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Insight into the Animal Models for Microbiome Studies

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Microbiome in Human Health and Disease

Abstract

The microbiomes, including bacteria, fungi, and viruses, exist within and on all the organisms, which is the current field of research. Particularly of interest are microbiome of human and its direct impact on human health. The health and fitness of animals, including humans, are influenced by the existence and composition of microbial communities of the host. To date, maximum microbiome research has been focused on the mouse as a model organism for studying the mechanisms of different processes occurring in the microbial communities. Mouse microbiome models have also been the primary choice for performing preclinical tests for studying relationships between the microbiomes and host physiological, metabolic, immune, and neurologic phenotypes. These were also used for developing methodologies to correct functional abnormalities in these communities that lead to disease. The mouse, however, is not a perfect model for studying different aspects of the microbiome and for studying the host stimuli and environmental responses. Hence, researchers have been conducting microbiome studies using other animals as well, for example, zebrafish, pigs, and Drosophila. This chapter summarizes the microbiome studies conducted using different models and an insight into its advantages.

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References

  • Al-Asmakh M, Anuar F, Zadjali F, Rafter J, Pettersson S (2012) Gut microbial communities modulating brain development and function. Gut Microbes 3:366–373

    Article  PubMed  PubMed Central  Google Scholar 

  • Al-Asmakh M, Stukenborg JB, Reda A, Anuar F, Strand ML, Hedin L (2014) The gut microbiota and developmental programming of the testis in mice. PLoS One 9:e103809

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Allen HK, Looft T, Bayles DO (2011) Antibiotics in feed induce prophages in swine fecal microbiomes. MBio 2:e00260

    Article  PubMed  PubMed Central  Google Scholar 

  • Alsop D, Vijayan MM (2009) Molecular programming of the corticosteroid stress axis during zebrafish development. Comp Biochem Physiol A Mol Integr Physiol 153:49–54

    Article  PubMed  CAS  Google Scholar 

  • Amacher SL (2008) Emerging gene knockout technology in zebrafish: zinc-finger nucleases. Brief Funct Genomic Proteomic 7:460–464

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arm HG, Floyd TM, Faber JE (1965) Use of ligated segments of rabbit small intestine in experimental shigellosis. J Bacteriol 89:803–809

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arthur JC, Jobin C (2013) The complex interplay between inflammation, the microbiota and colorectal cancer. Gut Microbes 4:253–258

    Article  PubMed  PubMed Central  Google Scholar 

  • Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y (2011) Induction of colonic regulatory T cells. Science 331:337–342

    Article  CAS  PubMed  Google Scholar 

  • Barszcz M, Taciak M, Skomial J (2016) The effects of inulin, dried Jerusalem artichoke tuber and a multispecies probiotic preparation on microbiota ecology and immune status of the large intestine in young pigs. Arch Anim Nutr 70:278–292

    Article  PubMed  CAS  Google Scholar 

  • Bates JM, Akerlund J, Mittge E (2007) Intestinal alkaline phosphatase detoxifies lipopolysaccharide and prevents inflammation in zebrafish in response to the gut microbiota. Cell Host Microbe 2:371–382

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bates JM, Mittge E, Kuhlman J (2006) Distinct signals from the microbiota promote different aspects of zebrafish gut differentiation. Dev Biol 297:374–386

    Article  CAS  PubMed  Google Scholar 

  • Bedell VM, Wang Y, Campbell JM, Poshusta TL, Starker CG, Krug RG II, Tan W, Penheiter SG, Ma AC, Leung AYH (2012) In vivo genome editing using a high-efficiency TALEN system. Nature 491:114–118

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Berding K, Wang M, Monaco MH (2016) Prebiotics and bioactive milk fractions affect gut development, microbiota, and neurotransmitter expression in piglets. J Pediatr Gastroenterol Nutr 63:688–697

    Article  CAS  PubMed  Google Scholar 

  • Berg M, Stenuit B, Ho J (2016) Assembly of the Caenorhabditis elegans gut microbiota from diverse soil microbial environments. ISME J 10:1998–2009

