Gnotobiotic experimentation helps define symbiogenesis in vertebrate evolution

References

• Asnicar F, Leeming ER, Dimidi E, Mazidi M, Franks PW, Al Khatib H, Valdes AM, Davies R, Bakker E, Francis L, et al. 2021 Sep. Blue poo: impact of gut transit time on the gut microbiome using a novel marker. Gut. 70(9):1665–1674. doi:10.1136/gutjnl-2020-323877.
   PubMed Web of Science ®Google Scholar
• Bäckhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF, Gordon JI. 2004 Nov 2. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A. 101(44):15718–15723. doi:10.1073/pnas.0407076101.
   PubMed Web of Science ®Google Scholar
• Badhan A, Low KE, Jones DR, Xing X, Milani MRM, Polo RO, Klassen L, Venketachalam S, Hahn MG, Abbott DW, McAllister TA. 2021 Dec 9. Mechanistic insights into the digestion of complex dietary fibre by the rumen microbiota using combinatorial high-resolution glycomics and transcriptomic analyses. Comput Struct Biotechnol J. 20:148–164. doi:10.1016/j.csbj.2021.12.009.
   PubMed Web of Science ®Google Scholar
• Ballard FJ, Hanson RW, Kronfeld DS. 1969. Gluconeogenesis and lipogenesis in tissue from ruminant and nonruminant animals. Fed Proc. 28:218–231.
   PubMedGoogle Scholar
• Barnes RD, Fairweather DV, Holliday J, Keane C, Piesowicz A, Soothill JF, Tuffrey M. 1969 Jan 25. A germfree infant. Lancet. 1(7587):168–171. doi:10.1016/s0140-6736(69)91187-8.
   PubMed Web of Science ®Google Scholar
• Barnes RH, Fiala G. 1959 Aug 10. Effects of the prevention of coprophagy in the rat. J Nutr. 68(4):603–614. doi:10.1093/jn/68.4.603.
   PubMed Web of Science ®Google Scholar
• Baumann P. 2005. Biology bacteriocyte-associated endosymbionts of plant sap-sucking insects. Annu Rev Microbiol. 59:155–189. doi:10.1146/annurev.micro.59.030804.121041.
   PubMed Web of Science ®Google Scholar
• Bealmear PM, South MA, Wilson R. 1985. David’s story: the gift of 12 years, 5 months, and 1 day. Prog Clin Biol Res. 181:475–489.
   PubMedGoogle Scholar
• Bercik P, Denou E, Collins J, Jackson W, Lu J, Jury J, Deng Y, Blennerhassett P, Macri J, McCoy KD, et al. 2011 Aug. The intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology. 141(2):599–609. 609.e1-3. doi: 10.1053/j.gastro.2011.04.052.
   PubMed Web of Science ®Google Scholar
• Beresford-Jones BS, Forster SC, Stares MD, Notley G, Viciani E, Browne HP, Boehmler DJ, Soderholm AT, Kumar N, Vervier K, et al. 2022 Jan 12. The mouse gastrointestinal bacteria catalogue enables translation between the mouse and human gut microbiotas via functional mapping. Cell Host Microbe. 30(1):124–138. e8. doi: 10.1016/j.chom.2021.12.003.
   PubMed Web of Science ®Google Scholar
• Bohnhoff M, Drake BL, Miller CP. 1954 May. Effect of streptomycin on susceptibility of intestinal tract to experimental salmonella infection. Proc Soc Exp Biol Med. 86(1):132–137. doi:10.3181/00379727-86-21030.
   PubMed Web of Science ®Google Scholar
• Carrier TJ, Reitzel AM. 2017 May 11. The hologenome across environments and the implications of a host-associated microbial repertoire. Front Microbiol. 8:802. doi:10.3389/fmicb.2017.00802.
   PubMed Web of Science ®Google Scholar
• Chen H, Nwe PK, Yang Y, Rosen CE, Bielecka AA, Kuchroo M, Cline GW, Kruse AC, Ring AM, Crawford JM, Palm NW. 2019 May 16. A forward chemical genetic screen reveals gut microbiota metabolites that modulate host physiology. Cell. 177(5):1217–1231. e18. doi: 10.1016/j.cell.2019.03.036.
   PubMed Web of Science ®Google Scholar
• Chu H, Mazmanian SK. 2013 Jul. Innate immune recognition of the microbiota promotes host-microbial symbiosis. Nat Immunol. 14(7):668–675. doi:10.1038/ni.2635.
