Abstract
Commonly, the ‘gut’ refers to the digestive (alimentary) canal between the pylorus and the anus. Other terms such as the ‘stomach’ and ‘intestinal tract’ are also frequently used in a more general sense. When referring to different kinds of animals, a more specific definition seems necessary. A clear distinction needs to be drawn between vertebrates and non-vertebrates, also with reference to the relative complexity and size of the alimentary tract. For vertebrates, the alimentary canal is generally being referred to as the gastrointestinal tract (GIT), implying a clear distinction between the stomach (with a low pH and generally a low microbial population) and both the small and large intestines (with an increasing pH and microbial numbers). The GI tract harbours the highest numbers of immune cells in our body. These sites are colonised by large numbers of autochthonous commensal microbiota, a healthy population that protects their ecological niche by different mechanisms such as reinforcing barrier immunity (Belkan and Hand 2014).
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abe F, Ishibashi N, Shimamura S (1995) Effect of administration of bifidobacteria and lactic acid bacteria to newborn calves and piglets. J Dairy Sci 78:2838–2846. https://doi.org/10.3168/jds.S0022-0302(95)76914-4
Adamczyk-Sowa M, Medrek A, Madej P, Michlicka W, Dobrakowski P (2017) Does the gut microbiota influence immunity and inflammation in multiple sclerosis pathophysiology? J Immunol Res 2017:7904821., 14 p. https://doi.org/10.1155/2017/7904821
Adams MC, Luo J, Rayward D, King S, Gibson R, Moghaddam GH (2008) Selection of a novel direct-fed microbial to enhance weight gain in intensively reared calves. Anim Feed Sci Technol 145:41–52. https://doi.org/10.1016/j.anifeedsci.2007.05.035
Aharon Y, Pasternak Z, Ben Yosef M, Behar A, Lauzon C, Yuval B et al (2012) Phylogenetic, metabolic, and taxonomic diversities shape Mediterranean fruit fly microbiotas during ontogeny. Appl Environ Microbiol 79:303–313. https://doi.org/10.1128/AEM.02761-12. pmid:23104413
Aharon Y, Pasternak Z, Ben Yosef M, Behar A, Lauzon C, Yuval B, Jurkevitch E (2013) Phylogenetic, metabolic, and taxonomic diversities shape Mediterranean fruit fly microbiotas during ontogeny. Appl Environ Microbiol 79:303–313
Akbari MR, Haghighi HR, Chambers JR, Brisbin J, Read LR, Sharif S (2008) Expression of antimicrobial peptides in cecal tonsils of chickens treated with probiotics and infected with Salmonella enterica serovar typhimurium. Clin Vaccine Immunol 15:1689–1693. https://doi.org/10.1128/CVI.00242-08
Aly SM, Ahmed YA, Ghareeb AA, Mohamed MF (2008) Studies on Bacillus subtilis and Lactobacillus acidophilus, as potential probiotics, on the immune response and resistance of tilapia nilotica (Oreochromis niloticus) to challenge infections. Fish Shellfish Immunol 25:128–136
Apajalahti J, Vienola K (2016) Interaction between chicken intestinal microbiota and protein digestion. Anim Feed Sci Tech 221:323–330. https://doi.org/10.1016/j.anifeedsci.2016.05.004
Asgari F, Madjd Z, Falak R, Bahar MA, Nasrabadi MH, Raiani M, Shekarabi M (2016) Probiotic feeding affects T cell populations in blood and lymphoid organs in chickens. Benef Microbes 28:1–8. https://doi.org/10.3920/BM2016.0014
Augustinos AA, Kyritsis GA, Papadopoulos NT, Abd-Alla AM, Cáceres C, Bourtzis K (2015) Exploitation of the medfly gut microbiota for the enhancement of sterile insect technique: use of Enterobacter sp. in larval diet-based probiotic applications. PLoS One 10(9):e0136459. https://doi.org/10.1371/journal.pone.0136459
Bager F, Aarestrup FM, Madsen M, Wegener HC (1999) Glycopeptide resistance in Enterococcus faecium from broilers and pigs following discontinued use of avoparcin. Microb Drug Resist 5:53–56
Balcázar JL, de Blas I, Ruiz-Zarzuela I, Vendrell D, Calvo AC, Márquez I, Gironés O, Muzquiz JL (2007a) Changes in intestinal microbiota and humoral immune response following probiotic administration in brown trout (Salmo trutta). Br J Nutr 97:522–527. https://doi.org/10.1017/S0007114507432986
Balcázar JL, de Blas I, Ruiz-Zarzuela I, Vendrell D, Gironés O, Muzquiz JL (2007b) Enhancement of the immune response and protection induced by probiotic lactic acid bacteria against furunculosis in rainbow trout (Oncorhynchus mykiss). FEMS Immunol Med Microbiol 51:185–193. https://doi.org/10.1111/j.1574-695X.2007.00294.x