    Article  PubMed  PubMed Central  Google Scholar 

  • Berg RD (1996) The indigenous gastrointestinal microflora. Trends Microbiol 4:430–435

    Article  CAS  PubMed  Google Scholar 

  • Bowey E, Adlercreutz H, Rowland I (2003) Metabolism of isoflavones and lignans by the gut microflora: a study in germ-free and human flora associated rats. Food Chem Toxicol 41:631–636

    Article  CAS  PubMed  Google Scholar 

  • Brugman S, Liu KY, Lindenbergh-Kortleve D (2009) Oxazolone-induced enterocolitis in zebrafish depends on the composition of the intestinal microbiota. Gastroenterologia 137:1757–1767

    Article  CAS  Google Scholar 

  • Cani PD, Osto M, Geurts L, Everard A (2012) Involvement of gut microbiota in the development of low grade inflammation and type 2 diabetes associated with obesity. Gut Microbes 3:279–288

    Article  PubMed  PubMed Central  Google Scholar 

  • Casteleyn C, Rekecki A, Van der Aa A, Simoens P, Van den Broeck W (2010) Surface area assessment of the murine intestinal tract as a prerequisite for oral dose translation from mouse to man. Lab Anim 44:176–183

    Article  CAS  PubMed  Google Scholar 

  • Chandler JA, Lang JM, Bhatnagar S, Eisen JA, Kopp A (2011) Bacterial communities of diverse Drosophila species: ecological context of a host-microbe model system. PLoS Genet 7:e1002272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Charroux B, Royet J (2012) Gut-microbiota interactions in nonmammals: what can we learn from drosophila? Semin Immunol 24:17–24

    Article  PubMed  Google Scholar 

  • Chaston J, Goodrich-Blair H (2010) Common trends in mutualism revealed by model associations between invertebrates and bacteria. FEMS Microbiol Reviews 34:41–58

    Article  CAS  Google Scholar 

  • Cho I, Yamanishi S, Cox L, Methe BA, Zavadil J, Li K, Gao Z, Mahana D, Raju K, Teitler I (2012) Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 488:621–626

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chu H, Mazmanian SK (2013) Innate immune recognition of the microbiota promotes host-microbial symbiosis. Nat Immunol 14:668–675

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clarke DJ (2008) Photorhabdus: a model for the analysis of pathogenicity and mutualism. Cell Microbiol 10:2159–2167

    Article  CAS  PubMed  Google Scholar 

  • Corby-Harris V, Pontaroli AC, Shimkets LJ, Bennetzen JL, Habel KE, Promislow DEL (2007) Geographical distribution and diversity of bacteria associated with natural populations of Drosophila melanogaster. Appl Environ Microbiol 73:3470–3479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cox CR, Gilmore MS (2007) Native microbial colonization of Drosophila melanogaster and its use as a model of Enterococcus faecalis pathogenesis. Infect Immun 75:1565–1576

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cunliffe RN, Rose FR, Keyte J, Abberley L, Chan WC, Mahida YR (2001) Human defensin 5 is stored in precursor form in normal Paneth cells and is expressed by some villous epithelial cells and by metaplastic Paneth cells in the colon in inflammatory bowel disease. Gut 48:176–185

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Davis DJ, Bryda EC, Gillespie CH (2016a) Microbial modulation of behavior and stress responses in zebrafish larvae. Behav Brain Res 311:219–227

    Article  PubMed  PubMed Central  Google Scholar 

  • Davis DJ, Doerr HM, Grzelak AK (2016b) Lactobacillus plantarum attenuates anxiety-related behavior and protects against stress-induced dysbiosis in adult zebrafish. Sci Rep 6:33726

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • De Rienzo G, Gutzman JH, Sive H (2012) Efficient shRNA mediated inhibition of gene expression in zebrafish. Zebrafish 9:97–107

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • De SN, Chatterje DN (1953) An experimental study of the mechanism of action of Vibrio cholerae on the intestinal mucous membrane. J Pathol Bacteriol 66:559–562

