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Feline gastrointestinal microbiota

  • Yasushi Minamoto (a1), Seema Hooda (a2), Kelly S. Swanson (a2) and Jan S. Suchodolski (a1)


The close relationship between gastrointestinal (GI) microbiota and its host has an impact on the health status of an animal that reaches beyond the GI tract. A balanced microbiome stimulates the immune system, aids in the competitive exclusion of transient pathogens and provides nutritional benefits to the host. With recent rapid advances in high-throughput sequencing technology, molecular approaches have become the routinely used tools for ecological studies of the feline microbiome, and have revealed a highly diverse and complex intestinal ecosystem in the feline GI tract. The major bacterial groups are similar to those found in other mammals, with Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria constituting more than 99% of intestinal microbiota. Several nutritional studies have demonstrated that the feline microbiota can be modulated by the amount of soluble fibers (i.e., prebiotics) and macronutrients (i.e., protein content) in the diet. Initial clinical studies have suggested the presence of a dysbiosis in feline inflammatory bowel disease (IBD). Recently, metagenomic approaches have attempted to characterize the microbial gene pool. However, more studies are needed to describe the phylogenetic and functional changes in the intestinal microbiome in disease states and in response to environmental and dietary modulations. This paper reviews recent studies cataloging the microbial phylotypes in the GI tract of cats.


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Abecia, LH, Hoyles, L, Khoo, C, Frantz, N and McCartney, AL (2010). Effects of a novel galactooligosaccharide on the faecal microbiota of healthy and inflammatory bowel disease cats during a randomized, double-blind, cross-over feeding study. International Journal of Probiotics and Prebiotics 5: 6168.
Amann, R, Ludwig, W and Schleifer, K (1995). Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59: 143169.
Bailey, MT, Dowd, SE, Parry, NM, Galley, JD, Schauer, DB and Lyte, M (2010). Stressor exposure disrupts commensal microbial populations in the intestines and leads to increased colonization by Citrobacter rodentium. Infection and Immunity 78: 15091519.
Baker, G, Smith, J and Cowan, D (2003). Review and re-analysis of domain-specific 16S primers. Journal of Microbiological Methods 55: 541555.
Barry, KA (2010). Indices of gut health and intestinal microbial ecology of the cat as affected by ingestion of select carbohydrates varying in fermentative capacity. PhD Thesis, University of Illinois.
Barry, KA, Wojcicki, BJ, Middelbos, IS, Vester, BM, Swanson, KS and Fahey, GC Jr (2010). Dietary cellulose, fructooligosaccharides, and pectin modify fecal protein catabolites and microbial populations in adult cats. Journal of Animal Science 88: 29782987.
Bartlett, JG (2009). Clostridium difficile infection: historic review. Anaerobe 15: 227229.
Benno, Y, Nakao, H, Uchida, K and Mitsuoka, T (1992). Impact of the advances in age on the gastrointestinal microflora of beagle dogs. Journal of Veterinary Medical Science 54: 703706.
Beutin, L (1999). Escherichia coli as a pathogen in dogs and cats. Veterinary Research 30: 285298.
Brosey, BP, Hill, RC and Scott, KC (2000). Gastrointestinal volatile fatty acid concentrations and pH in cats. American Journal of Veterinary Research 61: 359361.
Buddington, RK and Paulsen, DB (1998). Development of canine and feline gastrointestinal tract. In: Carey, DP and Reinhart, GA (eds.) 1998 IAMS Nutrition Symposium. Orange Frazer Press. Wilmington, Ohio, USA.
Bures, J, Cyrany, J, Kohoutova, D, Förstl, M, Rejchrt, S, Kvetina, J, Vorisek, V and Kopacova, M (2010). Small intestinal bacterial overgrowth syndrome. World Journal of Gastroenterology 16: 29782990.
Bybee, SN, Scorza, AV and Lappin, MR (2011). Effect of the probiotic Enterococcus faecium SF68 on presence of diarrhea in cats and dogs housed in an animal shelter. Journal of Veterinary Internal Medicine 25: 856860.
