Modeling microbiota-associated human diseases: from minimal models to complex systems

Abstract

Alterations in the intestinal microbiota are associated with various human diseases of the digestive system, including obesity and its associated metabolic diseases, inflammatory bowel diseases (IBD), and colorectal cancer (CRC). All three diseases are characterized by modifications of the richness, composition, and metabolic functions of the human intestinal microbiota. Despite being multi-factorial diseases, studies in germ-free animal models have unarguably identified the intestinal microbiota as a causal driver of disease pathogenesis. However, for an increased mechanistic understanding of microbial signatures in human diseases, models require detailed refinement to closely mimic the human microbiota and reflect the complexity and range of dysbiosis observed in patients. The transplantation of human fecal microbiota into animal models represents a powerful tool for studying the causal and functional role of the dysbiotic human microbiome in a pathological context. While human microbiota-associated models were initially employed to study obesity, an increasing number of studies have applied this approach in the context of IBD and CRC over the past decade. In this review, we discuss different approaches that allow the functional validation of the bacterial contribution to human diseases, with emphasis on obesity and its associated metabolic diseases, IBD, and CRC. We discuss the utility of simple models, such as in vitro fermentation systems of the human microbiota and ex vivo intestinal organoids, as well as more complex whole organism models. Our focus here lies on human microbiota-associated mouse models in the context of all three diseases, as well as highlighting the advantages and limitations of this approach.

Keywords

Human microbiota-associated mouse models / fecal microbiota transplantation / inflammatory bowel diseases / obesity / metabolic diseases / colorectal cancer / host-microbiota interactions

References

[1] Bäckhed F,Sonnenburg JL,Gordon JI.Host-bacterial mutualism in the human intestine.Science2005;307:1915-20

[2] Gilbert JA,Caporaso JG,Lynch SV.Current understanding of the human microbiome.Nat Med2018;24:392-400 PMCID:PMC7043356

[3] Qin J,Raes J.MetaHIT ConsortiumA human gut microbial gene catalogue established by metagenomic sequencing.Nature2010;464:59-65 PMCID:PMC3779803

[4] Natividad JM.Modulation of intestinal barrier by intestinal microbiota: pathological and therapeutic implications.Pharmacol Res2013;69:42-51

[5] Gensollen T,Kasper DL.How colonization by microbiota in early life shapes the immune system.Science2016;352:539-44 PMCID:PMC5050524

[6] Fischbach MA.Eating for two: how metabolism establishes interspecies interactions in the gut.Cell Host Microbe2011;10:336-47 PMCID:PMC3225337

[7] Ahmad A,Chen G.Analysis of gut microbiota of obese individuals with type 2 diabetes and healthy individuals.PLoS One2019;14:e0226372 PMCID:PMC6938335

[8] Cho I.The human microbiome: at the interface of health and disease.Nat Rev Genet2012;13:260-70 PMCID:PMC3418802

[9] Ferrer M,Lanza F.Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure.Environ Microbiol2013;15:211-26

[10] Turnbaugh PJ,Yatsunenko T.A core gut microbiome in obese and lean twins.Nature2009;457:480-4 PMCID:PMC2677729

[11] Zhang X,Fang Z.Human gut microbiota changes reveal the progression of glucose intolerance.PLoS One2013;8:e71108 PMCID:PMC3754967

[12] Gevers D,Denson LA.The treatment-naive microbiome in new-onset Crohn’s disease.Cell Host Microbe2014;15:382-92 PMCID:PMC4059512

[13] Lloyd-Price J,Ananthakrishnan AN.IBDMDB InvestigatorsMulti-omics of the gut microbial ecosystem in inflammatory bowel diseases.Nature2019;569:655-62 PMCID:PMC6650278

[14] Morgan XC,Sokol H.Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.Genome Biol2012;13:R79 PMCID:PMC3506950

[15] Pascal V,Borruel N.A microbial signature for Crohn’s disease.Gut2017;66:813-22 PMCID:PMC5531220

[16] Sartor RB.The intestinal microbiota in inflammatory bowel diseases.Nestle Nutr Inst Workshop Ser2014;79:29-39

[17] Schirmer M,Vlamakis H.Microbial genes and pathways in inflammatory bowel disease.Nat Rev Microbiol2019;17:497-511 PMCID:PMC6759048

[18] Baxter NT,Chen GY.Structure of the gut microbiome following colonization with human feces determines colonic tumor burden.Microbiome2014;2:20 PMCID:PMC4070349

