Hostname: page-component-586b7cd67f-tf8b9 Total loading time: 0 Render date: 2024-11-22T18:23:09.588Z Has data issue: false hasContentIssue false
  • English
  • Français

Characteristics of the gastrointestinal microbial communities, with special reference to the chicken

Published online by Cambridge University Press:  18 September 2007

J. Apajalahti ,
A. Kettunen  and
H. Graham
J. Apajalahti*
Affiliation:
Alimetrics Ltd, HÖyläämÖtie 14, FIN-00380, Helsinki, Finland
A. Kettunen
Affiliation:
Danisco Innovation, Sokeritehtaantie 20, 02460 Kantvik, Finland
H. Graham
Affiliation:
Danisco Animal Nutrition, Box 777, Marlborough, Wilts SN8 lXN, England
*
*Corresponding author: e-mail: [email protected]
Get access

Abstract

Bacteria in nature appear as diverse communities, which may comprise of hundreds of different species. The shared capacity of the bacterial communities to adapt in any imaginable set of conditions is remarkable. Many bacteria have growth requirements, as yet undiscovered, which are fulfilled by their natural habitats. Indeed, bacterial communities have members specialized on different functions and providing vital elements to other bacteria living in the same community. Therefore, most bacteria cannot easily be isolated from their habitats by the routine culturing methods used in most laboratories today. To overcome the difficulties in culturing of individual microbes, modern approaches analyse the structure of bacterial communities by determining the characteristic features of the microbial DNA extracted from the community samples. Using such techniques we have found that 90% of the bacteria in the chicken gastrointestinal tract represent previously unknown species. Furthermore, more than half of the 640 different species found represent previously unknown bacterial genera. Bacteria in the gastrointestinal tract derive most of their carbon and energy from dietary compounds which are either resistant to attack by digestive fluids or absorbed so slowly by the host that bacteria can successfully compete for them. The performance improvements on use of a growth promoting feed antibiotic is due to factors such as reduced competition for nutrients in the small intestine, reduced local inflammation due to control of pathogens, and reduced size of intestine. Since bacterial species differ in their substrate preferences and growth requirements, the chemical composition and structure of the digesta largely determines the species distribution of the bacterial community in the gastrointestinal tract. Consequently, it should be possible to shift the microbial community from harmful to non-harmful bacteria by changing the diet.

Keywords

Gastrointestinal tractbacteriachickenmicrobial communitiesnovel bacteriacommunity analysiscolonisation%G+G profiling16s rDNA sequencingbacterial densitybifidobacteria
Type
Research Article
Information
World's Poultry Science Journal , Volume 60 , Issue 2 , June 2004 , pp. 223 - 232
Copyright
Copyright © Cambridge University Press 2004