Caricilli, AM, Picardi, PK, de Abreu, LL, Ueno, M, Prada, PO, Ropelle, ER, Hirabara, SM, Castoldi, Â, Vieira, P, Camara, NO, Curi, R, Carvalheira, JB and Saad, MJ (2011). Gut microbiota is a key modulator of insulin resistance in TLR 2 knockout mice. PLoS Biology 9, e1001212.
Clooten, J, Kruth, S, Arroyo, L and Weese, JS (2008). Prevalence and risk factors for Clostridium difficile colonization in dogs and cats hospitalized in an intensive care unit. Veterinary Microbiology 129: 209214.
Desai, AR, Musil, KM, Carr, AP and Hill, JE (2008). Characterization and quantification of feline fecal microbiota using cpn60 sequence-based methods and investigation of animal-to-animal variation in microbial population structure. Veterinary Microbiology 137: 120128.
Dethlefsen, L, Huse, S, Sogin, ML and Relman, DA (2008). The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biology 6, e280.
Donaldson, RM (1965). Studies on the pathogenesis of steatorrhea in the blind loop syndrome. Journal of Clinical Investigation 44: 18151825.
Eckburg, PB, Bik, EM, Bernstein, CN, Purdom, E, Dethlefsen, L, Sargent, M, Gill, SR, Nelson, KE and Relman, DA (2005). Diversity of the human intestinal microbial flora. Science 308: 16351638.
Frank, DN, Amand, ALS, Feldman, RA, Boedeker, EC, Harpaz, N and Pace, NR (2007). Molecular–phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proceedings of the National Academy of Sciences of the United States of America 104: 1378013785.
Garcia-Mazcorro, JF, Lanerie, DJ, Dowd, SE, Paddock, CG, Grützner, N, Steiner, JM, Ivanek, R and Suchodolski, JS (2011). Effect of a multi-species synbiotic formulation on fecal bacterial microbiota of healthy cats and dogs as evaluated by pyrosequencing. FEMS Microbiology Ecology 78: 542554.
Gill, SR, Pop, M, Deboy, RT, Eckburg, PB, Turnbaugh, PJ, Samuel, BS, Gordon, JI, Relman, DA, Fraser-Liggett, CM and Nelson, KE (2006). Metagenomic analysis of the human distal gut microbiome. Science 312: 13551359.
Gronvold, AMR, L'Abee-Lund, TM, Sorum, H, Skancke, E, Yannarell, AC and Mackie, RI (2010). Changes in fecal microbiota of healthy dogs administered amoxicillin. FEMS Microbiology Ecology 71: 313326.
Hall, EJ (2011). Antibiotic-Responsive Diarrhea in Small Animals. Veterinary Clinics of North America: Small Animal Practice 41: 273286.
Hamer, HM, Jonkers, D, Venema, K, Vanhoutvin, S, Troost, FJ and Brummer, RJ (2008). Review article: the role of butyrate on colonic function. Alimentary Pharmacology and Therapeutics 27: 104119.
Handl, S, Dowd, SE, Garcia-Mazcorro, JF, Steiner, JM and Suchodolski, JS (2011). Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats. FEMS Microbiology Ecology 76: 301310.
Hansen, J, Gulati, A and Sartor, RB (2010). The role of mucosal immunity and host genetics in defining intestinal commensal bacteria. Current Opinion in Gastroenterology 26: 564571.
Hart, ML, Suchodolski, JS, Steiner, JM and Webb, CG (2012). Open-label trial of a multi-strain synbiotic in cats with chronic diarrhea. Journal of Feline Medicine and Surgery doi:. 14(4): 240245.
Inness, VL, McCartney, AL, Khoo, C, Gross, KL and Gibson, GR (2007). Molecular characterisation of the gut microflora of healthy and inflammatory bowel disease cats using fluorescence in situ hybridisation with special reference to Desulfovibrio spp. Journal of Animal Physiology and Animal Nutrition 91: 4853.
Janeczko, S, Atwater, D, Bogel, E, Greiter-Wilke, A, Gerold, A, Baumgart, M, Bender, H, McDonough, PL, McDonough, SP, Goldstein, RE and Simpson, KW (2008). The relationship of mucosal bacteria to duodenal histopathology, cytokine mRNA, and clinical disease activity in cats with inflammatory bowel disease. Veterinary Microbiology 128: 178193.