   PubMed Web of Science ®Google Scholar
• Coates ME, Davies MK, Kon SK. 1955. The effect of antibiotics on the intestine of the chick. Br J Nutr. 9(1):110–119. doi:10.1079/bjn19550016.
   PubMed Web of Science ®Google Scholar
• Cohen LJ, Esterhazy D, Kim SH, Lemetre C, Aguilar RR, Gordon EA, Pickard AJ, Cross JR, Emiliano AB, Han SM, et al. 2017 Sep 7. Commensal bacteria make GPCR ligands that mimic human signalling molecules. Nature. 549(7670):48–53. doi: 10.1038/nature23874. Erratum in: Nature. 2018 Apr 4;556(7699):135.
   PubMed Web of Science ®Google Scholar
• Collins A, Kelley E, Katz LA. 2019. The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis. J Exp Zool (Mol Dev Evol. 9:349–355.
   Web of Science ®Google Scholar
• Colosimo DA, Kohn JA, Luo PM, Piscotta FJ, Han SM, Pickard AJ, Rao A, Cross JR, Cohen LJ, Brady SF. 2019 Aug 14. Mapping interactions of microbial metabolites with human G-protein-coupled receptors. Cell Host Microbe. 26(2):273–282. e7. doi: 10.1016/j.chom.2019.07.002.
   PubMed Web of Science ®Google Scholar
• Copeland L, Blazek J, Salman H, Tang MC. 2009. Form and functionality of starch. Food Hydroll. 23:1527–1534.
   Web of Science ®Google Scholar
• Crumeyrolle-Arias M, Jaglin M, Bruneau A, Vancassel S, Cardona A, Daugé V, Naudon L, Rabot S. 2014 Apr. Absence of the gut microbiota enhances anxiety-like behavior and neuroendocrine response to acute stress in rats. Psychoneuroendocrinology. 42:207–217. doi:10.1016/j.psyneuen.2014.01.014.
   PubMed Web of Science ®Google Scholar
• Cryan JF, Mazmanian SK. 2022 May 27. Microbiota-brain axis: context and causality. Science. 376(6596):938–939. doi:10.1126/science.abo4442.
   PubMed Web of Science ®Google Scholar
• Cummings JH, Macfarlane GT. 1991. The control and consequences of bacterial fermentation in the human colon. J Appl Bacteriol. 70(6):443–459.
   PubMedGoogle Scholar
• Cummings JH, Stephen AM. 1980. The role of dietary fibre in the human colon. Can Med Assoc J. 123(11):1109–1114.
   PubMed Web of Science ®Google Scholar
• Das P, Babaei P, Nielsen J. 2019 Mar 12. Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome. BMC Genomics. 20(1):208. doi:10.1186/s12864-019-5591-7.
   PubMed Web of Science ®Google Scholar
• Douglas AE, Werren JH. 2016 Mar 31. Holes in the hologenome: Why host-microbe symbioses are not holobionts. mBio. 7(2):e02099. doi:10.1128/mBio.02099-15.
   PubMed Web of Science ®Google Scholar
• Ebino KY. 1993 Jan. Studies on coprophagy in experimental animals. Jikken Dobutsu. 42(1):1–9. doi:10.1538/expanim1978.42.1_1.
   PubMed Web of Science ®Google Scholar
• Ericsson AC, Franklin CL. 2021 Aug. The gut microbiome of laboratory mice: considerations and best practices for translational research. Mamm Genome. 32(4):239–250. doi:10.1007/s00335-021-09863-7.
   PubMed Web of Science ®Google Scholar
• Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML. 2014 Nov 15. Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Hum Mol Genet. 23(22):5866–5878. doi:10.1093/hmg/ddu309.
   PubMed Web of Science ®Google Scholar
• Fleissner CK, Huebel N, Abd El-Bary MM, Loh G, Klaus S, Blaut M. 2010 Sep. Absence of intestinal microbiota does not protect mice from diet-induced obesity. Br J Nutr. 104(6):919–929. doi:10.1017/S0007114510001303.
   PubMed Web of Science ®Google Scholar
• Flint HJ. 2020. Why gut microbes matter. understanding our microbiome. Cham: Springer Nature Switzerland AG.
