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Isolation of bacteria from mouse caecal samples and description of Bacteroides sartorii sp. nov

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Abstract

Caecal samples from wild-type and TNFdeltaARE mice were cultured on selective media containing bile salts, amino acids or casein macro-peptides. Twenty-two strains were isolated and identified by 16S rRNA gene sequencing. Twenty-one strains showed >98% similarity to known bacteria (Blautia spp., Clostridium innocuum, Enterococcus spp., Escherichia coli, Lactobacillus murinus, Parabacteroides goldsteinii and Shigella dysenteriae). One additional isolate, strain A-C2-0, was a new bacterium. The closest relatives were Bacteroides massiliensis, Bacteroides dorei and Bacteroides vulgatus (≤94% similarity). Strain A-C2-0 is a Gram-negative rod that does not form spores and has a G + C content of DNA of 41.5%. Its major cellular fatty acid is C15:0 ANTEISO, and its major respiratory quinone is MK-9. Cells are aerotolerant but grow only under strict anoxic conditions. They are resistant to cefotaxime and tobramycin. When compared with related Bacteroides spp., the new bacterium was positive for α-arabinosidase, negative for glutamyl glutamic acid arylamidase and did not metabolise galactose, glucose, fructose, mannose, raffinose and sucrose. Strain A-C2-0 therefore merits recognition as a member of a novel species within the genus Bacteroides, for which the name Bacteroides sartorii is proposed. The type strain is A-C2-0T (= DSM 21941T = CCUG 57211T).

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References

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    CAS  PubMed  Google Scholar 

  • Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ (2005) At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl Environ Microbiol 71:7724–7736

    Article  CAS  PubMed  Google Scholar 

  • Attebery HR, Finegold SM (1969) Combined screw-cap and rubber-stopper closure for Hungate tubes (pre-reduced anaerobically sterilized roll tubes and liquid media). Appl Microbiol 18:558–561

    CAS  PubMed  Google Scholar 

  • Backhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, Semenkovich CF, Gordon JI (2004) The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA 101:15718–15723

    Article  PubMed  CAS  Google Scholar 

  • Bakir MA, Sakamoto M, Kitahara M, Matsumoto M, Benno Y (2006) Bacteroides dorei sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 56:1639–1643

    Article  CAS  PubMed  Google Scholar 

  • Berg RD (1980) Inhibition of Escherichia coli translocation from the gastrointestinal tract by normal cecal flora in gnotobiotic or antibiotic-decontaminated mice. Infect Immun 29:1073–1081

    CAS  PubMed  Google Scholar 

  • Brook I (1989) Pathogenicity of the Bacteroides fragilis group. Ann Clin Lab Sci 19:360–376

    CAS  PubMed  Google Scholar 

  • Cashion P, Holder-Franklin MA, McCully J, Franklin M (1977) A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81:461–466

    Article  CAS  PubMed  Google Scholar 

  • Clavel T, Haller D (2007) Molecular interactions between bacteria, the epithelium, and the mucosal immune system in the intestinal tract: implications for chronic inflammation. Curr Issues Intest Microbiol 8:25–43

    CAS  PubMed  Google Scholar 

  • Clavel T, Henderson G, Alpert CA, Philippe C, Rigottier-Gois L, Dore J, Blaut M (2005) Intestinal bacterial communities that produce active estrogen-like compounds enterodiol and enterolactone in humans. Appl Environ Microbiol 71:6077–6085

    Article  CAS  PubMed  Google Scholar 

  • Clavel T, Charrier C, Braune A, Wenning M, Blaut M, Haller D (2009) Isolation of bacteria from the ileal mucosa of TNFdeltaARE mice and description of Enterorhabdus mucosicola gen. nov., sp. nov. Int J Syst Evol Microbiol 59:1805–1812

    Article  CAS  PubMed  Google Scholar 

  • Cole JR, Chai B, Marsh TL, Farris RJ, Wang Q, Kulam SA, Chandra S, McGarrell DM, Schmidt TM, Garrity GM, Tiedje JM (2003) The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res 31:442–443

    Article  CAS  PubMed  Google Scholar 

  • Dewhirst FE, Chien CC, Paster BJ, Ericson RL, Orcutt RP, Schauer DB, Fox JG (1999) Phylogeny of the defined murine microbiota: altered Schaedler flora. Appl Environ Microbiol 65:3287–3292

    CAS  PubMed  Google Scholar 

  • Eerola E, Lehtonen OP (1988) Optimal data processing procedure for automatic bacterial identification by gas-liquid chromatography of cellular fatty acids. J Clin Microbiol 26:1745–1753

    CAS  PubMed  Google Scholar 

  • Eggerth AH, Gagnon BH (1933) The Bacteroides of human feces. J Bacteriol 25:389–413

    CAS  PubMed  Google Scholar 

  • Fenner L, Roux V, Mallet MN, Raoult D (2005) Bacteroides massiliensis sp. nov., isolated from blood culture of a newborn. Int J Syst Evol Microbiol 55:1335–1337

    Article  CAS  PubMed  Google Scholar 

  • Finegold SM, Sutter VL, Mathisen GE (1983) Normal indigenous intestinal flora. In: Henteges DJ (ed) Human intestinal microflora in health and disease. Academic Press, New York, pp 3–31