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Amann, R.I., Ludwig, W. and Schleifer, K.H. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143–169.CrossRefGoogle ScholarPubMed
Apajalahti, J. and Bedford, M.R. (1999) Improve bird performance by feeding its microflora. World Poultry 15: 20–23.Google Scholar
Apajalahti, J.H., Kettunen, A., Bedford, M.R. and Holben, W.E. (2001) Percent G+C profiling accurately reveals diet-related differences in the gastrointestinal microbial community of broiler chickens. Appl. Environ. Microbiol. 67: 5656–5667.CrossRefGoogle ScholarPubMed
Apajalahti, J.H., Kettunen, H., Kettunen, A., Holben, W.E., Nurminen, P.H., Rautonen, N. and Mutanen, M. (2002) Culture-independent microbial community analysis reveals that inulin in the diet primarily affects previously unknown bacteria in the mouse ceacum. Appl. Environ. Microbiol. 68: 4986–4995.CrossRefGoogle Scholar
Apajalahti, J.H.A., Kettunen, A., Nurminen, P.H., Jatila, H. and Holben, W.E. (2003) Selective plating underestimates abundance and shows differential recovery of bifidobacterial species from human feces. Appl. Environ. Microbiol. 69: 5731–5735.CrossRefGoogle ScholarPubMed
Apajalahti, J.H.A., Sarkilahti, L.K., Maki, B.R., Heikkinen, J.P., Nurminen, P.H. and Holben, W.E. (1998) Effective recovery of bacterial DNA and percent-guanine-plus-cytosine- based analysis of community structure in the gastrointestinal tract of broiler chickens. Appl. Environ. Microbiol. 64: 4084–4088.CrossRefGoogle ScholarPubMed
Brenes, A., Smith, M., Guenter, W. and Marquardt, R.R. (1993) Effect of enzyme supplementation on the performance and digestive tract size of broiler chickens fed wheat and barley based diets. Poultry Science 72: 1731–1739.CrossRefGoogle ScholarPubMed
Cresci, A., Orpianesi, C., Silvi, S., Mastrandrea, V. and Dolara, P. (1999) The effect of sucrose or starch-based diet on short-chain fatty acids and faecal microflora in rats. Journal of Applied Microbiology 86: 245–250.CrossRefGoogle ScholarPubMed
Edelman, S., Leskela, S., Ron, E., Apajalahti, J. and Korhonen, T.K. (2003) In vitro adhesion of an avian pathogenic Escherichia coli O78 strain to surfaces of the chicken intestinal tract and to ileal mucus. Vet. Microbiol. 91: 41–56.CrossRefGoogle ScholarPubMed
Edelman, S., Westerlund-Wikstrom, B., Leskela, S., Kettunen, H., Rautonen, N., Apajalahti, J. and Korhonen, T.K. (2002) In vitro adhesion specificity of indigenous Lactobacilli within the avian intestinal tract. Appl. Environ. Microbiol. 68: 5155–5159.CrossRefGoogle ScholarPubMed
Felske, A., Akkermans, A.D.L. and De Vos, W.M. (1998) In situ detection of an uncultured predominant Bacillus in Dutch grassland soils. Appl. Environ. Microbiol. 64: 4588–4590.CrossRefGoogle ScholarPubMed
Fritsche, T.R., Horn, M., Seyedirashti, S., Gautom, R.K., Schleifer, K.H. and Wagner, M. (1999) In situ detection of novel bacterial endosymbionts of Acanthamoeba spp. phylogenetically related to members of the order Rickettsiales. Appl. Environ. Microbiol. 65: 206–212.CrossRefGoogle ScholarPubMed
Garriga, M., Pascual, M., Monfort, J.M. and Hugas, M. (1998) Selection of Lactobacilli for chicken probiotic adjuncts. J. Appl. Microbiol. 84: 125–132.CrossRefGoogle ScholarPubMed
Gibson, G.R., Willems, A., Reading, S. and Collins, M.D. (1996) Fermentation of non-digestible oligosaccharides by human colonic bacteria. Proc. Nutr. Soc. 55: 899–912.CrossRefGoogle ScholarPubMed
Gollnisch, K., Vahjen, W., Simon, O. and Schulz, E. (1996) Influence of an antimicrobial (avilamycin) and an enzymatic (xylanase) feed additive alone or in combination on pathogenic micro-organisms in the intestine of pigs (E. coli, C. perfringens). Landbauforschung Volkenrode 193: 337–342.Google Scholar
Gong, J., Forster, R.J., Yu, H., Chambers, J.R., Sabour, P.M., Wheatcroft, R., and Chen, S. (2002) Diversity and phylogenetic analysis of bacteria in the mucosa of chicken ceca and comparison with bacteria in the cecal lumen. FEMS Microbiol. Lett. 208: 1–7.CrossRefGoogle ScholarPubMed
Gusils, C., Chaia, A.P., Gonzalez, S. and Oliver, G. (1999) Lactobacilli isolated from chicken intestines: potential use as probiotics. Journal of Food Protection 62: 252–256.CrossRefGoogle ScholarPubMed
Hanson, R.S. and Hanson, T.E. (1996) Methanotrophic bacteria. Microbiol. Rev. 60: 439–471.CrossRefGoogle ScholarPubMed