    Article  CAS  PubMed  Google Scholar 

  • Delzenne NM, Neyrinck AM, Bäckhed F, Cani PD (2011) Targeting gut microbiota in obesity: effects of prebiotics and probiotics. Nat Rev Endocrinol 7:639–646

    Article  CAS  PubMed  Google Scholar 

  • Dewhirst FE, Chen T, Izard J (2010) The human oral microbiome. J Bacteriol 192:5002–5017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Diaz Heijtz R, Wang S, Anuar F, Qian Y, Bjorkholm B, Samuelsson A, Hibberd ML, Forssberg H, Pettersson S (2011) Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci 108:3047–3052

    Article  PubMed  Google Scholar 

  • Duncan CL, Sugiyama H, Strong DH (1968) Rabbit ileal loop response to strains of Clostridium perfringens. J Bacteriol 95:1560–1566

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Erb-Downward JR, Thompson DL, Han MK (2011) Analysis of the lung microbiome in the “healthy”smoker and in COPD. PLoS One 6:e16384

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ericsson AC, Personett AR, Grobman ME (2016) Composition and predicted metabolic capacity of upper and lower airway microbiota of healthy dogs in relation to the fecal microbiota. PLoS One 11:e0154646

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fontaine CA, Skorupski AM, Vowles CJ, Anderson NE, Poe SA, Eaton KA (2015) How free of germs is germ-free? Detection of bacterial contamination in a germ free mouse unit. Gut Microbes 6:225–233

    Article  PubMed  PubMed Central  Google Scholar 

  • Fritz JV, Desai MS, Shah P, Schneider JG, Wilmes P (2013) From meta-omics to causality: experimental models for human microbiome research. Microbiome 1:14

    Article  PubMed  PubMed Central  Google Scholar 

  • Gallo M, Poser H, Bottio T (2017) The Vietnamese pig as a translational animal model to evaluate tissue engineered heart valves: promising early experience. Int J Artif Organs 40:142–149

    Article  PubMed  Google Scholar 

  • Garrett WS, Gordon JI, Glimcher LH (2010) Homeostasis and inflammation in the intestine. Cell 140:859–870

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Geiger BM, Gras-Miralles B, Ziogas DC (2013) Intestinal upregulation of melanin-concentrating hormone in TNBS-induced enterocolitis in adult zebrafish. PLoS One 8:e83194

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Gérard P, Béguet F, Lepercq P, Rigottier-Gois L, Rochet V, Andrieux C, Juste C (2004) Gnotobiotic rats harboring human intestinal microbiota as a model for studying cholesterol-to-coprostanol conversion. FEMS Microbiol Ecol 47:337–343

    Article  PubMed  CAS  Google Scholar 

  • Ghosh D, Porter E, Shen B, Lee SK, Wilk D, Drazba J, Yadav SP, Crabb JW, Ganz T, Bevins CL (2002) Paneth cell trypsin is the processing enzyme for human defensin-5. Nat Immunol 3:583–590

    Article  CAS  PubMed  Google Scholar 

  • Giorgini E, Conti C, Ferraris P (2010) Effects of Lactobacillus rhamnosus on zebrafish oocyte maturation: in FTIR imaging and biochemical analysis. Anal Bioanal Chem 398:3063–3072

    Article  CAS  PubMed  Google Scholar 

  • Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, Dantas G, Gordon JI (2011) Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci U S A 108:6252–6257

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gootenberg DB, Turnbaugh PJ (2011) Companion animals symposium: humanized animal models of the microbiome. J Anim Sci 89:1531–1537

    Article  CAS  PubMed  Google Scholar 

  • Gordon HA, Pesti L (1971) The gnotobiotic animal as a tool in the study of host microbial relationships. Bacteriol Rev 35:390–429

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gorrel C (1998) Periodontal disease and diet in domestic pets. J Nutr 128:2712S–2714S

    Article  CAS  PubMed  Google Scholar 

  • Graf J, Kikuchi Y, Rio RV (2006) Leeches and their microbiota: naturally simple symbiosis models. Trends Microbiol 14:365–371