[19] Flemer B,Brown JM.Tumour-associated and non-tumour-associated microbiota in colorectal cancer.Gut2017;66:633-43 PMCID:PMC5529966

[20] Zeller G,Voigt AY.Potential of fecal microbiota for early-stage detection of colorectal cancer.Mol Syst Biol2014;10:766 PMCID:PMC4299606

[21] Blüher M.Obesity: global epidemiology and pathogenesis.Nat Rev Endocrinol2019;15:288-98

[22] Kaplan GG.The global burden of IBD: from 2015 to 2025.Nat Rev Gastroenterol Hepatol2015;12:720-7

[23] Saeedi P,Salpea P.IDF Diabetes Atlas CommitteeGlobal and regional diabetes prevalence estimates for 2019 and projections for 2030 and 2045: results from the International Diabetes Federation Diabetes Atlas, 9^th edition.Diabetes Res Clin Pract2019;157:107843

[24] Loos RJF.The genetics of obesity: from discovery to biology.Nat Rev Genet2022;23:120-33 PMCID:PMC8459824

[25] Bogaert J.Molecular genetics of colorectal cancer.Ann Gastroenterol2014;27:9-14. Available from: Last accessed on 5 May 2022] PMCID:PMC3959535

[26] Safiri S,Ikuta KS.The global, regional, and national burden of colorectal cancer and its attributable risk factors in 195 countries and territories, 1990-2017: a systematic analysis for the global burden of disease study 2017.2019;4:913-33 PMCID:PMC7026697

[27] Wu S,Zhu W.Substantial contribution of extrinsic risk factors to cancer development.Nature2016;529:43-7 PMCID:PMC4836858

[28] Guan Q.A comprehensive review and update on the pathogenesis of inflammatory bowel disease.J Immunol Res2019;2019:7247238 PMCID:PMC6914932

[29] Khor B,Xavier RJ.Genetics and pathogenesis of inflammatory bowel disease.Nature2011;474:307-17 PMCID:PMC3204665

[30] Round JL.The gut microbiota shapes intestinal immune responses during health and disease.Nat Rev Immunol2009;9:313-23 PMCID:PMC4095778

[31] Forslund K,Nielsen T.MetaHIT ConsortiumDisentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota.Nature2015;528:262-6 PMCID:PMC4681099

[32] He Y,Zheng HM.Regional variation limits applications of healthy gut microbiome reference ranges and disease models.Nat Med2018;24:1532-5

[33] Reitmeier S,Clavel T.Arrhythmic gut microbiome signatures predict risk of type 2 diabetes.Cell Host Microbe2020;28:258-272.e6

[34] Ananthakrishnan AN,Yajnik V.Gut microbiome function predicts response to anti-integrin biologic therapy in inflammatory bowel diseases.Cell Host Microbe2017;21:603-610.e3 PMCID:PMC5705050

[35] Frank DN,Feldman RA,Harpaz N.Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases.Proc Natl Acad Sci U S A2007;104:13780-5 PMCID:PMC1959459

[36] Sokol H,Watterlot L.Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients.Proc Natl Acad Sci U S A2008;105:16731-6 PMCID:PMC2575488

[37] Strauss J,Beck PL.Invasive potential of gut mucosa-derived Fusobacterium nucleatum positively correlates with IBD status of the host.Inflamm Bowel Dis2011;17:1971-8

[38] Ahn J,Pei Z.Human gut microbiome and risk for colorectal cancer.J Natl Cancer Inst2013;105:1907-11 PMCID:PMC3866154

[39] Wang T,Qiu Y.Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers.ISME J2012;6:320-9 PMCID:PMC3260502

[40] Viljoen KS,Goldberg P.Quantitative profiling of colorectal cancer-associated bacteria reveals associations between fusobacterium spp., enterotoxigenic Bacteroides fragilis (ETBF) and clinicopathological features of colorectal cancer.PLoS One2015;10:e0119462 PMCID:PMC4353626

[41] Bäckhed F,Wang T.The gut microbiota as an environmental factor that regulates fat storage.Proc Natl Acad Sci U S A2004;101:15718-23 PMCID:PMC524219

[42] Bäckhed F,Semenkovich CF.Mechanisms underlying the resistance to diet-induced obesity in germ-free mice.Proc Natl Acad Sci U S A2007;104:979-84 PMCID:PMC1764762