Bauer KC, Huus KE, Finlay BB (2016) Microbes and the mind: emerging hallmarks of the gut microbiota-brain axis. Cell Microbiol 18(5):632–644. https://doi.org/10.1111/cmi.12585
Behar A, Yuval B, Jurkevitch E (2005) Enterobacteria-mediated nitrogen fixation in natural populations of the fruit fly Ceratitis capitata. Mol Ecol 14:2637–2643. https://doi.org/10.1111/j.1365-294X.2005.02615.x
Behar A, Jurkevitch E, Yuval B (2008a) Bringing back the fruit into fruit fly-bacteria interactions. Mol Ecol 17:1375–1386. https://doi.org/10.1111/j.1365-294X.2008.03674.x
Behar A, Yuval B, Jurkevitch E (2008b) Community structure of the Mediterranean fruit fly microbiota: seasonal and spatial sources of variation. Israel J Ecol Evol 54(2):181–191. https://doi.org/10.1080/15659801.2008.10639612
Behar A, Yuval B, Jurkevitch E (2008c) Gut bacterial communities in the Mediterranean fruit fly (Ceratitis capitata) and their impact on host longevity. J Insect Physiol 54:1377–1383. https://doi.org/10.1016/j.jinsphys.2008.07.011
Belkan Y, Hand T (2014) Role of the microbiota in immunity and inflammation. Cell 157(1):121–141. https://doi.org/10.1016/j.cell.2014.03.011
Ben Ami E, Yuval B, Jurkevitch E (2010) Manipulation of the microbiota of mass-reared Mediterranean fruit flies Ceratitis capitata (Diptera: Tephritidae) improves sterile male sexual performance. ISME J 4:28–37. https://doi.org/10.1038/ismej.2009.82
Benson AK, Kelly SA, Legge R, Ma F, Low SJ, Kim J, Zhang M, Oh PL, Nehrenberg D, Hua K, Kachman SD, Moriyama EN, Walter J, Peterson DA, Pomp D (2010) Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. PNAS 107(44):18933–18938. www.pnas.org/cgi/doi/10.1073/pnas.1007028107
Ben-Yosef M, Jurkevitch E, Yuval B (2008a) Effect of bacteria on nutritional status and reproductive success of the Mediterranean fruitfly Ceratitis capitata. Physiol Entomol 33:145–154
Ben-Yosef M, Behar A, Jurkevitch E, Yuval B (2008b) Bacteria-diet interactions affect longevity in the medfly Ceratitis capitata. J Appl Entomol 132:690–694
Bhandari SK, Opapeju FO, Krause DO, Nyachoti CM (2010) Dietary protein level and probiotic supplementation effects on piglet response to Escherichia coli K88 challenge: performance and gut microbial population. Livest Sci 133:185–188. https://doi.org/10.1016/j.livsci.2010.06.060
Borie C, Albala I, Sánchez P, Sánchez ML, Ramírez S, Navarro C, Morales MA, Retamales AJ, Robeson J (2008) Bacteriophage treatment reduces Salmonella colonization of infected chickens. Avian Dis 52:64–67. https://doi.org/10.1637/8091-082007-Reg
Borie C, Sánchez ML, Navarro C, Ramírez S, Morales MA, Retamales J, Robeson J (2009) Aerosol spray treatment with bacteriophages and competitive exclusion reduces Salmonella enteritidis infection in chickens. Avian Dis 53:250–254. https://doi.org/10.1637/8406-071008-Reg.1
Brisbin JT, Haghighi HR, Kulkarni R, Sharif S (2007) Regulation of the intestinal immune system by commensal microbiota in avian and ruminant species. CAB Rev Perspect Agric Nutr Nat Resour 2(8). https://doi.org/10.1079/PAVSNNR20072008. http://www.cababstractsplus.org/cabreviews
Brisbin JT, Gong J, Orouji S, Esufali J, Mallick AI, Parvizi P, Shewen PE, Sharif S (2011) Oral treatment of chickens with lactobacilli influences elicitation of immune responses. Clin Vaccine Immunol 18:1447–1455. https://doi.org/10.1128/CVI.05100-11
Brown R, Clarke TB (2016) The regulation of host defences to infection by the microbiota. Immunology 150:1–6. https://doi.org/10.1111/imm.12634
Browne HP, Foster SC, Anonye BO, Kumar N, Neville BAS, Stares MD, Goulding D, Lawley TD (2016) Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation. Nature 533:543–546. https://doi.org/10.1038/nature17645
Brunt J, Austin B (2005) Use of a probiotic to control lactococcosis and streptococcosis in rainbow trout, Oncorhynchus mykiss (Walbaum). J Fish Dis 28:693–701. https://doi.org/10.1111/j.1365-2761.2005.00672.x
Buchon N, Broderick AN, Lemaitre B (2013) The gut microbiota—masters of host development and physiology. Nat Rev Microbiol 10:1038
Cerf-Bensussan N, Gaboriau-Routhiau V (2010) The immune system and the gut microbiota: friends or foes? Nat Rev Immunol 10(10):735–744
Chambers JR, Gong J (2011) The intestinal microbiota and its modulation for Salmonella control in chickens. Food Res Int 44:3149–3159