    Article  CAS  PubMed  Google Scholar 

  • Haenen D, Zhang J, Souza da Silva C (2013) A diet high in resistant starch modulates microbiota composition, SCFA concentrations, and gene expression in pig intestine. J Nutr 143:274–283

    Article  CAS  PubMed  Google Scholar 

  • Harvey CE (1998) Periodontal disease in dogs. Etiopathogenesis, prevalence, and significance. Vet Clin North Am Small Anim Pract 28:1111–1128

    Article  CAS  PubMed  Google Scholar 

  • Hazenberg MP, Bakker M, Verschoor-Burggraaf A (1981) Effects of the human intestinal flora on germ-free mice. J Appl Bacteriol 50:95–106

    Article  CAS  PubMed  Google Scholar 

  • Heinritz SN, Weiss E, Eklund M (2016) Intestinal microbiota and microbial metabolites are changed in a pig model fed a high-fat/low-fiber or a low-fat/high-fiber diet. PLoS One 11:e0154329

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Hirayama K (1999) Ex-germfree mice harboring intestinal microbiota derived from other animal species as an experimental model for ecology and metabolism of intestinal bacteria. Exp Anim 48:219–227

    Article  CAS  PubMed  Google Scholar 

  • Hooper LV, Littman DR, Macpherson AJ (2012) Interactions between the microbiota and the immune system. Science 336:1268–1273

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hughes HC (1986) Swine in cardiovascular research. Lab Anim Sci 36:348–350

    CAS  PubMed  Google Scholar 

  • Ji Y, Guo Q, Yin Y (2018) Dietary proline supplementation alters colonic luminal microbiota and bacterial metabolite composition between days 45 and 70 of pregnancy in Huanjiang mini-pigs. J Anim Sci Biotechnol 9:18

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI (2011) Human nutrition, the gut microbiome and the immune system. Nature 474:327–336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kibe RM, Sakamoto H, Yokota H, Ishikawa Y, Aiba Y, Koga Y, Benno (2005) Movement and fixation of intestinal microbiota after administration of human feces to germ free mice. Appl Environ Microbiol 71:3171–3178

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kietz C, Pollari V, Meinander A (2018) Generating germfree drosophila to study gut-microbe interactions: protocol to rear Drosophila under axenic conditions. Curr Protoc Toxicol 77:e52

    Article  PubMed  Google Scholar 

  • Kostic AD, Howitt MR, Garrett WS (2013) Exploring host microbiota interactions in animal models and humans. Genes Dev 27:701–718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lai HC, Young J, Lin CS, Chang CJ, Lu CC, Martel J (2014) Impact of the gut microbiota, prebiotics, and probiotics on human health and disease. Biom J 37:259–268

    Google Scholar 

  • Lanning D, Sethupathi P, Rhee KJ (2000) Intestinal microflora and diversification of the rabbit antibody repertoire. J Immunol 165:2012–2019

    Article  CAS  PubMed  Google Scholar 

  • Littman DR, Pamer EG (2011) Role of the commensal microbiota in normal and pathogenic host immune responses. Cell Host Microbe 10:311–323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu H, Ivarsson E, Dicksved J (2012) Inclusion of chicory (Cichorium intybus L.) in pigs’ diets affects the intestinal microenvironment and the gut microbiota. Appl Environ Microbiol 78:4102–4109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Looft T, Johnson TA, Allen HK (2012) In-feed antibiotic effects on the swine intestinal microbiome. Proc Natl Acad Sci U S A 109:1691–1696

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Macdonald RS, Wagner K (2012) Influence of dietary phytochemicals and microbiota on colon cancer risk. J Agric Food Chem 60:6728–6735

    Article  CAS  PubMed  Google Scholar 

  • Maynard CL, Elson CO, Hatton RD, Weaver CT (2012) Reciprocal interactions of the intestinal microbiota and immune system. Nature 489:231–241

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McFall-Ngai M (2007) Adaptive immunity: care for the community. Nature 445:153

    Article  CAS  PubMed  Google Scholar 

  • McFall-Ngai M (2014) Divining the essence of symbiosis: insights from the squid-vibrio model. PLoS Biol 12:e1001783