Hillman, K. (1999) Manipulation of the intestinal microflora for improved health and growth in pigs. Proc. WPSA Spring MeetingScarborough22–24 March: 59–61.Google Scholar
Hock, E., Halle, I., Matthes, S. and Jeroch, H. (1997) Investigations on the composition of the ileal and caecal microflora of broiler chicks in consideration to dietary enzyme preparation and zinc bacitracin in wheat-based diets. Agribiological Research-Zeitschrift für Agrarbiologie Agrikulturchemie Okologie 50: 85–95.Google Scholar
Holben, W.E., Noto, K., Sumino, T. and Suwa, Y. (1998) Molecular analysis of bacterial communities in a three-compartment granular activated sludge system indicates community-level control by incompatible nitrification processes. Appl. Environ. Microbiol. 64: 2528–2532.CrossRefGoogle Scholar
Holben, W.E., Sarkilahti, L.K., Williams, P., Saarinen, M. and Apajalahti, J.H.A. (2002) Phylogenetic analysis of intestinal microflora indicates a novel Mycoplasma phylotype in farmed and wild salmon. Microb. Ecol. 44: 175–185.CrossRefGoogle ScholarPubMed
Izat, A.L., Hierholzer, R.E., Kopek, J.M.,Adams, M.H., Reiber, M.A. and McGinnis, J.P. (1990) Effects of D-mannose on incidence and levels of salmonellae in ceca and carcass samples of market age broilers. Poultry Science 69: 2244–2247.CrossRefGoogle ScholarPubMed
Jin, L.Z., Ho, Y.W., Abdullah, N., Ali, M.A. and Jalaludin, S. (1998) Effects of adherent Lactobacillus cultures on growth, weight of organs and intestinal microflora and volatile fatty acids in broilers. Anim. Feed Sci. Technol. 70: 197–209.CrossRefGoogle Scholar
Kleessen, B., Hartmann, L. and Blaut, M. (2001) Oligofructose and long-chain inulin: influence on the gut microbial ecology of rats associated with a human faecal flora. Br: J. Nutr. 86: 291–300.Google ScholarPubMed
Maidak, B.L., Cole, J.R., Parker, C.T. Jr, Garrity, G.M., Larsen, N., Li, B., Lilburn, T.G., McCaughey, M.J., Olsen, G.J., Overbeek, R., Pramanik, S., Schmidt, T.M., Tiedje, J.M. and Woese, C.R. (1999) A new version of the RDP (Ribosomal Database Project). Nucleic Acids Res. 27: 171–173.CrossRefGoogle ScholarPubMed
Mortensen, P.B. and Clausen, M.R. (1996) Short-chain fatty acids in the human colon: relation to gastrointestinal health and disease. Scand. J. Gasrroenterol. Suppl 216: 132–148.CrossRefGoogle ScholarPubMed
Ohkuma, M. and Kudo, T. (1996) Phylogenetic diversity of the intestinal bacterial community in the termite Reticulitermes speratus. Appl. Environ. Microbiol. 62: 461–468.CrossRefGoogle ScholarPubMed
Reid, C.-A. and Hillman, K. (1999) The effects of retrogradation and amylose/amylopectin ratio of starches on carbohydrate fermentation and microbial populations in the porcine colon. Animal Science 68: 503–510.CrossRefGoogle Scholar
Savory, C.J. (l992(Enzyme supplementation, degradation and metabolism of three U- 14C-labelled cell-wall substrates in the fowl. Br. J. Nutr. 67: 91–102.CrossRefGoogle Scholar
Simon, O. (1998) The mode of action of NSP hydrolysing enzymes in the gastrointestinal tract. J. Anim. Feed Sci. 7: 115–123.CrossRefGoogle Scholar
Thomke, S. and Elwinger, K. (l998a) Growth promotants in feeding pigs and poultry. II. Mode of action of antibiotic growth promotants. Ann. Zootech. 47: 153–167.CrossRefGoogle Scholar
Thomke, S. and Elwinger, K. (1998b) Growth promotants in feeding pigs and poultry. I. Growth and feed efficiency responses to antibiotic growth promotants. Ann. Zootech. 47: 85–97.CrossRefGoogle Scholar
Vahjen, W., Glaser, K., Schafer, K. and Simon, O. (1998) Influence of xylanase-supplemented feed on the development of selected bacterial groups in the intestinal tract of broiler chicks. J. Agric. Sci. Camb. 130: 489–500.CrossRefGoogle Scholar
Van Der Meulen, J., Bakker, J.G.M., Smits, B. and De Visser, H. (1997) Effect of source of starch on net portal flux of glucose, lactate, volatile fatty acids and amino acids in the pig. Br. J. Nutr. 78: 533–544.CrossRefGoogle ScholarPubMed
Wagner, D.D. and Thomas, O.P. (1987) Influence of diets containing rye or pectin on the intestinal flora of chicks. Poultry Science 57: 971–975.Google Scholar
Zhu, X.Y., Zhong, T., Pandya, Y. and Joerger, R.D. (2002) 16S rRNA-based analysis of microbiota from the caecum of broiler chickens. Appl. Environ. Microbiol. 68: 124–137.CrossRefGoogle ScholarPubMed