Chaucheyras-Durand F, Durand H (2010) Probiotics in animal nutrition and health. Benef Microbes 1:3–9. https://doi.org/10.3920/BM2008.1002
Chiquette J, Allison MJ, Rasmussen MA (2008) Prevotella bryantii 25A used as a probiotic in early-lactation dairy cows: effect on ruminal fermentation characteristics, milk production, and milk composition. J Dairy Sci 91:3536–3543. https://doi.org/10.3168/jds.2007-0849
Clarke G, Stilling RM, Kennedy PJ, Stanton C, Cryan JF, Dinan TG (2014) Gut microbiota: the neglected endocrine organ. Mol Endocrinol 28:1221–1238. https://doi.org/10.1210/me.2014-1108
Collier CT, Carroll JA, Ballou MA, Starkey JD, Sparks JC (2011) Oral administration of Saccharomyces cerevisiae boulardii reduces mortality associated with immune and cortisol responses to Escherichia coli endotoxin in pigs. J Anim Sci 89:52–58. https://doi.org/10.2527/jas.2010-2944
Collington GK, Parker DS, Armstrong DG (1990) The influence of inclusion of either an antibiotic or a probiotic in the diet on the development of digestive enzyme activity in the pig. Br J Nutr 64:59–70. https://doi.org/10.1079/BJN19900009
Cruywagen CW, Jordaan I, Venter L (1996) Effect of Lactobacillus acidophilus supplementation of milk replacer on preweaning performance of calves. J Dairy Sci 79:483–486. https://doi.org/10.3168/jds.S0022-0302(96)76389-0
D’Argenio V, Salvatore F (2015) The role of the gut microbiome in the healthy adult status. Clin Chim Acta 451:97–102. https://doi.org/10.1016/j.cca.2015.01.003
Dillon RJ, Vennard CT, Buckling A, Charnley AK (2005) Diversity of locust gut bacteria protects against pathogen invasion. Ecol Lett 8:1291–1298
Dinan TG, Cryan JF (2017) Gut–brain axis in 2016: brain–gut–microbiota axis—mood, metabolism and behaviour. Nat Rev Gastroenterol Hepatol 14:69–70. https://doi.org/10.1038/nrgastro.2016.200
Douglas AE (2009) The microbial dimension in insect nutritional ecology. Funct Ecol 23:38–47. https://doi.org/10.1111/j.1365-2435.2008.01442.x
Duncker SC, Lorentz A, Schroeder B, Breves G, Bischoff SC (2006) Effect of orally administered probiotic E. coli strain Nissle 1917 on intestinal mucosal immune cells of healthy young pigs. Vet Immunol Immunopathol 111:239–250. https://doi.org/10.1016/j.vetimm.2006.01.017
du Toit M, Franz CM, Dicks LM, Schillinger U, Haberer P, Warlies B, Ahrens F, Holzapfel WH (1998) Characterisation and selection of probiotic lactobacilli for a preliminary minipig feeding trial and their effect on serum cholesterol levels, faeces pH and faeces moisture content. Int J Food Microbiol 40:93–104. https://doi.org/10.1016/S0168-1605(98)00024-5
Dyck VA, Hendrichs JP, Robinson AS (eds) (2005) The sterile insect technique: principles and practice in area-wide integrated pest management. Springer, Dordrecht
Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308:1635–1638
Elam NA, Gleghorn JF, Rivera JD, Galyean ML, Defoor PJ, Brashears MM, Younts-Dahl SM (2003) Effects of live cultures of Lactobacillus acidophilus (strains NP45 and NP51) and Propionibacterium freudenreichii on performance, carcass, and intestinal characteristics, and Escherichia coli strain O157 shedding of finishing beef steers. J Anim Sci 81:2686–2698
Engel P, Morgan NA (2013) The gut microbiota of insects—diversity in structure and Function. FEMS Microbiol Rev 37:699–735. https://doi.org/10.1111/1574-6976.12025
Fasano A (2017) Celiac disease, gut-brain axis, and behavior: cause, consequence, or merely epiphenomenon? Pediatrics 139(3):e20164323
Feldhaar H (2011) Bacterial symbionts as mediators of ecologically important traits of insect hosts. Ecol Entomol 36:533–543. https://doi.org/10.1111/j.1365-2311.2011.01318.x
Fischbach MA, Segre JA (2016) Signaling in host-associated microbial communities. Cell 164:1288–1300. https://doi.org/10.1016/j.cell.2016.02.037
Fowler ME, Bravo WP (2010) Chapter 1: General biology and evolution. In: Medicine and surgery of camelids, 3rd edn. Wiley-Blackwell, Ames
Frizzo LS, Soto LP, Zbrun MV, Bertozzi E, Sequeira G, Armesto RR, Rosmini MR (2010) Lactic acid bacteria to improve growth performance in young calves fed milk replacer and spray-dried whey powder. Anim Feed Sci Technol 157:159–167. https://doi.org/10.1016/j.anifeedsci.2010.03.005