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • McVey Neufeld KA, Perez-Burgos A, Mao YK, Bienenstock J, Kunze WA (2015) The gut microbiome restores intrinsic and extrinsic nerve function in germ-free mice accompanied by changes in calbindin. Neurogastroenterol Motil 27:627–636

    Article  CAS  PubMed  Google Scholar 

  • Melling J, Capel BJ, Turnbull PC (1976) Identification of a novel enterotoxigenic activity associated with Bacillus cereus. J Clin Pathol 29:938–940

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Misic AM, Davis MF, Tyldsley AS (2015) The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites. Microbiome 3:2

    Article  PubMed  PubMed Central  Google Scholar 

  • Nasevicius A, Ekker SC (2000) Effective targeted gene ‘knockdown’ in zebrafish. Nat Genet 26:216–220

    Article  CAS  PubMed  Google Scholar 

  • Neufeld KM, Kang N, Bienenstock J, Foster JA (2011) Reduced anxiety-like behavior and central neurochemical change in germ-free mice. Neurogastroenterol Motil 23:255–264

    Article  CAS  PubMed  Google Scholar 

  • Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W, Pattersson S (2012) Host-gut microbiota metabolic interactions. Science 336:1262–1267

    Article  CAS  PubMed  Google Scholar 

  • Nicklas W, Keubler L, Bleich A (2015) Maintaining and monitoring the defined microbiota status of gnotobiotic rodents. ILAR J 56:241–249

    Article  CAS  PubMed  Google Scholar 

  • Norman JM, Handley SA, Virgin HW (2014) Kingdom agnostic metagenomics and the importance of complete characterization of enteric microbial communities. Gastroenterology 146:1459–1469

    Article  CAS  PubMed  Google Scholar 

  • Norton WH, Folchert A, Bally-Cuif L (2008) Comparative analysis of serotonin receptor (HTR1A/HTR1B families) and transporter (slc6a4a/b) gene expression in the zebrafish brain. J Comp Neurol 511:521–542

    Article  CAS  PubMed  Google Scholar 

  • Ouellette AJ, Selsted ME (1996) Paneth cell defensins: endogenous peptide components of intestinal host defense. FASEB J 10:1280–1289

    Article  CAS  PubMed  Google Scholar 

  • Palm NW, de Zoete MR, Flavell RA (2015) Immune microbiota interactions in health and disease. Clin Immunol 159:122–127

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Panasevich MR, Wankhade UD, Chintapalli SV (2018) Cecal versus fecal microbiota in Ossabaw swine and implications for obesity. Physiol Genomics 50:355–368

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pang X, Hua X, Yang Q, Ding D, Che C, Cui L, Jia W, Bucheli P, Zhao L (2007) Inter-species transplantation of gut microbiota from human to pigs. ISME J 1:156–162

    Article  CAS  PubMed  Google Scholar 

  • Patton EE, Zon LI (2001) The art and design of genetic screens: zebrafish. Nat Rev Genet 2:956–966

    Article  CAS  PubMed  Google Scholar 

  • Pedersen R, Ingerslev HC, Sturek M (2013) Characterisation of gut microbiota in Ossabaw and Gottingen minipigs as models of obesity and metabolic syndrome. PLoS One 8:e56612

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Perleberg C, Kind A, Schnieke A (2018) Genetically engineered pigs as models for human disease. Disease Mod Mech 11:dmm030783

    Article  CAS  Google Scholar 

  • Pham LN, Kanther M, Semova I, Rawls JF (2008) Methods for generating and colonizing gnotobiotic zebrafish. Nat Protoc 3:1862–1875

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qin C, Xu L, Yang Y (2014) Comparison of fecundity and offspring immunity in zebrafish fed Lactobacillus rhamnosus CICC 6141 and Lactobacillus casei BL23. Reproduction 147:53–64

    Article  CAS  PubMed  Google Scholar 

  • Qin C, Zhang Z, Wang Y (2017) EPSP of L. casei BL23 protected against the infection caused by Aeromonas veronii via enhancement of immune response in zebrafish. Front Microbiol 8:2406