Jia, J, Frantz, N, Khoo, C, Gibson, GR, Rastall, RA and McCartney, AL (2011a). Investigation of the faecal microbiota of geriatric cats. Letters in Applied Microbiology 53: 288293.
Jia, J, Frantz, N, Khoo, C, Gibson, GR, Rastall, RA and McCartney, AL (2011b). Investigation of the faecal microbiota of kittens: monitoring bacterial succession and effect of diet. FEMS Microbiology Ecology 78: 395404.
Johnston, KL, Lamport, AI, BallŠvre, OP and Batt, RM (2000). Effects of oral administration of metronidazole on small intestinal bacteria and nutrients of cats. American Journal of Veterinary Research 61: 11061112.
Johnston, KL, Swift, NC, Forster-van Hijfte, M, Rutgers, HC, Lamport, A, Ballevre, O and Batt, RM (2001). Comparison of the bacterial flora of the duodenum in healthy cats and cats with signs of gastrointestinal tract disease. Journal of the American Veterinary Medical Association 218: 4851.
Kanakupt, K, Vester Boler, BM, Dunsford, BR and Fahey, GC Jr (2011). Effects of short-chain fructooligosaccharides and galactooligosaccharides, individually and in combination, on nutrient digestibility, fecal fermentative metabolite concentrations, and large bowel microbial ecology of healthy adults cats. Journal of Animal Science 89: 13761384.
Krogius-Kurikka, L, Kassinen, A, Paulin, L, Corander, J, Mäkivuokko, H, Tuimala, J and Palva, A (2009). Sequence analysis of percent G+C fraction libraries of human faecal bacterial DNA reveals a high number of Actinobacteria. BMC Microbiology 9: 68.
Ley, RE, Hamady, M, Lozupone, C, Turnbaugh, PJ, Ramey, RR, Bircher, JS, Schlegel, ML, Tucker, TA, Schrenzel, MD, Knight, R and Gordon, JI (2008). Evolution of mammals and their gut microbes. Science 320: 16471651.
Marks, SL, Rankin, SC, Byrne, BA and Weese, JS (2011). Enteropathogenic bacteria in dogs and cats: diagnosis, epidemiology, treatment, and control. Journal of Veterinary Internal Medicine 25: 11951208.
McClane, BA (1996). An overview of Clostridium perfringens enterotoxin. Toxicon 34: 1335–1143.
Moter, A and Göbel, UB (2000). Fluorescence in situ hybridization (FISH) for direct visualization of microorganisms. Journal of Microbiological Methods 41: 85–112.
O'Keefe, SJ, Ou, J, Aufreiter, S, O'Connor, D, Sharma, S, Sepulveda, J, Fukuwatari, T, Shibata, K and Mawhinney, T (2009). Products of the colonic microbiota mediate the effects of diet on colon cancer risk. Journal of Nutrition 139: 20442048. Orange Frazer Press. Wilmington, Ohio, USA
Osbaldiston, GW and Stowe, EC (1971). Microflora of alimentary tract of cats. American Journal of Veterinary Research 32: 13991405.
Ott, SJ, Musfeldt, M, Timmis, KN, Hampe, J, Wenderoth, DF and Schreiber, S (2004). In vitro alterations of intestinal bacterial microbiota in fecal samples during storage. Diagnostic Microbiology and Infectious Disease 50: 237245.
Packer, RA, Moore, GE, Chang, CY, Zello, GA, Abeysekara, S, Naylor, JM, Steiner, JM, Suchodolski, JS and O'Brien, DP (2012). Serum d-lactate concentrations in cats with gastrointestinal disease. Journal of Veterinary Internal Medicine, doi:. [Epub ahead of print]. 22(3): 292301.
Packey, CD and Sartor, RB (2009). Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases. Current Opinion in Infectious Diseases 22: 292301.
Palmer, C, Bik, EM, DiGiulio, DB, Relman, DA and Brown, PO (2007). Development of the human infant intestinal microbiota. PLoS Biology 5, e177.
Queen, EV, Marks, SL and Farver, TB (2012). Prevalence of selected bacterial and parasitic agents in feces from diarrheic and healthy control cats from Northern California. Journal of Veterinary Internal Medicine 26: 5460.