Gavriel S, Jurkevitch E, Gazit Y, Yuval B (2011) Bacterially enriched diet improves sexual performance of sterile male Mediterranean fruit flies. J Appl Entomol 135:564–573. https://doi.org/10.1111/j.1439-0418.2010.01605.x
Ghorbani GR, Morgavi DP, Beauchemin KA, Leedle JAZ (2002) Effects of bacterial direct-fed microbials on ruminal fermentation, blood variables, and the microbial populations of feedlot cattle. J Anim Sci 80:1977–1985. https://doi.org/10.2527/2002.8071977x
Giri SS, Sukumaran V, Oviya M (2013) Potential probiotic Lactobacillus plantarum VSG3 improves the growth, immunity, and disease resistance of tropical freshwater fish, Labeo rohita. Fish Shellfish Immunol 34:660–666. https://doi.org/10.1016/j.fsi.2012.12.008
Godon J-J, Aulazhagan P, Steyer J-P, Hamelin J (2016) Vertebrate bacterial gut diversity: size also matters. BMC Ecol 16:12. https://doi.org/10.1186/s12898-016-0071-2
Gopalakannan A, Arul V (2011) Inhibitory activity of probiotic Enterococcus faecium MC13 against Aeromonas hydrophila confers protection against hemorrhagic septicemia in common carp Cyprinus carpio. Aquacult Int 19:973–985. https://doi.org/10.1007/s10499-011-9415-2
Gordon JI (2012) Honor thy gut symbionts redux. Science 336:1251–1253
Ha CW, Lam YY, Holmes AJ (2014) Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health. World J Gastroenterol 20:16498–16517
Hamden H, Guerfali MM, Fadhl S, Saidi M, Chevrier C (2013) Fitness improvement of mass-reared sterile males of Ceratitis capitata (Vienna 8 strain) (Diptera: Tephritidae) after gut enrichment with probiotics. J Econ Entomol 106:641–647. https://doi.org/10.1603/EC12362. pmid:23786049
Harikrishnan R, Kim MC, Kim JS, Balasundaram C, Heo MS (2011) Protective effect of herbal and probiotics enriched diet on haematological and immunity status of Oplegnathus fasciatus (Temminck & Schlegel) against Edwardsiella tarda. Fish Shellfish Immunol 30:886–893. https://doi.org/10.1016/j.fsi.2011.01.013
Hayakawa T, Masuda T, Kurosawa D, Tsukahara T (2016) Dietary administration of probiotics to sows and/or their neonates improves the reproductive performance, incidence of post-weaning diarrhea and histopathological parameters in the intestine of weaned piglets. Anim Sci J 87(12):1501–1510. https://doi.org/10.1111/asj.12565
He S, Zhou Z, Meng K, Zhao H, Yao B, Ringø E, Yoon I (2011) Effects of dietary antibiotic growth promoter and Saccharomyces cerevisiae fermentation product on production, intestinal bacterial community, and nonspecific immunity of hybrid tilapia (Oreochromis niloticus female × Oreochromis aureus male). J Anim Sci 89:84–92. https://doi.org/10.2527/jas.2010-3032
Hildebrandt MA, Hoffmann C, Sherrill-Mix SA, Keilbaugh SA, Hamady M, Chen Y-Y, Knight R, Ahima RS, Bushman F, Wu GD (2009) High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 137:1716–1724
Ivanov I, Honda K (2012) Intestinal commensal microbes as immune modulators. Cell Host Microbe 12:496–506
Jami E, Israel A, Kotser A, Mizrahi I (2013) Exploring the bovine rumen bacterial community from birth to adulthood. ISME J 7:1069–1079. https://doi.org/10.1038/ismej.2013.2
Jatkauskas J, Vrotniakiene V (2010) Effects of probiotic dietary supplementation on diarrhoea patterns, faecal microbiota and performance of early-weaned calves. Vet Med Czech 55:494–503
Jones BV, Fung S, Marchesi JR (2010) Comparative metagenomic analysis of plasmid encoded functions in the human gut microbiome. BMC Genomics 11:46. http://www.biomedcentral.com/1471-2164/11/46
Karasov WH, Douglas AE (2013) Comparative digestive physiology. Compr Physiol 3(2):741–783. https://doi.org/10.1002/cphy.c110054
Kikuchi Y, Hayatsu M, Hosokawa T, Nagayama A, Tago K, Fukatsu T (2012) Symbiont-mediated insecticide resistance. Proc Natl Acad Sci U S A 109:8618–8622. www.pnas.org/cgi/doi/10.1073/pnas.1200231109
Kim D, Beck BR, Heo SB, Kim J, Kim HD, Lee SM, Kim Y, Oh SY, Lee K, Do H, Lee K, Holzapfel WH, Song SK (2013) Lactococcus lactis BFE920 activates the innate immune system of olive flounder (Paralichthys olivaceus), resulting in protection against Streptococcus iniae infection and enhancing feed efficiency and weight gain in large-scale field studies. Fish Shellfish Immunol 35:1585–1590. https://doi.org/10.1016/j.fsi.2013.09.008
Kohl KD, Weiss RB, Cox J, Dale C, Dearing D (2014) Gut microbes of mammalian herbivores facilitate intake of plant toxins. Ecol Lett 17:1238–1246