    Article  PubMed  PubMed Central  Google Scholar 

  • Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, MetaHIT Consortium (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rawls JF, Mahowald MA, Goodman AL, Trent CM, Gordon JI (2007) In vivo imaging and genetic analysis link bacterial motility and symbiosis in the zebrafish gut. Proc Natl Acad Sci U S A 104:7622–7627

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Reinhardt C, Bergentall M, Greiner TU, Schaffner F, Ostergren-Lunden G, Petersen LC, Ruf W, Backhed F (2012) Tissue factor and PAR1 promote microbiota-induced intestinal vascular remodelling. Nature 483:627–631

    Article  CAS  PubMed  Google Scholar 

  • Ren C, Webster P, Finkel SE, Tower J (2007) Increased internal and external bacterial load during Drosophila aging without life-span trade-off. Cell Metab 6:144–152

    Article  CAS  PubMed  Google Scholar 

  • Riboulet-Bisson E, Sturme MH, Jeffery IB (2012) Effect of Lactobacillus salivarius bacteriocin Abp118 on the mouse and pig intestinal microbiota. PLoS One 7:e31113

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rio RV, Maltz M, McCormick B (2009) Symbiont succession during embryonic development of the European medicinal leech, Hirudo verbana. Appl Environ Microbiol 75:6890–6895

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roura E, Koopmans SJ, Lalles JP (2016) Critical review evaluating the pig as a model for human nutritional physiology. Nutr Res Rev 29:60–90

    Article  CAS  PubMed  Google Scholar 

  • Russo P, Iturria I, Mohedano ML (2015) Zebrafish gut colonization by mCherry-labelled lactic acid bacteria. Appl Microbiol Biotechnol 99:3479–3490

    Article  CAS  PubMed  Google Scholar 

  • Ryu J, Prather RS, Lee K (2018) Use of gene-editing technology to introduce targeted modifications in pigs. J Anim Sci Biotechnol 9:5

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Ryu JH, Kim SH, Lee HY, Bai JY, Nam YD, Bae JW, Lee DG, Shin SC, Ha EM, Lee WJ (2008) Innate immune homeostasis by the homeobox gene caudal and commensal-gut mutualism in Drosophila. Science 319:777–782

    Article  CAS  PubMed  Google Scholar 

  • Sakamoto M, Umeda M, Benno Y (2005) Molecular analysis of human oral microbiota. J Periodontal Res 40:277–285

    Article  CAS  PubMed  Google Scholar 

  • Sanyal SC, Singh SJ, Sen PC (1995) Enteropathogenicity of Aeromonas hydrophila and Plesiomonas shigelloides. J Med Microbiol 8:195–198

    Article  Google Scholar 

  • Schleicher TR, Nyholm SV (2011) Characterizing the host and symbiont proteomes in the association between the bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri. PLoS One 6:e25649

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schousboe LP, Rasmussen LM, Ovesen T (2001) Induction of mucin and adhesion molecules in middle ear mucosa. Acta Otolaryngol 121:596–601

    Article  CAS  PubMed  Google Scholar 

  • Schubert AM, Sinani H, Schloss PD (2015) Antibiotic-induced alterations of the murine gut microbiota and subsequent effects on colonization resistance against Clostridium difficile. MBio 6:e00974-15

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Shen J, Zhang B, Wei H (2010) Assessment of the modulating effects of fructo-oligosaccharides on fecal microbiota using human flora-associated piglets. Arch Microbiol 192:959–968

    Article  CAS  PubMed  Google Scholar 

  • Shimizu K, Muranaka Y, Fujimura R, Ishida H, Tazume S, Shimamura T (1998) Normalization of reproductive function in germfree mice following bacterial contamination. Exp Anim 47:151–158

    Article  CAS  PubMed  Google Scholar 

  • Shin SC, Kim SH, You H, Kim B, Kim AC, Lee KA, Yoon JH, Ryu JH, Lee WJ (2011) Drosophila microbiome modulates host developmental and metabolic homeostasis via insulin signaling. Science 334:670–674