   Google Scholar
• Floch MH, Gershengoren W, Elliott S, Spiro HM. 1971 Aug. Bile acid inhibition of the intestinal microflora - a function for simple bile acids? Gastroenterol. 61(2):228–233.
   PubMed Web of Science ®Google Scholar
• Furness JB, Boyle EK, Fakhry J, Gajewski J, Fothergill LJ. 2019. Digerstive system. In: Brune M, Schiefenhovel W, editor. Oxford handbook of evolutionary medicine. Oxford: Oxford Academic; p. 532–562. doi:10.1093/oxfordhb/9780198789666.001.0001
   Google Scholar
• Gordon HA, Pesti L. 1971 Dec. The gnotobiotic animal as a tool in the study of host microbial relationships. Bacteriol Rev. 35(4):390–429. doi:10.1128/br.35.4.390-429.1971.
   PubMedGoogle Scholar
• Gordon HA. 1968. Is the germfree animal normal? In: M. E. Coates, editor. The germfree animal in research. New York: Academic Press Inc; p. 127–150.
   Google Scholar
• Grice EA, Segre JA. 2012. The human microbiome: our second genome. Annu Rev Genomics Hum Genet. 13:151–170. doi:10.1146/annurev-genom-090711-163814.
   PubMed Web of Science ®Google Scholar
• Guerrero R, Margulis L, Berlanga M. 2013 Sep. Symbiogenesis: the holobiont as a unit of evolution. Int Microbiol. 16(3):133–143. doi:10.2436/20.1501.01.188.
   PubMed Web of Science ®Google Scholar
• Gustafsson BE. 1959 May 8. Vitamin K deficiency in germfree rats. Ann N Y Acad Sci. 78:166–174. doi:10.1111/j.1749-6632.1959.tb53101.x.
   PubMed Web of Science ®Google Scholar
• Hofmann AF, Hagey LR, Krasowski MD. 2010 Feb. Bile salts of vertebrates: structural variation and possible evolutionary significance. J Lipid Res. 51(2):226–246. doi:10.1194/jlr.R000042.
   PubMed Web of Science ®Google Scholar
• Hooks KB, Konsman JP, O’Malley MA. 2019. Microbiota-gut-brain research: A critical analysis. Behav Brain Sci. 42:e60. 1–53. doi:10.1017/S0140525X18002133.
   Web of Science ®Google Scholar
• Høverstad T. 1986. Studies of short-chain fatty acid absorption in man. Scand J Gastroenterol. 21(3):257–260.
   PubMed Web of Science ®Google Scholar
• Hugenholtz F, de Vos WM. 2018 Jan. Mouse models for human intestinal microbiota research: a critical evaluation. Cell Mol Life Sci. 75(1):149–160. doi:10.1007/s00018-017-2693-8.
   PubMed Web of Science ®Google Scholar
• Karl JP, Meydani M, Barnett JB, Vanegas SM, Barger K, Fu X, Goldin B, Kane A, Rasmussen H, Vangay P, et al. 2017 Oct. Fecal concentrations of bacterially derived vitamin K forms are associated with gut microbiota composition but not plasma or fecal cytokine concentrations in healthy adults. Am J Clin Nutr. 106(4):1052–1061. doi:10.3945/ajcn.117.155424.
   PubMed Web of Science ®Google Scholar
• Kieser S, Zdobnov EM, Trajkovski M. 2022 Mar 8. Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart. PLoS Comput Biol. 18(3):e1009947. doi:10.1371/journal.pcbi.1009947.
   PubMed Web of Science ®Google Scholar
• Kirk RGW. 2012. Life in a germ-free world: isolating life from the laboratory animal to the bubble boy. Bull Hist Med. 8:237–275.
   Web of Science ®Google Scholar
• Koo H, Hakim JA, Crossman DK, Lefkowitz EJ, Morrow CD. 2019. Sharing of gut microbial strains between selected individual sets of twins cohabitating for decades. PLoS One. 14:e0226111.
   PubMed Web of Science ®Google Scholar
• Krych L, Hansen CH, Hansen AK, van den Berg FW, Nielsen DS. 2013 May 1. Quantitatively different, yet qualitatively alike: a meta-analysis of the mouse core gut microbiome with a view towards the human gut microbiome. PLoS One. 8(5):e62578. doi:10.1371/journal.pone.0062578.
   PubMed Web of Science ®Google Scholar
• Kumar J, Rani K, Datt C. 2020 Aug. Molecular link between dietary fibre, gut microbiota and health. Mol Biol Rep. 47(8):6229–6237. doi:10.1007/s11033-020-05611-3.