König H (2006) Bacillus species in the intestine of termites and other soil invertebrates. J Appl Microbiol 101(3):620–627. https://doi.org/10.1111/j.1365-2672.2006.02914.x
Koutsos EA, Matson KD, Klasing KC (2001) Nutrition of birds in the order of Psittaciformes: a review. J Avian Med Surg 15(4):257–275. https://doi.org/10.1647/1082-6742(2001)015[0257:NOBITO]2.0.CO;2
Kritas SK, Govaris A, Christodoulopoulos G, Burriel AR (2006) Effect of Bacillus licheniformis and Bacillus subtilis supplementation of ewe’s feed on sheep milk production and young lamb mortality. J Vet Med A Physiol Pathol Clin Med 53:170–173. https://doi.org/10.1111/j.1439-0442.2006.00815.x
Kwong WK, Moran NA (2016) Gut microbial communities of social bees. Nat Rev Microbiol 14:374–384. https://doi.org/10.1038/nrmicro.2016.43
Kwong KW, Engel P, Koch H, Moran NA (2014) Genomics and host specialization of honey bee and bumble bee gut symbionts. PNAS 111:11509–11514. www.pnas.org/cgi/doi/10.1073/pnas.1405838111
Lagier JC, Hugon P, Khelaifia S, Fournier PE, La Scola B, Raoult D (2015) The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 28:237–264. https://doi.org/10.1128/CMR.00014-14
Lagier JC, Khelaifia S, Tidjani M et al (2016) Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol 1:16203. https://doi.org/10.1038/NMICROBIOL.2016.203
Lamari F, Mahdhi A, Chakroun I, Esteban MA, Mazurais D, Amina B, Gatesoupe FJ (2016) Interactions between candidate probiotics and the immune and antioxidative responses of European sea bass (Dicentrarchus labrax) larvae. J Fish Dis 39:1421–1432. https://doi.org/10.1111/jfd.12479
Lau JT, Whelan FJ, Herath I, Lee CH, Collins SM, Bercik P, Surette MG (2016) Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling. Genome Med 8:72. https://doi.org/10.1186/s13073-016-0327-7
Lauzon CR, Potter SE (2012) Description of the irradiated and nonirradiated midgut of Ceratitis capitata Wiedemann (Diptera: Tephritidae) used for sterile insect technique. J Pest Sci 85(2):217–226
Lee IK, Yoon Chul Kye YC, Kim G, Kim HW, Gu MJ, Umboh J, Maaruf K, Kim SW, Yun C-H (2016) Stress, nutrition, and intestinal immune responses in pigs—a review. Asian Australas J Anim Sci 29(8):1075–1082. https://doi.org/10.5713/ajas.16.0118
Lee SH, Hosseindoust AR, Kim JS, Choi YH, Lee JH, Kwon IK, Chae BJ (2016) Bacteriophages as a promising anti-pathogenic option in creep-feed for suckling piglets: targeted to control Clostridium spp. and coliforms faecal shedding. Livest Sci 191:161–164. https://doi.org/10.1016/j.livsci.2016.08.003
Li RW, Connor EE, Li C, Baldwin Vi RL, Sparks ME (2012) Characterization of the rumen microbiota of pre-ruminant calves using metagenomic tools. Environ Microbiol 14:129–139. https://doi.org/10.1111/j.1462-2920.2011.02543.x
Loor JJ, Elolimy AA, McCann JC (2016) Dietary impacts on rumen microbiota in beef and dairy production. Anim Front 6(3):22–29
Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R (2012) Diversity, stability and resilience of the human gut microbiota. Nature 489:220–230. https://doi.org/10.1038/nature11550
Malik R, Bandla S (2010) Effect of source and dose of probiotics and exogenous fibrolytic enzymes (EFE) on intake, feed efficiency, and growth of male buffalo (Bubalus bubalis) calves. Trop Anim Health Prod 42:1263–1269. https://doi.org/10.1007/s11250-010-9559-5
Maltz MA, Weiss BL, O’Neill M, Wu Y, Aksoy S (2012) OmpA-mediated biofilm formation is essential for the commensal bacterium Sodalis glossinidius to colonize the tsetse fly gut. Appl Environ Microbiol 78(21):7760–7768
Mann ER, Landy JD, Bernardo D, Peake STC, Hart AL, Al-Hassi HO, Knight S (2013) Intestinal dendritic cells: their role in intestinal inflammation, manipulation by the gut microbiota and differences between mice and men. Immunol Lett 150:30–40. https://doi.org/10.1016/j.imlet.2013.01.007
Mappley LJ, Tchórzewska MA, Nunez A, Woodward MJ, Bramley PM, La Ragione RM (2013) Oral treatment of chickens with Lactobacillus reuteri LM1 reduces Brachyspira pilosicoli-induced pathology. J Med Microbiol 62:287–296. https://doi.org/10.1099/jmm.0.051862-0
McFall-Ngaia M, Hadfield MG, Bosch TGC, Carey HV, Domazet-Loso T et al (2013) Animals in a bacterial world, a new imperative for the life sciences. Proc Natl Acad Sci U S A 110:3229–3236. https://doi.org/10.1073/pnas.1218525110
McFarland LV (2014) Use of probiotics to correct dysbiosis of normal microbiota following disease or disruptive events: a systematic review. Br Med J 10:1136