    Article  CAS  PubMed  Google Scholar 

  • Sicard M, Ferdy JB, Pages S (2004) When mutualists are pathogens: an experimental study of the symbioses between Steinernema (entomopathogenic nematodes) and Xenorhabdus (bacteria). J Evol Biol 17:985–993

    Article  CAS  PubMed  Google Scholar 

  • Singer JT, Phennicie RT, Sullivan MJ (2010) Broad-host range plasmids for red fluorescent protein labeling of gram-negative bacteria for use in the zebrafish model system. Appl Environ Microbiol 76:3467–3474

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh S, Orr D, Divinagracia E (2015) Role of secondary metabolites in establishment of the mutualistic partnership between Xenorhabdus nematophila and the entomopathogenic nematode Steinernema carpocapsae. Appl Environ Microbiol 81:754–764

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sinkora M, Butler JE (2016) Progress in the use of swine in developmental immunology of B and T lymphocytes. Dev Comp Immunol 58:1–17

    Article  CAS  PubMed  Google Scholar 

  • Sjogren K, Engdahl C, Henning P, Lerner UH, Tremaroli V, Lagerquist MK (2012a) The gut microbiota regulates bone mass in mice. J Bone Miner Res 27:1357–1367

    Article  PubMed  CAS  Google Scholar 

  • Sjogren K, Engdahl C, Henning P, Lerner UH, Tremaroli V, Lagerquist MK, Backhed F, Ohlsson C (2012b) The gut microbiota regulates bone mass in mice. J Bone Miner Res 27:1357–1367

    Article  PubMed  CAS  Google Scholar 

  • Smith K, McCoy KD, Macpherson AJ (2007) Use of axenic animals in studying the adaptation of mammals to their commensal intestinal microbiota. Semin Immunol 19:59–69

    Article  CAS  PubMed  Google Scholar 

  • Sommer F, Backhed F (2013) The gut microbiota – masters of host development and physiology. Nat Rev Microbiol 11:227–238

    Article  CAS  PubMed  Google Scholar 

  • Song SJ, Lauber C, Costello EK (2013) Cohabiting family members share microbiota with one another and wit their dogs. Elife 2:e00458

    Article  PubMed  PubMed Central  Google Scholar 

  • Spor A, Koren O, Ley R (2011) Unravelling the effects of the environment and host genotype on the gut microbiome. Nat Rev Microbiol 9:279–290

    Article  CAS  PubMed  Google Scholar 

  • Stappenbeck TS, Hooper LV, Gordon JI (2002) Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. Proc Natl Acad Sci 99:15451–15455

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stepankova R, Tonar Z, Bartova J, Nedorost L, Rossman P, Poledne R (2010) Absence of microbiota (germ-free conditions) accelerates the atherosclerosis in ApoE-deficient mice fed standard low cholesterol diet. J Atheroscler Thromb 17:796–804

    Article  CAS  PubMed  Google Scholar 

  • Taylor J, Maltby MP, Payne JM (1958) Factors influencing the response of ligated rabbit-gut segments to injected Escherichia coli. J Pathol Bacteriol 76:491–499

    Article  CAS  PubMed  Google Scholar 

  • Trede NS, Langenau DM, Traver D (2004) The use of zebrafish to understand immunity. Immunity 20:367–379

    Article  CAS  PubMed  Google Scholar 

  • Treuting PM, Dintzis SM (2012) Lower gastrointestinal tract, in comparative anatomy and histology – a mouse and human atlas. In: Dintzis SM, Frevert CW, Liggitt HD, Montine KS, Treuting PM (eds) , 1st edn. Elsevier, Amsterdam

    Google Scholar 

  • Turnbaugh PJ, Gordon JI (2009) The core gut microbiome, energy balance and obesity. J Physiol 587:4153–4158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Turnbaugh PJ, Ley RE, Mahowald MA (2006) An obesity- associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031

    Article  PubMed  Google Scholar 

  • Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI (2009) The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 1:ra14

    Article  CAS  Google Scholar 

  • Vodicka P, Smetana K Jr, Dvorankova B (2005) The miniature pig as an animal model in biomedical research. Ann N Y Acad Sci 1049:161–171