   PubMed Web of Science ®Google Scholar
• Lawley TD, Young VB. 2013 Dec. Murine models to study Clostridium difficile infection and transmission. Anaerobe. 24:94–97. doi:10.1016/j.anaerobe.2013.09.008.
   PubMed Web of Science ®Google Scholar
• Li J, Zhong H, Ramayo-Caldas Y, Terrapon N, Lombard V, Potocki-Veronese G, Estellé J, Popova M, Yang Z, Zhang H, et al. 2020b Jun 1. A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment. Gigascience. 9(6):giaa057. doi:10.1093/gigascience/giaa057.
   PubMed Web of Science ®Google Scholar
• Li X, Zhou J, Fang M, Yu B. 2020a. Pregnancy immune tolerance at the maternal-fetal interface. Int Rev Immunol. 39(6):247–263. doi:10.1080/08830185.2020.1777292.
   PubMed Web of Science ®Google Scholar
• Liu CH, Lee SM, Vanlare JM, Kasper DL, Mazmanian SK. 2008 Mar 11. Regulation of surface architecture by symbiotic bacteria mediates host colonization. Proc Natl Acad Sci U S A. 105(10):3951–3956. doi:10.1073/pnas.0709266105.
   PubMed Web of Science ®Google Scholar
• Liu L, Huh JR, Shah K. 2022 Mar. Microbiota and the gut-brain-axis: implications for new therapeutic design in the CNS. EBioMedicine. 77:103908. doi:10.1016/j.ebiom.2022.103908.
   PubMed Web of Science ®Google Scholar
• Louis P, Duncan SH, McCrae SI, Millar J, Jackson MS, Flint HJ. 2004. Restricted distribution of the butyrate kinase pathway among butyrate-producing bacteria from the human colon. J Bacteriol. 186:2099–2106.
   PubMed Web of Science ®Google Scholar
• Luckey TD. 1963. Germfree life and gnotobiology. USA: Academic Press. ISBN 978-0124143920.
   Google Scholar
• Luczynski P, McVey Neufeld KA, Oriach CS, Clarke G, Dinan TG, Cryan JF. 2016 Aug 12. Growing up in a bubble: using germ-free animals to assess the influence of the gut microbiota on brain and behavior. Int J Neuropsychopharmacol. 19(8):pyw020.. doi: 10.1093/ijnp/pyw020.
   PubMed Web of Science ®Google Scholar
• Macpherson AJ, Geuking MB, McCoy KD. 2005 Jun. Immune responses that adapt the intestinal mucosa to commensal intestinal bacteria. Immunology. 115(2):153–162. doi:10.1111/j.1365-2567.2005.02159.x.
   PubMed Web of Science ®Google Scholar
• Magnúsdóttir S, Ravcheev D, de Crécy-Lagard V, Thiele I. 2015 Apr 20. Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes. Front Genet. 6:148. doi:10.3389/fgene.2015.00148.
   PubMed Web of Science ®Google Scholar
• Magulis L. 1991. Symbiogenesis and symbionticism. In: Margulis L, Fester R, editor. Symbiosis as a source of evolutionary innovation: speciation and morphogenesis. Cambridge, MA: MIT Press; p. 1–14.
   Google Scholar
• Malinak LR, Wilson R, South MA, Montgomery JR, Mumford DM, Jr FC. 1973 May 15. Germ-free delivery. The initiation of management of infants with a high probability of congenital immune deficiency states. Am J Obstet Gynecol. 116(2):201–204. doi:10.1016/0002-9378(73)91051-x.
   PubMed Web of Science ®Google Scholar
• Margulis L. 1993. Origins of species: acquired genomes and individuality. Biosystems. 31(2-3):121–125. doi:10.1016/0303-2647(93)90039-f.
   PubMed Web of Science ®Google Scholar
• Margulis L. 2004. Serial endosymbiotic theory (SET) and composite individuality. Transition from bacterial to eukaryotic genomes. Microbiol Today. 31:172–174.
   Google Scholar
• Meynell GG. 1963 Apr. Antibacterial mechanisms of the mouse gut. II. The role of Eh and volatile fatty acids in the normal gut. Br J Exp Pathol. 44(2):209–219.