[43] Fleissner CK,Abd El-Bary MM,Klaus S.Absence of intestinal microbiota does not protect mice from diet-induced obesity.Br J Nutr2010;104:919-29

[44] Kübeck R,Hoffmann C.Dietary fat and gut microbiota interactions determine diet-induced obesity in mice.Mol Metab2016;5:1162-74 PMCID:PMC5123202

[45] Adolph TE,Niederreiter L.Paneth cells as a site of origin for intestinal inflammation.Nature2013;503:272-6 PMCID:PMC3862182

[46] Kaser A,Franke A.XBP1 links ER stress to intestinal inflammation and confers genetic risk for human inflammatory bowel disease.Cell2008;134:743-56 PMCID:PMC2586148

[47] Roulis M,Armaka M.Host and microbiota interactions are critical for development of murine Crohn’s-like ileitis.Mucosal Immunol2016;9:787-97 PMCID:PMC5027991

[48] Schaubeck M,Calasan J.Dysbiotic gut microbiota causes transmissible Crohn’s disease-like ileitis independent of failure in antimicrobial defence.Gut2016;65:225-37 PMCID:PMC4752651

[49] Steck N,Sava IG.Enterococcus faecalis metalloprotease compromises epithelial barrier and contributes to intestinal inflammation.Gastroenterology2011;141:959-971

[50] Lengfelder I,Hansen JJ.Complex bacterial consortia reprogram the colitogenic activity of Enterococcus faecalis in a gnotobiotic mouse model of chronic, immune-mediated colitis.Front Immunol2019;10:1420 PMCID:PMC6596359

[51] Chu FF,Chu PG.Bacteria-induced intestinal cancer in mice with disrupted Gpx1 and Gpx2 genes.Cancer Res2004;64:962-8

[52] Uronis JM,Herfarth HH,Jones GS.Modulation of the intestinal microbiota alters colitis-associated colorectal cancer susceptibility.PLoS One2009;4:e6026 PMCID:PMC2696084

[53] Coleman OI,Bierwirth S.Activated ATF6 induces intestinal dysbiosis and innate immune response to promote colorectal tumorigenesis.Gastroenterology2018;155:1539-1552.e12

[54] Benchimol EI,To T.Asthma, type 1 and type 2 diabetes mellitus, and inflammatory bowel disease amongst South Asian immigrants to Canada and their children: a population-based cohort study.PLoS One2015;10:e0123599 PMCID:PMC4388348

[55] Britton GJ,Mogno I.Microbiotas from humans with inflammatory bowel disease alter the balance of gut Th17 and RORγt⁺ regulatory T cells and exacerbate colitis in mice.Immunity2019;50:212-224.e4 PMCID:PMC6512335

[56] Goodrich JK,Poole AC.Human genetics shape the gut microbiome.Cell2014;159:789-99 PMCID:PMC4255478

[57] Kaiser T,Zhu Z.Donor microbiota composition and housing affect recapitulation of obese phenotypes in a human microbiota-associated murine model.Front Cell Infect Microbiol2021;11:614218 PMCID:PMC7937608

[58] Lavoie S,Lassen KG.The Crohn’s disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response.Elife2019;8:e39982 PMCID:PMC6342529

[59] Li L,Zhong W.Gut microbiota from colorectal cancer patients enhances the progression of intestinal adenoma in Apc^min/+ mice.EBioMedicine2019;48:301-15 PMCID:PMC6838415

[60] Metwaly A,Waldschmitt N.Integrated microbiota and metabolite profiles link Crohn’s disease to sulfur metabolism.Nat Commun2020;11:4322 PMCID:PMC7456324

[61] Nagao-Kitamoto H,Gillilland MG 3rd.Functional characterization of inflammatory bowel disease-associated gut dysbiosis in gnotobiotic mice.Cell Mol Gastroenterol Hepatol2016;2:468-81 PMCID:PMC5042563

[62] Parker KD,Ibrahim H.Dietary rice bran-modified human gut microbial consortia confers protection against colon carcinogenesis following fecal transfaunation.Biomedicines2021;9:144 PMCID:PMC7913285

[63] Ridaura VK,Rey FE.Gut microbiota from twins discordant for obesity modulate metabolism in mice.Science2013;341:1241214 PMCID:PMC3829625

[64] Soderborg TK,Mulligan CE.The gut microbiota in infants of obese mothers increases inflammation and susceptibility to NAFLD.Nat Commun2018;9:4462 PMCID:PMC6203757