    Article  PubMed  Google Scholar 

  • Wang M, Donovan SM (2015) Human microbiota-associated swine: current progress and future opportunities. ILAR J/National Res Council Inst Lab Animal Res 56:63–73

    CAS  Google Scholar 

  • Wang Y, Ren Z, Fu L (2016) Two highly adhesive lactic acid bacteria strains are protective in zebrafish infected with Aeromonas hydrophila by evocation of gut mucosal immunity. J Appl Microbiol 120:441–451

    Article  CAS  PubMed  Google Scholar 

  • Wen K, Tin C, Wang H (2014) Probiotic Lactobacillus rhamnosus GG enhanced Th1 cellular immunity but did not affect antibody responses in a human gut microbiota transplanted neonatal gnotobiotic pig model. PLoS One 9:e94504

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wollenberg AC, Jagdish T, Slough G (2016) Death becomes them: bacterial community dynamics and stilbene antibiotic production in cadavers of Galleria mellonella killed by Heterorhabditis and Photorhabdus spp. Appl Environ Microbiol 82:5824–5837

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wong CNA, Ng P, Douglas AE (2011) Low-diversity bacterial community in the gut of the fruitfly Drosophila melanogaster. Environ Microbiol 13:1889–1900

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wong RY, Oxendine SE, Godwin J (2013) Behavioral and neurogenomic transcriptome changes in wild-derived zebrafish with fluoxetine treatment. BMC Genomics 14:348

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wostmann BS (1996) Germfree and gnotobiotic animal models: background and applications. CRC Press, Boca Raton

    Google Scholar 

  • Yang Y, Tomkovich S, Jobin C (2014) Could a swimming creature inform us on intestinal diseases? Lessons from zebrafish. Inflamm Bowel Dis 20:956–966

    Article  PubMed  Google Scholar 

  • Yi P, Li L (2012) The germfree murine animal: an important animal model for research on the relationship between gut microbiota and the host. Vet Microbiol 157:1–7

    Article  PubMed  Google Scholar 

  • Zackular JP, Baxter NT, Chen GY, Schloss PD (2016) Manipulation of the gut microbiota reveals role in colon tumorigenesis. mSphere 1:e00001

    Article  PubMed  Google Scholar 

  • Zhang H, Wang H, Shepherd M (2014) Probiotics and virulent human rotavirus modulate the transplanted human gut microbiota in gnotobiotic pigs. Gut Pathog 6:39

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhao W, Wang Y, Liu S (2015) The dynamic distribution of porcine microbiota across different ages and gastrointestinal tract segments. PLoS One 10:e0117441

    Article  PubMed  PubMed Central  CAS  Google Scholar 

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Acknowledgement

The authors are grateful to their respective institutions for encouragement and support.

Conflict of Interest

The authors declare no conflict of interests.

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Authors and Affiliations

  1. Marine Microbiology, School of Earth, Ocean and Atmospheric Sciences (SEOAS), Goa University, Taleigao Plateau, Goa, India

    Chanda Vikrant Berde

  2. Gogate Jogalekar College, Ratnagiri, Maharashtra, India

    P. Salvi Sagar, V. Kajarekar Kunal & A. Joshi Suyoj

  3. Department of Zoology, Arts, Commerce and Science College, Lanja, Maharashtra, India

    B. Berde Vikrant

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  1. Chanda Vikrant Berde
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  2. P. Salvi Sagar
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  3. V. Kajarekar Kunal
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  4. A. Joshi Suyoj
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  5. B. Berde Vikrant
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  1. Department of Biotechnology, Krishna University, Machilipatnam, Andhra Pradesh, India

    Pallaval Veera Bramhachari

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Vikrant Berde, C., Salvi Sagar, P., Kajarekar Kunal, V., Joshi Suyoj, A., Berde Vikrant, B. (2021). Insight into the Animal Models for Microbiome Studies. In: Bramhachari, P.V. (eds) Microbiome in Human Health and Disease. Springer, Singapore. https://doi.org/10.1007/978-981-16-3156-6_13

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