   PubMedGoogle Scholar
• Moran NA, Degnan PH. 2006 Apr. Functional genomics of Buchnera and the ecology of aphid hosts. Mol Ecol. 15(5):1251–1261. doi:10.1111/j.1365-294X.2005.02744.x. PMID: 16626452.
   PubMed Web of Science ®Google Scholar
• Moran NA, Plague GR, Sandström JP, Wilcox JL. 2003 Nov 25. A genomic perspective on nutrient provisioning by bacterial symbionts of insects. Proc Natl Acad Sci U S A. 100(Suppl 2):14543–14548. doi:10.1073/pnas.2135345100.
   PubMed Web of Science ®Google Scholar
• Moran NA, Sloan DB. 2015 Dec 4. The hologenome concept: helpful or hollow? PLoS Biol. 13(12):e1002311. doi:10.1371/journal.pbio.1002311.
   PubMed Web of Science ®Google Scholar
• Morrison DJ, Preston T. 2016. Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism. Gut Microbes. 7(3):189–200. doi:10.1080/19490976.2015.1134082.
   PubMed Web of Science ®Google Scholar
• Müller M, Hermes GDA, Canfora EE, Smidt H, Masclee AAM, Zoetendal EG, Blaak EE. 2020 Feb 1. Distal colonic transit is linked to gut microbiota diversity and microbial fermentation in humans with slow colonic transit. Am J Physiol Gastrointest Liver Physiol. 318(2):G361–G369. doi:10.1152/ajpgi.00283.2019.
   PubMed Web of Science ®Google Scholar
• Nguyen TL, Vieira-Silva S, Liston A, Raes J. 2015 Jan. How informative is the mouse for human gut microbiota research? Dis Model Mech. 8(1):1–16. doi:10.1242/dmm.017400.
   PubMed Web of Science ®Google Scholar
• O’Keefe SJD. 2019. Plant-based foods and the microbiome in the preservation of health and prevention of disease. Am J Clin Nutr. 110:265–266.
   PubMed Web of Science ®Google Scholar
• O’Malley MA. 2017 Dec 7. From endosymbiosis to holobionts: evaluating a conceptual legacy. J Theor Biol. 434:34–41. doi:10.1016/j.jtbi.2017.03.008.
   PubMed Web of Science ®Google Scholar
• Pawlowski SW, Calabrese G, Kolling GL, Platts-Mills J, Freire R, AlcantaraWarren C, Liu B, Sartor RB, Guerrant RL. 2010 Dec 1. Murine model of Clostridium difficile infection with aged gnotobiotic C57BL/6 mice and a BI/NAP1 strain. J Infect Dis. 202(11):1708–1712. doi:10.1086/657086. Erratum in: J Infect Dis. 2011 May 15;203(10):1505. Platts-Mills, J [added].
   PubMed Web of Science ®Google Scholar
• Perry GH, Kistler L, Kelaita MA, Sams AJ. 2015. Insights into hominin phenotypic and dietary evolution from ancient DNA sequence data. J Human Evol. 79:55–63.
   PubMed Web of Science ®Google Scholar
• Perry RJ, Peng L, Barry NA, Cline GW, Zhang D, Cardone RL, Petersen KF, Kibbey RG, Goodman AL, Shulman GI. 2016 Jun 9. Acetate mediates a microbiome-brain-β-cell axis to promote metabolic syndrome. Nature. 534(7606):213–217. doi: 10.1038/nature18309. PMID: 27279214; PMCID: PMC4922538.
   PubMed Web of Science ®Google Scholar
• Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. 2010 Mar 4. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 464(7285):59–65. doi:10.1038/nature08821.
   PubMed Web of Science ®Google Scholar
• Reichardt N, Duncan SH, Young P, Belenguer A, McWilliam Leitch C, Scott KP, Flint HJ, Louis P. 2014 Jun. Phylogenetic distribution of three pathways for propionate production within the human gut microbiota. ISME J. 8(6):1323–1335. doi:10.1038/ismej.2014.14. Epub 2014 Feb 20. Erratum in: ISME J. 2014 Jun;8(6):1352.
   PubMed Web of Science ®Google Scholar
• Rolfe RD. 1984 Jul. Role of volatile fatty acids in colonization resistance to clostridium difficile. Infect Immun. 45(1):185–191. doi:10.1128/iai.45.1.185-191.1984.