[65] Torres J,Seki A.Infants born to mothers with IBD present with altered gut microbiome that transfers abnormalities of the adaptive immune system to germ-free mice.Gut2020;69:42-51

[66] Wong SH,Zhang X.Gavage of fecal samples from patients with colorectal cancer promotes intestinal carcinogenesis in germ-free and conventional mice.Gastroenterology2017;153:1621-1633.e6

[67] Zhang L,Roager HM.Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans.ISME J2017;11:676-90 PMCID:PMC5322303

[68] Ahmed BA,Barra NG.Lower brown adipose tissue activity is associated with non-alcoholic fatty liver disease but not changes in the gut microbiota.Cell Rep Med2021;2:100397

[69] Arnoriaga-Rodríguez M,Burokas A.Obesity impairs short-term and working memory through gut microbial metabolism of aromatic amino acids.Cell Metab2020;32:548-560.e7

[70] Fujimoto K,Shimohigoshi M.Antigen-specific mucosal immunity regulates development of intestinal bacteria-mediated diseases.Gastroenterology2019;157:1530-1543.e4

[71] Halatchev IG,Hibberd MC.Applying indirect open-circuit calorimetry to study energy expenditure in gnotobiotic mice harboring different human gut microbial communities.Microbiome2019;7:158 PMCID:PMC6909537

[72] Trikha SRJ,Ecton KE.Transplantation of an obesity-associated human gut microbiota to mice induces vascular dysfunction and glucose intolerance.Gut Microbes2021;13:1940791 PMCID:PMC8317959

[73] Walter J,Finlay BB.Establishing or exaggerating causality for the gut microbiome: lessons from human microbiota-associated rodents.Cell2020;180:221-32

[74] Lee M.Inflammatory bowel diseases (IBD) and the microbiome-searching the crime scene for clues.Gastroenterology2021;160:524-37 PMCID:PMC8098834

[75] Leystra AA.Gut microbiota influences experimental outcomes in mouse models of colorectal cancer.Genes (Basel)2019;10:900 PMCID:PMC6895921

[76] Muscogiuri G,Cassarano S.On Behalf of the Obesity Programs of NutritionEducationResearch and Assessment (OPERA) GroupGut microbiota: a new path to treat obesity.Int J Obes Suppl2019;9:10-9 PMCID:PMC6683132

[77] Nguyen TL,Liston A.How informative is the mouse for human gut microbiota research?.Dis Model Mech2015;8:1-16 PMCID:PMC4283646

[78] Park JC.Of men in mice: the development and application of a humanized gnotobiotic mouse model for microbiome therapeutics.Exp Mol Med2020;52:1383-96 PMCID:PMC8080820

[79] Zihler Berner A,Dostal A.Novel polyfermentor intestinal model (PolyFermS) for controlled ecological studies: validation and effect of pH.PLoS One2013;8:e77772 PMCID:PMC3813750

[80] Tanner SA,Rigozzi E,Chassard C.In vitro continuous fermentation model (PolyFermS) of the swine proximal colon for simultaneous testing on the same gut microbiota.PLoS One2014;9:e94123 PMCID:PMC3978012

[81] Dostal A,Bircher L.Iron modulates butyrate production by a child gut microbiota in vitro.mBio2015;6:e01453-15 PMCID:PMC4659462

[82] Geirnaert A,Tinck M.Interindividual differences in response to treatment with butyrate-producing butyricicoccus pullicaecorum 25-3T studied in an in vitro gut model.FEMS Microbiol Ecol2015;91:fiv054

[83] Lacroix C,Chassard C.Integrated multi-scale strategies to investigate nutritional compounds and their effect on the gut microbiota.Curr Opin Biotechnol2015;32:149-55

[84] McDonald JA,Schroeter K.Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model.J Microbiol Methods2015;108:36-44

[85] Payne AN,Chassard C.Advances and perspectives in in vitro human gut fermentation modeling.Trends Biotechnol2012;30:17-25

[86] Cinquin C,Fliss I.New three-stage in vitro model for infant colonic fermentation with immobilized fecal microbiota.FEMS Microbiol Ecol2006;57:324-36

[87] Cinquin C,Fliss I.Immobilization of infant fecal microbiota and utilization in an in vitro colonic fermentation model.Microb Ecol2004;48:128-38