Mead GC (2000) Prospects for ‘competitive exclusion’ treatment to control salmonellas and other food-borne pathogens in poultry. Vet J 159:111–123
Miller MB, Bassler BL (2001) Quorum sensing in bacteria. Annu Rev Microbiol 55:165–199. https://doi.org/10.1146/annurev.micro.55.1.165
Mohapatra S, Chakraborty T, Kumar V, DeBoeck G, Mohanta KN (2012) J Animal Phys Anim Nutr 97:405–430. https://doi.org/10.1111/j.1439-0396.2012.01301.x
Montalban AA, De Schryver P, Bossier P, Gorkiewicz G, Mulero V, Monroe DG, Galindo-Villegas J (2015) Selective manipulation of the gut microbiota improves immune status in vertebrates. Front Immunol 6:512. https://doi.org/10.3389/fimmu.2015.00512
Moran NA, Hansen AK, Powell JE, Sabree ZL (2012) Distinctive gut microbiota of honey bees assessed using deep sampling from individual worker bees. PLoS One 7(4):e36393
Morgan XC, Huttenhower C (2012) Chapter 12: Human microbiome analysis. PLoS Comput Biol 8(12):e1002808. https://doi.org/10.1371/journal.pcbi.1002808
Mortha A, Chudnovskiy A, Hashimoto D, Bogunovic M, Spencer SP, Belkaid Y, Merad M (2014) Microbiota-dependent crosstalk between macrophages and ILC3 promotes intestinal homeostasis. Science 343(6178):1249288. https://doi.org/10.1126/science.1249288
Mountzouris KC, Tsirtsikos P, Kalamara E, Nitsch S, Schatzmayr G, Fegeros K (2007) Evaluation of the efficacy of a probiotic containing Lactobacillus, Bifidobacterium, Enterococcus, and Pediococcus strains in promoting broiler performance and modulating cecal microflora composition and metabolic activities. Poult Sci 86:309–317. https://doi.org/10.1093/ps/86.2.309
Muegge BD, Kuczynski J, Knights D, Clemente JC, González A, Fontana L, Henrissat B, Knight R, Gordon JI (2011) Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332(6032):970–974
Nagaraja TG, Titgemeyer EC (2007) Ruminal acidosis in beef cattle: the current microbiological and nutritional outlook. J Dairy Sci 90(Suppl 1):E17–E38. https://doi.org/10.3168/jds.2006-478
Nayak SK, Swain P, Mukherjee SC (2007) Effect of dietary supplementation of probiotic and vitamin C on the immune response of Indian major carp, Labeo rohita (Ham.) Fish Shellfish Immunol 23:892–896. https://doi.org/10.1016/j.fsi.2007.02.008
Nikoskelainen S, Ouwehand AC, Bylund G, Salminen S, Lilius EM (2003) Immune enhancement in rainbow trout (Oncorhynchus mykiss) by potential probiotic bacteria (Lactobacillus rhamnosus). Fish Shellfish Immunol 15:443–452. https://doi.org/10.1016/S1050-4648(03)00023-8
Nurmi E, Rantala M (1973) New aspects of Salmonella infection in broiler production. Nature 241:210–211
Oakley BB, Lillehoj HS, Kogut MH, Kim WK, Maurer JJ et al (2014) The chicken gastrointestinal microbiome. FEMS Microbiol Lett 360:100–112
Ohland LC, Jobin C (2015) Microbial activities and intestinal homeostasis: a delicate balance between health and disease. Cell Mol Gastroenterol Hepatol 1:28–40
Panda AK, Rama Rao SV, Raju MVLN, Shyam Sunder G (2009) Effect of butyric acid on performance, gastrointestinal tract health and carcass characteristics in broiler chickens. Asian Aust J Anim Sci 22:1026–1031
Panigrahi A, Kiron V, Satoh S, Hirono I, Kobayashi T, Sugita H, Puangkaew J, Aoki T (2007) Immune modulation and expression of cytokine genes in rainbow trout Oncorhynchus mykiss upon probiotic feeding. Dev Comp Immunol 31:372–382. https://doi.org/10.1016/j.dci.2006.07.004
Park SC, Shimamura I, Fukunaga M, Mori KI, Nakai T (2000) Isolation of bacteriophages specific to a fish pathogen, Pseudomonas plecoglossicida, as a candidate for disease control. Appl Environ Microbiol 66:1416–1422. https://doi.org/10.1128/AEM.66.4.1416-1422.2000
Penry DL, Jumars PA (1987) Modeling animal guts as chemical reactors. Am Nat 129:69–96
Pernice M, Simpson SJ, Ponton F (2014) Towards an integrated understanding of gut microbiota using insects as model systems. J Insect Physiol 69:12–18. https://doi.org/10.1016/j.jinsphys.2014.05.016
Pollmann M, Nordhoff M, Pospischil A, Tedin K, Wieler LH (2005) Effects of a probiotic strain of Enterococcus faecium on the rate of natural chlamydia infection in swine. Infect Immun 73:4346–4353. https://doi.org/10.1128/IAI.73.7.4346-4353.2005
Pourabedin M (2015) Effects of mannan-oligosaccharides and xylo-oligosaccharides on the chicken gut microbiota. PhD-Thesis, McGill University, Montreal