   PubMed Web of Science ®Google Scholar
• Rosenberg E, Zilber-Rosenberg I. 2016 Mar 31. Microbes drive evolution of animals and plants: the hologenome concept. mBio. 7(2):e01395. doi:10.1128/mBio.01395-15.
   PubMed Web of Science ®Google Scholar
• Round JL, Mazmanian SK. 2010 Jul 6. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proc Natl Acad Sci U S A. 107(27):12204–12209. doi:10.1073/pnas.0909122107.
   PubMed Web of Science ®Google Scholar
• Said HM, Mohammed ZM. 2006 Mar. Intestinal absorption of water-soluble vitamins: an update. Curr Opin Gastroenterol. 22(2):140–146. doi:10.1097/01.mog.0000203870.22706.52.
   PubMed Web of Science ®Google Scholar
• Savage DC, Siegel JE, Snellen JE, Whitt DD. 1981 Dec. Transit time of epithelial cells in the small intestines of germfree mice and ex-germfree mice associated with indigenous microorganisms. Appl Environ Microbiol. 42(6):996–1001. doi:10.1128/aem.42.6.996-1001.1981.
   PubMed Web of Science ®Google Scholar
• Savage DC, Whitt DD. 1982 Aug. Influence of the indigenous microbiota on amounts of protein, DNA, and alkaline phosphatase activity extractable from epithelial cells of the small intestines of mice. Infect Immun. 37(2):539–549. doi:10.1128/iai.37.2.539-549.1982.
   PubMed Web of Science ®Google Scholar
• Savage DC. 1972 Dec. Associations and physiological interactions of indigenous microorganisms and gastrointestinal epithelia. Am J Clin Nutr. 25(12):1372–1379. doi:10.1093/ajcn/25.12.1372.
   PubMed Web of Science ®Google Scholar
• Savage DC. 1977. Microbial ecology of the gastrointestinal tract. Annu Rev Microbiol. 31:107–133. doi:10.1146/annurev.mi.31.100177.000543.
   PubMed Web of Science ®Google Scholar
• Schächtle MA, Rosshart SP. 2021 Jul 15. The microbiota-gut-brain axis in health and disease and Its implications for translational research. Front Cell Neurosci. 15:698172. doi:10.3389/fncel.2021.698172.
   PubMed Web of Science ®Google Scholar
• Schoeb TR, Eaton KA. 2017. Gnotobiotics. UK: Academic Press (Elsevier). ISBN 978-0-12-804561-9.
   Google Scholar
• Seedorf H, Griffin NW, Ridaura VK, Reyes A, Cheng J, Rey FE, Smith MI, Simon GM, Scheffrahn RH, Woebken D, et al. 2014 Oct 9. Bacteria from diverse habitats colonize and compete in the mouse gut. Cell. 159(2):253–266. doi:10.1016/j.cell.2014.09.008.
   PubMed Web of Science ®Google Scholar
• Sender R, Fuchs S, Milo R. 2016 Aug 19. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 14(8):e1002533. doi:10.1371/journal.pbio.1002533.
   PubMed Web of Science ®Google Scholar
• Sharma V, Rodionov DA, Leyn SA, Tran D, Iablokov SN, Ding H, Peterson DA, Osterman AL, Peterson SN. 2019 Jul 2. B-Vitamin sharing promotes stability of Gut microbial communities. Front Microbiol. 10:1485. doi:10.3389/fmicb.2019.01485.
   PubMed Web of Science ®Google Scholar
• Simon JC, Marchesi JR, Mougel C, Selosse MA. 2019 Jan 11. Host-microbiota interactions: from holobiont theory to analysis. Microbiome. 7(1):5. doi:10.1186/s40168-019-0619-4.
   PubMed Web of Science ®Google Scholar
• Simons C, Köhle K, Genscher U, Dietrich M. 1973. The impact of reverse isolation on early childhood development. Two and a half years of treatment in plastic isolation systems. Psychother Psychosom. 22(2):300–309. doi:10.1159/000286535.
   PubMed Web of Science ®Google Scholar
• Sims IM, Frese SA, Walter J, Loach D, Wilson M, Appleyard K, Eason J, Livingston M, Baird M, Cook G, Tannock GW. 2011. Structure and functions of exopolysaccharide produced by gut commensal Lactobacillus reuteri 100-23. ISME J. 5:1115–1124.