Rastogi, R, Wu, M, Dasgupta, I and Fox, GE (2009). Visualization of ribosomal RNA operon copy number distribution. BMC Microbiology 9, 208.
Ritchie, LE, Burke, KF, Garcia-Mazcorro, JF, Steiner, JM and Suchodolski, JS (2010). Characterization of fecal microbiota in cats using universal 16S rRNA gene and group-specific primers for Lactobacillus and Bifidobacterium spp. Veterinary Microbiology 144: 140146.
Ritchie, LE, Steiner, JM and Suchodolski, JS (2008). Assessment of microbial diversity along the feline intestinal tract using 16S rRNA gene analysis. FEMS Microbiology Ecology 66: 590598.
Rondeau, MP, Meltzer, K, Michel, KE, McManus, CM and Washabau, RJ (2003). Short chain fatty acids stimulate feline colonic smooth muscle contraction. Journal of Feline Medicine and Surgery 5: 167173.
Round, JL and Mazmanian, SK (2009). The gut microbiota shapes intestinal immune responses during health and disease. Nature Reviews Immunology 9: 313323.
Scanlan, PD and Marchesi, JR (2008). Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. ISME Journal 2: 11831193.
Seksik, P (2010). Gur mircrobiota and IBD. Gastroenterologie clinique et biologique 34: S44S51.
Shindo, K, Machida, M, Koide, K, Fukumura, M and Yamazaki, R (1998). Deconjugation ability of bacteria isolated from the jejunal fluid of patients with progressive systemic sclerosis and its gastric pH. Hepato-gastroenterology 45.
Simpson, J, Martineau, B, Jones, W, Ballam, J and Mackie, R (2002). Characterization of fecal bacterial populations in canines: effects of age, breed and dietary fiber. Microbial Ecology 44: 112.
Simpson, KW and Jergens, AE (2011). Pitfalls and progress in the diagnosis and management of canine inflammatory bowel disease. Veterinary Clinics of North America: Small Animal Practice 41: 381398.
Sparkes, AH, Papasouliotis, K, Sunvold, G, Werrett, G, Clarke, C, Jones, M, Gruffydd-Jones, TJ and Reinhart, G (1998a). Bacterial flora in the duodenum of healthy cats, and effect of dietary supplementation with fructo-oligosaccharides. American Journal of Veterinary Research 59: 431435.
Sparkes, AH, Papasouliotis, K, Sunvold, G, Werrett, G, Gruffydd-Jones, EA, Egan, K, Gruffydd-Jones, TJ and Reinhart, G (1998b). Effect of dietary supplementation with fructo-oligosaccharides on fecal flora of healthy cats. American Journal of Veterinary Research 59: 436440.
Suchodolski, JS, Ruaux, CG, Steiner, JM, Fetz, K and Williams, DA (2005). Assessment of the qualitative variation in bacterial microflora among compartments of the intestinal tract of dogs by use of a molecular fingerprinting technique. American Journal of Veterinary Research 66: 15561562.
Suchodolski, JS, Camacho, J and Steiner, JM (2008). Analysis of bacterial diversity in the canine duodenum, jejunum, ileum, and colon by comparative 16S rRNA gene analysis. FEMS Microbiology Ecology 66: 567578.
Suchodolski, JS, Dowd, SE, Westermarck, E, Steiner, JM, Wolcott, RD, Spillmann, T and Harmoinen, JA (2009). The effect of the macrolide antibiotic tylosin on microbial diversity in the canine small intestine as demonstrated by massive parallel 16S rRNA gene sequencing. BMC Microbiology 9, 210.
Suchodolski, JS, Xenoulis, PG, Paddock, CG, Steiner, JM and Jergens, AE (2010a). Molecular analysis of the bacterial microbiota in duodenal biopsies from dogs with idiopathic inflammatory bowel disease. Veterinary Microbiology 142: 394400.
Suchodolski, JS, Gossett, NM, Aicher, KM, Heilmann, RM, Xenoulis, PG and Steiner, JM (2010b). Molecular assay for the detection of Campylobacter spp. in canine and feline fecal samples. Journal of Veterinary Internal Medicine 24: 748749.