Qin J, Li R, Raes J, Arumugam M, Burgdorf KS et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65
Rajilic-Stojanovic M, De Vos WM (2014) The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiol Rev 8:996–1047
Ran C, Huang L, Hu J, Tacon P, He S, Li Z, Wang Y, Liu Z, Xu L, Yang Y, Zhou Z (2016) Effects of dietary live and heat-inactive baker’s yeast on growth, gut health, and disease resistance of Nile tilapia under high rearing density. Fish Shellfish Immunol 56:263–271. https://doi.org/10.1016/j.fsi.2016.07.001
Reece WO (2013) Functional anatomy and physiology of domestic animals, 4th edn. Wiley, Hoboken, p 359. ISBN 111868589X, 9781118685891
Ringø E, Vadstein O (1998) Colonization of Vibrio pelagius and Aeromonas caviae in early developing turbot (Scophthalmus maximus L.) larvae. J Appl Microbiol 84:227–233. https://doi.org/10.1046/j.1365-2672.1998.00333.x
Roos TB, Tabeleão VC, Dümmer LA, Schwegler E, Goulart MA, Moura SV, Corrêa MN, Leite FPL, Gil-Turnes C (2010) Effect of Bacillus cereus var. Toyoi and Saccharomyces boulardiion the immune response of sheep to vaccines. Food Agric Immunol 21:113–118. https://doi.org/10.1080/09540100903443691
Sanders JG, Powell S, Kronauer DJ, Vasconcelos HL, Frederickson ME, Pierce NE (2014) Stability and phylogenetic correlation in gut microbiota: lessons from ants and apes. Mol Ecol 23(6):1268–1283. https://doi.org/10.1111/mec.12611
Sandhu KV, Sherwin E, Schellekens H, Stanton H, Dinan TG, Cryan JF (2017) Feeding the microbiota-gut-brain axis: diet, microbiome, and neuropsychiatry. Transl Res 179:223–244. https://doi.org/10.1016/j.trsl.2016.10.002
Sekirov I, Russell SL, Antunes LC, Finlay BB (2010) Gut microbiota in health and disease. Physiol Rev 90:859–904. https://doi.org/10.1152/physrev.00045.2009
Sen S, Ingale SL, Kim YW, Kim JS, Lohakare JD, Kim EK, Kim HS, Ryu MH, Kwon IK, Chae BL (2012) Effect of supplementation of Bacillus subtilis LS 1-2 to broiler diets on growth performance, nutrient retention, caecal microbiology and small intestinal morphology. Res Vet Sci 93:264–268. https://doi.org/10.1016/j.rvsc.2011.05.021
Shaufi MAM, Sieo CC, Chong CW, Gan HM, Ho YW (2015) Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses. Gut Pathogens 7:4. https://doi.org/10.1186/s13099-015-0051-7
Smith PA (2015) Brain, meet gut. Nature 526:312–314
Sommer F, Bäckhed F (2013) The gut microbiota—masters of host development and physiology. Nat Rev Microbiol 10:1038
Spanggaard B, Huber I, Nielsen J, Sick EB, Pipper CB, Martinussen T, Slierendrecht WJ, Gram L (2001) The probiotic potential against vibriosis of the indigenous microflora of rainbow trout. Environ Microbiol 3:755–765. https://doi.org/10.1046/j.1462-2920.2001.00240.x
Sudo N (2014) Microbiome, HPA axis and production of endocrine hormones in the gut. Adv Exp Med Biol 817:177–194. https://doi.org/10.1007/978-1-4939-0897-4_8. In: Mark L, Cryan JF (eds) Microbial endocrinology: the microbiota-gut-brain axis in health and disease. Springer, New York, Heidelberg
Taheri HR, Moravej H, Tabandeh F, Zaghari M, Shivazad M (2010) Efficacy of combined or single use of Lactobacillus crispatus LT116 and L. johnsonii LT171 on broiler performance. Br Poult Sci 51:580–585. https://doi.org/10.1080/00071668.2010.508491
Tajima K, Aminov RJ, Nagamine T, Matsui H, Nakamura M, Benno Y (2001) Diet-dependent shifts in the bacterial population of the rumen revealed with realtime PCR. Appl Environ Microbiol 67:2766–2774. https://doi.org/10.1128/ AEM.67.6.2766-2774.2001
Taoka Y, Maeda H, Jo JY, Jeon MJ, Bai SC, Lee WJ, Yuge K, Koshio S (2006) Growth, stress tolerance and nonspecific immune response of Japanese flounder Paralichthys olivaceus to probiotics in a closed recirculating system. Fish Sci 72:310–321. https://doi.org/10.1111/j.1444-2906.2006.01152.x
Thaiss CA, Zmora N, Levy M, Elinav E (2016) The microbiome and innate immunity. Nature 535:65–74. https://doi.org/10.1038/nature18847
Toro H, Price SB, McKee AS, Hoerr FJ, Krehling J, Perdue M, Bauermeister L (2005) Use of bacteriophages in combination with competitive exclusion to reduce Salmonella from infected chickens. Avian Dis 49:118–124. https://doi.org/10.1637/7286-100404R
Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human microbiome project. Nature 449(7164):804–810