[88] Macfarlane GT.Models for intestinal fermentation: association between food components, delivery systems, bioavailability and functional interactions in the gut.Curr Opin Biotechnol2007;18:156-62

[89] Van den Abbeele P,Marzorati M.Microbial community development in a dynamic gut model is reproducible, colon region specific, and selective for bacteroidetes and clostridium cluster IX.Appl Environ Microbiol2010;76:5237-46 PMCID:PMC2916472

[90] Pompei A,Raimondi S.In vitro comparison of the prebiotic effects of two inulin-type fructans.Anaerobe2008;14:280-6

[91] Gumienna M,Czarnecki Z.Bioconversion of grape and chokeberry wine polyphenols during simulated gastrointestinal in vitro digestion.Int J Food Sci Nutr2011;62:226-33

[92] Lesmes U,Gibson GR,Shimoni E.Effects of resistant starch type III polymorphs on human colon microbiota and short chain fatty acids in human gut models.J Agric Food Chem2008;56:5415-21

[93] Day-Walsh P,Saha S.The use of an in-vitro batch fermentation (human colon) model for investigating mechanisms of TMA production from choline, L-carnitine and related precursors by the human gut microbiota.Eur J Nutr2021;60:3987-99 PMCID:PMC8437865

[94] Macfarlane GT,Cummings JH.Comparison of fermentation reactions in different regions of the human colon.J Appl Bacteriol1992;72:57-64

[95] Macfarlane GT,Gibson GR.Validation of a three-stage compound continuous culture system for investigating the effect of retention time on the ecology and metabolism of bacteria in the human colon.Microb Ecol1998;35:180-7

[96] Molly K,Verstraete W.Development of a 5-step multi-chamber reactor as a simulation of the human intestinal microbial ecosystem.Appl Microbiol Biotechnol1993;39:254-8

[97] Venema K.Experimental models of the gut microbiome.Best Pract Res Clin Gastroenterol2013;27:115-26

[98] Sato T,Snippert HJ.Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche.Nature2009;459:262-5

[99] Sato T,Ferrante M.Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett’s epithelium.Gastroenterology2011;141:1762-72

[100] Kretzschmar K.Organoids: modeling development and the stem cell niche in a dish.Dev Cell2016;38:590-600

[101] Nagpal R,Wang S,Lovato JF.Obesity-linked gut microbiome dysbiosis associated with derangements in gut permeability and intestinal cellular homeostasis independent of diet.J Diabetes Res2018;2018:3462092 PMCID:PMC6140100

[102] Howell KJ,Nayak KM.DNA methylation and transcription patterns in intestinal epithelial cells from pediatric patients with inflammatory bowel diseases differentiate disease subtypes and associate with outcome.Gastroenterology2018;154:585-98 PMCID:PMC6381389

[103] d’Aldebert E,Sébert M.Characterization of human colon organoids from inflammatory bowel disease patients.Front Cell Dev Biol2020;8:363 PMCID:PMC7287042

[104] Nanki K,Shimokawa M.Somatic inflammatory gene mutations in human ulcerative colitis epithelium.Nature2020;577:254-9

[105] Fujii M,Date S.A colorectal tumor organoid library demonstrates progressive loss of niche factor requirements during tumorigenesis.Cell Stem Cell2016;18:827-38

[106] van de Wetering M,Francis JM.Prospective derivation of a living organoid biobank of colorectal cancer patients.Cell2015;161:933-45 PMCID:PMC6428276

[107] Vlachogiannis G,Vatsiou A.Patient-derived organoids model treatment response of metastatic gastrointestinal cancers.Science2018;359:920-6 PMCID:PMC6112415

[108] Hasan NM,Yin J.Intestinal stem cell-derived enteroids from morbidly obese patients preserve obesity-related phenotypes: Elevated glucose absorption and gluconeogenesis.Mol Metab2021;44:101129 PMCID:PMC7770968

[109] Mohammadi S,Wright CW.Assessing donor-to-donor variability in human intestinal organoid cultures.Stem Cell Reports2021;16:2364-78 PMCID:PMC8452536

[110] Yin X,van Es JH,Langer R.Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny.Nat Methods2014;11:106-12 PMCID:PMC3951815

[111] Boonekamp KE,Clevers H.Intestinal organoids as tools for enriching and studying specific and rare cell types: advances and future directions.J Mol Cell Biol2020;12:562-8 PMCID:PMC7683021