Suchodolski, JS (2011). Intestinal Microbiota of Dogs and Cats: a Bigger World than We Thought. Veterinary Clinics of North America: Small Animal Practice 41: 261272.
Suchodolski, JS, Steinberg, BR, Butterfield, A and Steiner, JM (2011). Prevalence of archaea in the gastrointestinal tract of dogs and cats. 21th ECVIM-CA Congress, 2011, p. 236.
Sunvold, GD, Titgemeyer, EC, Bourquin, LD, Fahey, GC Jr and Reinhart, GA (1994). Fermentability of selected fibrous substrates by cat fecal microflora. Journal of Nutrition 124: 2721S2722S.
Swanson, KS, Dowd, SE, Suchodolski, JS, Middelbos, IS, Vester, BM, Barry, KA and Fahey, GC Jr (2011). Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. ISME Journal 5: 639649.
Swidsinski, A, Weber, J, Loening-Baucke, V, Hale, LP and Lochs, H (2005). Spatial organization and composition of the mucosal flora in patients with inflammatory bowel disease. Journal of Clinical Microbiology 43: 33803389.
Tabaqchali, S and Booth, CC (1967). Relationship of the intestinal bacterial flora to absorption. British Medical Bulletin 23: 285290.
Terada, A, Hara, H, Kato, S, Kimura, T, Fujimori, I, Hara, K, Maruyama, T and Mitsuoka, T (1993). Effect of lactosucrose (4G-beta-D-galactosylsucrose) on fecal flora and fecal putrefactive products of cats. Journal of Veterinary Medical Science 55: 291295.
Tun, HM, Brar, MS, Khin, N, Jun, L, Hui, RK, Dowd, SE and Leung, FC (2012). Gene-centric metagenomics analysis of feline intestinal microbiome using 454 junior pyrosequencing. Journal of Microbiological Methods 88: 369376.
Van den Abbeele, P, Van de Wiele, T, Verstraete, W and Possemiers, S (2011). The host selects mucosal and luminal associations of coevolved gut microorganisms: a novel concept. FEMS Microbiology Reviews 35: 681704.
Van Immerseel, F, Pasmans, F, De Buck, J, Rychlik, I, Hradecka, H, Collard, JM, Wildemauwe, C, Heyndrickx, M, Ducatelle, R and Haesebrouck, F (2004). Cats as a risk for transmission of antimicrobial drug-resistant Salmonella. Emerging Infectious Diseases 10: 21692174.
Van Nimwegen, FA, Penders, J, Stobberingh, EE, Postma, DS, Koppelman, GH, Kerkhof, M, Reijmerink, NE, Dompeling, E, van den Brandt, PA, Ferreira, I, Mommers, M and Thijs, C (2011). Mode and place of delivery, gastrointestinal microbiota, and their influence on asthma and atopy. Journal of Allergy and Clinical Immunology 128: 948955, e1e3.
Vester, BM, Dalsing, BL, Middelbos, IS, Apanavicius, CJ, Lubbs, DC and Swanson, KS (2009). Faecal microbial populations of growing kittens fed high- or moderate-protein diets. Archives of Animal Nutrition 63: 254265.
Viswanathan, VK, Hodges, K and Hecht, G (2009). Enteric infection meets intestinal function: how bacterial pathogens cause diarrhoea. Nature Reviews Microbiology 7: 110119.
Welkos, SL, Toskes, PP and Baer, H (1981). Importance of anaerobic bacteria in the cobalamin malabsorption of the experimental rat blind loop syndrome. Gastroenterology 80: 313320.
Woodmansey, EJ (2007). Intestinal bacteria and ageing. Journal of Applied Microbiology 102: 11781186.
Xenoulis, PG, Palculict, B, Allenspach, K, Steiner, JM, Van House, AM and Suchodolski, JS (2008). Molecular–phylogenetic characterization of microbial communities imbalances in the small intestine of dogs with inflammatory bowel disease. FEMS Microbiology Ecology 66: 579589.
Zoetendal, EG, Collier, CT, Koike, S, Mackie, RI and Gaskins, HR (2004). Molecular ecological analysis of the gastrointestinal microbiota: a review. Journal of Nutrition 134: 465472.



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