE, Plugge CM, de Vos WM. 2004. Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int. J. Syst. Evol. Microbiol. 54:51469–76
    [Google Scholar]
  84. 84.
    Depommier C, Everard A, Druart C, Plovier H, Van Hul M et al. 2019. Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study. Nat. Med. 25:71096–103
    [Google Scholar]
  85. 85.
    Plovier H, Everard A, Druart C, Depommier C, Van Hul M et al. 2017. A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and diabetic mice. Nat. Med. 23:1107–13
    [Google Scholar]
  86. 86.
    Oliveira RA, Pamer EG. 2023. Assembling symbiotic bacterial species into live therapeutic consortia that reconstitute microbiome functions. Cell Host Microbe 31:472–84
    [Google Scholar]
  87. 87.
    Tvede M, Rask-Madsen J. 1989. Bacteriotherapy for chronic relapsing Clostridium difficile diarrhoea in six patients. Lancet 1:86481156–60
    [Google Scholar]
  88. 88.
    Petrof EO, Gloor GB, Vanner SJ, Weese SJ, Carter D et al. 2013. Stool substitute transplant therapy for the eradication of Clostridium difficile infection: “RePOOPulating” the gut. Microbiome 1:3
    [Google Scholar]
  89. 89.
    Louie T, Golan Y, Khanna S, Bobilev D, Erpelding N et al. 2023. VE303, a defined bacterial consortium, for prevention of recurrent Clostridioides difficile infection: a randomized clinical trial. JAMA 329:161356–66
    [Google Scholar]
  90. 90.
    Arpaia N, Campbell C, Fan X, Dikiy S, van der Veeken J et al. 2013. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 504:7480451–55
    [Google Scholar]
  91. 91.
    Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G et al. 2013. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 504:7480446–50
    [Google Scholar]
  92. 92.
    Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC et al. 2018. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nat. Biotechnol. 36:4359–67
    [Google Scholar]
  93. 93.
    Zenner C, Hitch TCA, Riedel T, Wortmann E, Tiede S et al. 2021. Early-life immune system maturation in chickens using a synthetic community of cultured gut bacteria. mSystems 6:3e01300–20
    [Google Scholar]
  94. 94.
    Kollarcikova M, Faldynova M, Matiasovicova J, Jahodarova E, Kubasova T et al. 2020. Different Bacteroides species colonise human and chicken intestinal tract. Microorganisms 8:101483
    [Google Scholar]
  95. 95.
    Medvecky M, Cejkova D, Polansky O, Karasova D, Kubasova T et al. 2018. Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures. BMC Genom. 19:1561
    [Google Scholar]
  96. 96.
    Crhanova M, Karasova D, Juricova H, Matiasovicova J, Jahodarova E et al. 2019. Systematic culturomics shows that half of chicken caecal microbiota members can be grown in vitro except for two lineages of Clostridiales and a single lineage of Bacteroidetes. Microorganisms 7:11496
    [Google Scholar]
  97. 97.
    Kubasova T, Kollarcikova M, Crhanova M, Karasova D, Cejkova D et al. 2019. Gut anaerobes capable of chicken caecum colonisation. Microorganisms 7:12597
    [Google Scholar]
  98. 98.
    Ramayo-Caldas Y, Mach N, Lepage P, Levenez F, Denis C et al. 2016. Phylogenetic network analysis applied to pig gut microbiota identifies an ecosystem structure linked with growth traits. ISME J. 10:122973–77
    [Google Scholar]
  99. 99.
    Mackie RI, White BA. 1990. Recent advances in rumen microbial ecology and metabolism: potential impact on nutrient output. J. Dairy Sci. 73:102971–95
    [Google Scholar]
  100. 100.
    Gilmore SP, Lankiewicz TS, Wilken SE, Brown JL, Sexton JA et al. 2019. Top-down enrichment guides in formation of synthetic microbial consortia for biomass degradation. ACS Synth. Biol. 8:92174–85
    [Google Scholar]
  101. 101.
    Peng X, Wilken SE, Lankiewicz TS, Gilmore SP, Brown JL et al. 2021. Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes. Nat. Microbiol. 6:4499–511
    [Google Scholar]
  102. 102.
    Meyer JR, Agrawal AA, Quick RT, Dobias DT, Schneider D, Lenski RE. 2010. Parallel changes in host resistance to viral infection during 45,000 generations of relaxed selection. Evolution 64:103024–34
    [Google Scholar]
  103. 103.
    Yilmaz B, Mooser C, Keller I, Li H, Zimmermann J et al. 2021. Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice. Cell Host Microbe 29:4650–63.e9
    [Google Scholar]
  104. 104.
    Eberl C, Ring D, Münch PC, Beutler M, Basic M et al. 2020. Reproducible colonization of germ-free mice with the oligo-mouse-microbiota in different animal facilities. Front. Microbiol. 10:2999
    [Google Scholar]
  105. 105.
    Archer D, Elisa M, Tollenaar S, Veniamin S, Cheng CC et al. 2023. The importance of the timing of microbial signals for perinatal immune system development. Microbiome Res. Rep. 2:11
    [Google Scholar]
  106. 106.
    Schäpe SS, Krause JL, Engelmann B, Fritz-Wallace K, Schattenberg F et al. 2019. The simplified human intestinal microbiota (SIHUMIx) shows high structural and functional resistance against changing transit times in in vitro bioreactors. Microorganisms 7:12641
    [Google Scholar]
  107. 107.
    Uchimura Y, Wyss M, Brugiroux S, Limenitakis JP, Stecher B et al. 2016. Complete genome sequences of 12 species of stable defined moderately diverse mouse microbiota 2. Genome Announc. 4:5e00951–16
    [Google Scholar]
  108. 108.
    Studer N, Desharnais L, Beutler M, Brugiroux S, Terrazos MA et al. 2016. Functional intestinal bile acid 7α-dehydroxylation by Clostridium scindens associated with protection from Clostridium difficile infection in a gnotobiotic mouse model. Front. Cell. Infect. Microbiol. 6:191
    [Google Scholar]
  109. 109.
    Khan M, Backhed F 2022. Faecalibacterium prausnitzii and Desulfovibrio piger for use in the treatment or prevention of diabetes and bowel diseases. US Patent US20220133814A1
  110. 110.
    Eng A, Borenstein E. 2019. Microbial community design: methods, applications, and opportunities. Curr. Opin. Biotechnol. 58:117–28
    [Google Scholar]
  111. 111.
    Kumar N, Hitch TCA, Haller D, Lagkouvardos I, Clavel T. 2021. MiMiC: a bioinformatic approach for generation of synthetic communities from metagenomes. Microb. Biotechnol. 14:41757–70
    [Google Scholar]
  112. 112.
    Stein RR, Tanoue T, Szabady RL, Bhattarai SK, Olle B et al. 2018. Computer-guided design of optimal microbial consortia for immune system modulation. eLife 7:e30916
    [Google Scholar]
  113. 113.
    van den Berg NI, Machado D, Santos S, Rocha I, Chacón J et al. 2022. Ecological modelling approaches for predicting emergent properties in microbial communities. Nat. Ecol. Evol. 6:7855–65
    [Google Scholar]
  114. 114.
    Huang Y, Sheth RU, Zhao S, Cohen LA, Dabaghi K et al. 2023. High-throughput microbial culturomics using automation and machine learning. Nat. Biotechnol. https://doi.org/10.1038/s41587-023-01674-2
    [Google Scholar]
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