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(6):6ra14. https://doi.org/10.1126/scitranslmed.3000322
Van den Bogaard AE, Stobberingh EE (1999) Antibiotic usage in animals: impact on bacterial resistance and public health. Drugs 58:589–607
Van den Bogaard AE, Bruinsma N, Stobberingh EE (2000) The effect of banning avoparcin on VRE carriage in The Netherlands. J Antimicrob Chemother 46:146–148
Villena J, Saavedra L, Hebert EM, Suda Y, Masumizu Y, Albarracin L, Clua P, Ikeda-Ohtsubo W, Kitazawa H (2017) Draft genome sequence of L. plantarum MPL16, a wakame-utilizing immunobiotic strain isolated from swine feces. Genome Announc 5:e00006–e00017. https://doi.org/10.1128/genomeA.00006-17
Walter J, Britton RA, Roos S (2011) Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm. Proc Natl Acad Sci U S A 108(Suppl 1):4645–4652. www.pnas.org/cgi/doi/10.1073/pnas.1000099107
Wanapat M, Ngarmsang A, Korkhuntot S, Nontaso N, Wachirapakorn C, Beakes G, Rowlinson P (2000) A comparative study on the rumen microbial population of cattle and swamp buffalo raised under traditional village conditions in the northeast of Thailand. Asian Australas J Anim Sci 13(7):918–921
Wang F, Roy S (2016) Gut homeostasis, microbial dysbiosis, and opioids. Toxicol Pathol 45:150–156
Wang X, Farnell YZ, Peebles ED, Kiess AS, Wamsley KG, Zhai W (2016) Effects of prebiotics, probiotics, and their combination on growth performance, small intestine morphology, and resident Lactobacillus of male broilers. Poult Sci 95:1332–1340. https://doi.org/10.3382/ps/pew030
Williams BB, Van Benschoten AH, Cimermancic P, Donia MS, Zimmermann M, Taketani M, Ishihara A, Kashyap PC, Fraser JS, Fischbach MS (2014) Discovery and characterization of gut microbiota decarboxylases that can produce the neurotransmitter tryptamine. Cell Host Microbe 16(4):495–503. https://doi.org/10.1016/j.chom.2014.09.001
Wu GD, Chen J, Hoffmann C et al (2009) Linking long-term dietary patterns with gut microbial enterotypes. Science 334(6052):105–108. https://doi.org/10.1126/science.1208344
Yang Y, Iji PA, Choct M (2009) Dietary modulation of gut microflora in broiler chickens; a review of the role of six kinds of alternatives to in-feed antibiotics. Worlds Poult Sci J 65:97–114. https://doi.org/10.1017/S0043933909000008
Yang F, Hou C, Zeng X, Qiao S (2015) The use of lactic acid bacteria as a probiotic in swine diets. Pathogens 4:34–45. https://doi.org/10.3390/pathogens4010034
Yeo S, Park H, Ji Y, Park S, Yang Y, Lee J, Mathara JM, Shin HK, Holzapfel W (2015) Influence of gastrointestinal stress on autoinducer-2 activity of two Lactobacillus species. FEMS Microbiol Ecol 91:fiv065. https://doi.org/10.1093/femsec/fiv065
Yeo S, Lee S, Park H, Shin H, Holzapfel W, Huh CS (2016) Development of putative probiotics as feed additives: validation in a porcine-specific gastrointestinal tract model. Appl Microbiol Biotechnol 100:10043–10054. https://doi.org/10.1007/s00253-016-7812-1
Yeoman CJ, Chia N, Jeraldo P, Sipos M (2014) The microbiome of the chicken gastrointestinal tract. Anim Health Rev 13(1):89–99. https://doi.org/10.1017/S1466252312000138
Yu HF, Wang AN, Li XJ, Qiao SY (2008) Effect of viable Lactobacillus fermentum on the growth performance, nutrient digestibility and immunity of weaned pigs. J Anim Feed Sci 17:61–69
Yuval B, Hendrichs J (2000) Behavior of flies in the genus Ceratitis (Dacinae: Ceratidini). In: Aluja M, Norrbom A (eds) Fruit flies (Tehpritidae): phylogeny and evolution of behavior. CRC Press, Boca Raton, pp 429–457
Zhang ZF, Kim IH (2014) Effects of multistrain probiotics on growth performance, apparent ileal nutrient digestibility, blood characteristics, cecal microbial shedding, and excreta odor contents in broilers. Poult Sci 93:364–370. https://doi.org/10.3382/ps.2013-03314
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer International Publishing AG
About this chapter
Cite this chapter
Park, H., Yeo, S., Arellano, K., Kim, H.R., Holzapfel, W. (2018). Role of the Gut Microbiota in Health and Disease. In: Di Gioia, D., Biavati, B. (eds) Probiotics and Prebiotics in Animal Health and Food Safety. Springer, Cham. https://doi.org/10.1007/978-3-319-71950-4_2
Download citation
DOI: https://doi.org/10.1007/978-3-319-71950-4_2
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-71948-1
Online ISBN: 978-3-319-71950-4
eBook Packages: MedicineMedicine (R0)