[112] Hofer M.Engineering organoids.Nat Rev Mater2021;6:402-20 PMCID:PMC7893133

[113] Han X,Davies E,Allaire JM.Creating a more perfect union: modeling intestinal bacteria-epithelial interactions using organoids.Cell Mol Gastroenterol Hepatol2021;12:769-82 PMCID:PMC8273413

[114] Hentschel V,Armacki M.Intestinal organoids in coculture: redefining the boundaries of gut mucosa ex vivo modeling.Am J Physiol Gastrointest Liver Physiol2021;321:G693-704

[115] Bartfeld S,van de Wetering M.In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection.Gastroenterology2015;148:126-136.e6 PMCID:PMC4274199

[116] Co JY,Li X.Controlling epithelial polarity: a human enteroid model for host-pathogen interactions.Cell Rep2019;26:2509-2520.e4 PMCID:PMC6391775

[117] Shin YC,Koh D.Three-dimensional regeneration of patient-derived intestinal organoid epithelium in a physiodynamic mucosal interface-on-a-chip.Micromachines (Basel)2020;11:663 PMCID:PMC7408321

[118] Zhang J,Yoon JY.Primary human colonic mucosal barrier crosstalk with super oxygen-sensitive Faecalibacterium prausnitzii in continuous culture.Med (N Y)2021;2:74-98.e9 PMCID:PMC7839961

[119] Morse H. The mouse in biomedical research. 2^nd ed. New York: Elsevier; 1981. Available from: https://books.google.com.hk/books?id=Vt6nUmz1yEQC&pg=PA144&lpg=PA144&dq=Morse,+H.+and+Fox,+J.,+The+mouse+in+biomedical+research.+1981:+Academic,+New+York&source=bl&ots=epxwhP32B4&sig=ACfU3U0SqkHTjy35-wpwzsLQ-LOJphIANA&hl=zh-CN&sa=X&ved=2ahUKEwjqneDDz7j3AhUDL6YKHX8HC4wQ6AF6BAgCEAM#v=onepage&q=Morse%2C%20H.%20and%20Fox%2C%20J.%2C%20The%20mouse%20in%20biomedical%20research.%201981%3A%20Academic%2C%20New%20York&f=false [Last accessed on 5 May 2022]

[120] Zinkernagel RM.Immunological surveillance against altered self components by sensitised T lymphocytes in lymphocytic choriomeningitis.Nature1974;251:547-8

[121] Zinkernagel RM.Restriction of in vitro T cell-mediated cytotoxicity in lymphocytic choriomeningitis within a syngeneic or semiallogeneic system.Nature1974;248:701-2

[122] Walburg HE Jr,Cosgrove GE,Robie DM.Microbiological evaluation of an isolation facility for the production of specific-pathogen-free mice.Lab Anim Care1965;15:208-16

[123] Cox LM,Sohn J.Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences.Cell2014;158:705-21 PMCID:PMC4134513

[124] Olszak T,Zeissig S.Microbial exposure during early life has persistent effects on natural killer T cell function. Science 2012;336:489-493. PMCID:PMC3437652

[125] Hintze KJ,Rompato G.Broad scope method for creating humanized animal models for animal health and disease research through antibiotic treatment and human fecal transfer.Gut Microbes2014;5:183-91 PMCID:PMC4063843

[126] Manichanh C,Gibert P.Reshaping the gut microbiome with bacterial transplantation and antibiotic intake.Genome Res2010;20:1411-9 PMCID:PMC2945190

[127] Wos-Oxley M,Oxley AP.Comparative evaluation of establishing a human gut microbial community within rodent models.Gut Microbes2012;3:234-49 PMCID:PMC3427216

[128] Gonzalez-Perez G,Tekieli TM,Williams BL.Maternal antibiotic treatment impacts development of the neonatal intestinal microbiome and antiviral immunity.J Immunol2016;196:3768-79

[129] Lamousé-Smith ES,Starnbach MN.The intestinal flora is required to support antibody responses to systemic immunization in infant and germ free mice.PLoS One2011;6:e27662 PMCID:PMC3219679

[130] Li F,Chen Y.The microbiota maintain homeostasis of liver-resident γδT-17 cells in a lipid antigen/CD1d-dependent manner.Nat Commun2017;7:13839 PMCID:PMC5227332

[131] Houtkooper RH,Ryu D.Mitonuclear protein imbalance as a conserved longevity mechanism.Nature2013;497:451-7 PMCID:PMC3663447