   PubMed Web of Science ®Google Scholar
• Sjögren YM, Tomicic S, Lundberg A, Böttcher MF, Björkstén B, Sverremark-Ekström E, Jenmalm MC. 2009. Influence of early gut microbiota on the maturation of childhood mucosal and systemic immune responses. Clin Exp Allergy. 39:1842–1851.
   PubMed Web of Science ®Google Scholar
• Soto-Martin EC, Warnke I, Farquharson FM, Christodoulou M, Horgan G, Derrien M, Faurie JM, Flint HJ, Duncan SH, Louis P. 2020 Jul 14. Vitamin biosynthesis by human Gut butyrate-producing bacteria and cross-feeding in synthetic microbial communities. mBio. 11(4):e00886–20. doi:10.1128/mBio.00886-20.
   PubMed Web of Science ®Google Scholar
• Stencel A, Wloch-Salamon DM. 2018 Nov. Some theoretical insights into the hologenome theory of evolution and the role of microbes in speciation. Theory Biosci. 137(2):197–206. doi:10.1007/s12064-018-0268-3. Epub 2018 Jul 31. Erratum in: Theory Biosci. 2018 Sep 21.
   PubMed Web of Science ®Google Scholar
• Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N, Yu XN, Kubo C, Koga Y. 2004 Jul 1. Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice. J Physiol. 558(Pt 1):263–275. doi:10.1113/jphysiol.2004.063388.
   PubMed Web of Science ®Google Scholar
• Tannock GW, Blumershine RV, Savage DC. 1975 Feb. Association of Salmonella typhimurium with, and its invasion of, the ileal mucosa in mice. Infect Immun. 11(2):365–370. doi:10.1128/iai.11.2.365-370.1975.
   PubMed Web of Science ®Google Scholar
• Tannock GW. 2004 Jun. A special fondness for lactobacilli. Appl Environ Microbiol. 70(6):3189–3194. doi:10.1128/AEM.70.6.3189-3194.2004.
   PubMed Web of Science ®Google Scholar
• Tannock GW. 2017. Understanding the gut microbiota. New York: John Wiley & Sons.
   Google Scholar
• Tannock GW. 2021 Oct 28. Building robust assemblages of bacteria in the human gut in early life. Appl Environ Microbiol. 87(22):e0144921. doi:10.1128/AEM.01449-21.
   PubMed Web of Science ®Google Scholar
• Tannock GW. 2022 Sep 22. Exploring bacterial attributes that underpin symbiont life in the monogastric gut. Appl Environ Microbiol. 88(18):e0112822. doi:10.1128/aem.01128-22.
   PubMed Web of Science ®Google Scholar
• Teller WM. 1973. Rearing of non-identical twins with lymphopenic hypogammaglobulinaemia under gnotobiotic conditions. Acta Paediatr Scand Suppl. 240:1–45.
   PubMedGoogle Scholar
• Tigchelaar EF, Bonder MJ, Jankipersadsing SA, Fu J, Wijmenga C, Zhernakova A. 2016 Mar. Gut microbiota composition associated with stool consistency. Gut. 65(3):540–542. doi:10.1136/gutjnl-2015-310328.
   PubMed Web of Science ®Google Scholar
• Tims S, Derom C, Jonkers DM, Vlietinck R, Saris WH, Kleerebezem M, de Vos WM, Zoetendal EG. 2013. Microbiota conservation and BMI signatures in adult monozygotic twins. ISME J. 7:707–717.
   PubMed Web of Science ®Google Scholar
• Tramontano M, Andrejev S, Pruteanu M, Klünemann M, Kuhn M, Galardini M, Jouhten P, Zelezniak A, Zeller G, Bork P, et al. 2018 Apr. Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. Nat Microbiol. 3(4):514–522. doi:10.1038/s41564-018-0123-9.
   PubMed Web of Science ®Google Scholar
• Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, et al. 2009 Jan 22. A core gut microbiome in obese and lean twins. Nature. 457 (7228):480-484. doi: 10.1038/nature07540.
   Web of Science ®Google Scholar
• van der Waaij LA, Limburg PC, Mesander G, van der Waaij D. 1996 Mar. In vivo IgA coating of anaerobic bacteria in human faeces. Gut. 38(3):348–354. doi:10.1136/gut.38.3.348.
   PubMed Web of Science ®Google Scholar
• Vandeputte D, Falony G, Vieira-Silva S, Tito RY, Joossens M, Raes J. 2016 Jan. Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates. Gut. 65(1):57–62. doi:10.1136/gutjnl-2015-309618.
   PubMed Web of Science ®Google Scholar
• Vighi G, Marcucci F, Sensi L, Di Cara G, Frati F. 2008 Sep. Allergy and the gastrointestinal system. Clin Exp Immunol. 153(Suppl 1):3–6. doi:10.1111/j.1365-2249.2008.03713.x.
   PubMed Web of Science ®Google Scholar
• Visek WJ. 1978. The mode of growth promotion by antibiotics. J Anim Sci. 46:1447–1469.
   Web of Science ®Google Scholar
• Wenderlein J, Kienzle E, Straubinger RK, Schöl H, Ulrich S, Böswald LF. 2022 Apr 7. Morphology of starch particles along the passage through the gastrointestinal tract in laboratory mice fed extruded and pelleted diets. Animals (Basel. 12(8):952. doi:10.3390/ani12080952.
   PubMedGoogle Scholar
• Werren JH, Baldo L, Clark ME. 2008 Oct. Wolbachia: master manipulators of invertebrate biology. Nat Rev Microbiol. 6(10):741–751. doi:10.1038/nrmicro1969. PMID: 18794912.
   PubMed Web of Science ®Google Scholar
• Whitt DD, Savage DC. 1981 Sep. Influence of indigenous microbiota on amount of protein and activities of alkaline phosphatase and disaccharidases in extracts of intestinal mucosa in mice. Appl Environ Microbiol. 42(3):513–520. doi:10.1128/aem.42.3.513-520.1981.
   PubMed Web of Science ®Google Scholar
• Whitt DD, Savage DC. 1987 Feb. Lactobacilli as effectors of host functions: no influence on the activities of enzymes in enterocytes of mice. Appl Environ Microbiol. 53(2):325–330. doi:10.1128/aem.53.2.325-330.1987.
   PubMed Web of Science ®Google Scholar
• Whitt DD, Savage DC. 1988 Oct. Influence of indigenous microbiota on activities of alkaline phosphatase, phosphodiesterase I, and thymidine kinase in mouse enterocytes. Appl Environ Microbiol. 54(10):2405–2410. doi:10.1128/aem.54.10.2405-2410.1988.
   PubMed Web of Science ®Google Scholar
• World Health Organisation. 2021. Obesity and overweight. www.who.int/news-room/fact-sheets/detail/obesity-and-overweight.
   Google Scholar
• Wostman BS. 1996. Germfree and gnotobiotic animal models. background and applications. Boca Raton, FL: CRC Press. ISBN 0-8493-4008-X.
   Google Scholar
• Wostmann BS. 1981. The germfree animal in nutritional studies. Annu Rev Nutr. 1:257–279. doi:10.1146/annurev.nu.01.070181.001353.
   PubMed Web of Science ®Google Scholar
• Xiao L, Feng Q, Liang S, Sonne SB, Xia Z, Qiu X, Li X, Long H, Zhang J, Zhang D, et al. 2015 Oct. A catalog of the mouse gut metagenome. Nat Biotechnol. 33(10):1103–1108. doi:10.1038/nbt.3353.
   PubMed Web of Science ®Google Scholar
• Yadav M, Verma MJ, Chauhab NS. 2018. A review of metabolic potential of human gut microbiome in human nutrition. Arch Microbiol. 200:203–217. doi:10.1007/s00203-017-1459-x.
   PubMed Web of Science ®Google Scholar
• Yolton DP, Savage DC. 1976 Jun. Influence of certain indigenous gastrointestinal microorganisms on duodenal alkaline phosphatase in mice. Appl Environ Microbiol. 31(6):880–888. doi:10.1128/aem.31.6.880-888.1976.
   PubMed Web of Science ®Google Scholar
• Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, et al. 2014 Nov 20. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515(7527):355–364. doi:10.1038/nature13992.
   PubMed Web of Science ®Google Scholar
• Zeng H, Lazarova DL, Bordonaro M. 2014. Mechanisms linking dietary fiber, gut microbiota and colon cancer prevention. World J Gastrointest Oncol. 6(2):41–51. doi:10.4251/wjgo.v6.i2.41.
   PubMed Web of Science ®Google Scholar
• Zoetendal EG, Akkermans ADL, Akkermans-van Vliet VM, de Visser AGM, de Vos WM. 2001. The host genotype affects the bacterial community in the human gastrointestinal tract. Microb Ecol Health Dis. 13:129–134.
   Google Scholar