[132] McKee EE,Bentley AT.Inhibition of mammalian mitochondrial protein synthesis by oxazolidinones. Antimicrob Agents Chemother 2006;50:2042-9. PMCID:PMC1479116

[133] Kalghatgi S,Costello JC.Bactericidal antibiotics induce mitochondrial dysfunction and oxidative damage in mammalian cells.Sci Transl Med2013;5:192ra85 PMCID:PMC3760005

[134] Rosshart SP,Angeletti D.Wild mouse gut microbiota promotes host fitness and improves disease resistance.Cell2017;171:1015-1028.e13 PMCID:PMC6887100

[135] Rosshart SP,Vassallo BG.Laboratory mice born to wild mice have natural microbiota and model human immune responses.Science2019;365:eaaw4361 PMCID:PMC7377314

[136] Arnesen H,Steppeler C.Naturalizing laboratory mice by housing in a farmyard-type habitat confers protection against colorectal carcinogenesis.Gut Microbes2021;13:1993581 PMCID:PMC7377314

[137] Turnbaugh PJ,Faith JJ,Knight R.The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice.Sci Transl Med2009;1:6ra14 PMCID:PMC2894525

[138] Arrieta MC,Finlay BB.Human microbiota-associated mice: a model with challenges.Cell Host Microbe2016;19:575-8

[139] Abarca-gómez L,Hamid ZA.Worldwide trends in body-mass index, underweight, overweight, and obesity from 1975 to 2016: a pooled analysis of 2416 population-based measurement studies in 128·9 million children, adolescents, and adults.The Lancet2017;390:2627-42 PMCID:PMC5735219

[140] Wostmann BS,Moriarty A.Dietary intake, energy metabolism, and excretory losses of adult male germfree Wistar rats.Lab Anim Sci1983;33:46-50

[141] Hild B,Oh JH.Neonatal exposure to a wild-derived microbiome protects mice against diet-induced obesity.Nat Metab2021;3:1042-57

[142] Kleinert M,Hofmann SM.Animal models of obesity and diabetes mellitus.Nat Rev Endocrinol2018;14:140-62

[143] Dalby MJ,Walker AW.Dietary uncoupling of gut microbiota and energy harvesting from obesity and glucose tolerance in mice.Cell Rep2017;21:1521-33 PMCID:PMC5695904

[144] Bloom SM,Nava GM.Commensal bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease.Cell Host Microbe2011;9:390-403 PMCID:PMC3241010

[145] Ocvirk S,Lengfelder I.Surface-associated lipoproteins link enterococcus faecalis virulence to colitogenic activity in IL-10-deficient mice independent of their expression levels.PLoS Pathog2015;11:e1004911 PMCID:PMC4466351

[146] Eun CS,Wohlgemuth S.Induction of bacterial antigen-specific colitis by a simplified human microbiota consortium in gnotobiotic interleukin-10-/- mice.Infect Immun2014;82:2239-46 PMCID:PMC4019192

[147] Bray F,Soerjomataram I,Torre LA.Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.CA Cancer J Clin2018;68:394-424

[148] Moser AR,Dove WF.A dominant mutation that predisposes to multiple intestinal neoplasia in the mouse.Science1990;247:322-4

[149] De Filippo C,Di Paola M.Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.Proc Natl Acad Sci U S A2010;107:14691-6 PMCID:PMC2930426

[150] Smith MI,Manary MJ.Gut microbiomes of malawian twin pairs discordant for kwashiorkor.Science2013;339:548-54 PMCID:PMC3667500

[151] Subramanian S,Yatsunenko T.Persistent gut microbiota immaturity in malnourished Bangladeshi children.Nature2014;510:417-21 PMCID:PMC4189846

[152] Turnbaugh PJ,Mahowald MA,Mardis ER.An obesity-associated gut microbiome with increased capacity for energy harvest.Nature2006;444:1027-31

[153] Chung H,Hill JA.Gut immune maturation depends on colonization with a host-specific microbiota.Cell2012;149:1578-93 PMCID:PMC3442780

[154] Kibe R,Yokota H.Movement and fixation of intestinal microbiota after administration of human feces to germfree mice.Appl Environ Microbiol2005;71:3171-8 PMCID:PMC1151853

[155] Marcobal A,Nelson TA.A metabolomic view of how the human gut microbiota impacts the host metabolome using humanized and gnotobiotic mice.ISME J2013;7:1933-43 PMCID:PMC3965317