    Google Scholar 

  • Garner CD, Antonopoulos DA, Wagner B, Duhamel GE, Keresztes I, Ross DA, Young VB, Altier C (2009) Perturbation of the small intestine microbial ecology by streptomycin alters pathology in a Salmonella enterica serovar typhimurium murine model of infection. Infect Immun 77:2691–2702

    Article  CAS  PubMed  Google Scholar 

  • Hall TA (1999) Bioedit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nuc Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  • Holdeman LV, Kelley RW, Moore WEC (1984) Genus I. Bacteroides. In: Holt GJ (ed) Bergey’s manual systematic bacteriology. Williams & Wilkins, Baltimore, pp 610–613

    Google Scholar 

  • Hooper LV, Xu J, Falk PG, Midtvedt T, Gordon JI (1999) A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. Proc Natl Acad Sci USA 96:9833–9838

    Article  CAS  PubMed  Google Scholar 

  • Hormannsperger G, Clavel T, Hoffmann M, Reiff C, Kelly D, Loh G, Blaut M, Holzlwimmer G, Laschinger M, Haller D (2009) Post-translational inhibition of IP-10 secretion in IEC by probiotic bacteria: impact on chronic inflammation. PLoS One 4:e4365

    Article  PubMed  CAS  Google Scholar 

  • Kageyama A, Benno Y, Nakase T (1999) Phylogenetic evidence for the transfer of Eubacterium lentum to the genus Eggerthella as Eggerthella lenta gen. nov., comb. nov. Int J Syst Bacteriol 49:1725–1732

    Article  CAS  PubMed  Google Scholar 

  • Katakura K, Lee J, Rachmilewitz D, Li G, Eckmann L, Raz E (2005) Toll-like receptor 9-induced type I IFN protects mice from experimental colitis. J Clin Invest 115:695–702

    CAS  PubMed  Google Scholar 

  • Kim SC, Tonkonogy SL, Albright CA, Tsang J, Balish EJ, Braun J, Huycke MM, Sartor RB (2005) Variable phenotypes of enterocolitis in interleukin 10-deficient mice monoassociated with two different commensal bacteria. Gastroenterology 128:891–906

    Article  CAS  PubMed  Google Scholar 

  • Kontoyiannis D, Pasparakis M, Pizarro TT, Cominelli F, Kollias G (1999) Impaired on/off regulation of TNF biosynthesis in mice lacking TNF AU-rich elements: implications for joint and gut-associated immunopathologies. Immunity 10:387–398

    Article  CAS  PubMed  Google Scholar 

  • Langendijk PS, Schut F, Jansen GJ, Raangs GC, Kamphuis GR, Wilkinson MH, Welling GW (1995) Quantitative fluorescence in situ hybridization of Bifidobacterium spp. with genus-specific 16S rRNA-targeted probes and its application in fecal samples. Appl Environ Microbiol 61:3069–3075

    CAS  PubMed  Google Scholar 

  • Lee WK, Fujisawa T, Kawamura S, Itoh K, Mitsuoka T (1991) Isolation and identification of clostridia from the intestine of laboratory animals. Lab Anim 25:9–15

    Article  CAS  PubMed  Google Scholar 

  • Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, Bircher JS, Schlegel ML, Tucker TA, Schrenzel MD, Knight R, Gordon JI (2008) Evolution of mammals and their gut microbes. Science 320:1647–1651

    Article  CAS  PubMed  Google Scholar 

  • Lievin-Le Moal V, Servin AL (2006) The front line of enteric host defense against unwelcome intrusion of harmful microorganisms: mucins, antimicrobial peptides, and microbiota. Clin Microbiol Rev 19:315–337

    Article  CAS  PubMed  Google Scholar 

  • Lucke K, Miehlke S, Jacobs E, Schuppler M (2006) Prevalence of Bacteroides and Prevotella spp. in ulcerative colitis. J Med Microbiol 55:617–624

    Article  CAS  PubMed  Google Scholar 

  • Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL, Gaynor EC, Finlay BB (2007) Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe 2:204

    Article  CAS  PubMed  Google Scholar 

  • Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, Roca J, Dore J (2006) Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55:205–211

    Article  CAS  PubMed  Google Scholar 

  • Martens EC, Koropatkin NM, Smith TJ, Gordon JI (2009) Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J Biol Chem 284:24673–24677

    Article  CAS  PubMed  Google Scholar 

  • Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL (2005) An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122:107–118

    Article  CAS  PubMed  Google Scholar 

  • Mendoza JL, Lana R, Diaz-Rubio M (2009) Mycobacterium avium subspecies paratuberculosis and its relationship with Crohn’s disease. World J Gastroenterol 15:417–422

    Article  CAS  PubMed  Google Scholar 

  • Mesbah M, Premachandran U, Whitman W (1989) Precise measurement of the G + C content of deoxyribonucleic acid by high performance liquid chromatography. Int J Syst Bact 39:159–167

    Article  CAS  Google Scholar 

  • Muller S, Arni S, Varga L, Balsiger B, Hersberger M, Maly F, Seibold F (2006) Serological and DNA-based evaluation of Chlamydia pneumoniae infection in inflammatory bowel disease. Eur J Gastroenterol Hepatol 18:889–894

    Article  PubMed  Google Scholar 

  • Onderdonk AB, Franklin ML, Cisneros RL (1981) Production of experimental ulcerative colitis in gnotobiotic guinea pigs with simplified microflora. Infect Immun 32:225–231

    CAS  PubMed  Google Scholar 

  • Rath HC, Wilson KH, Sartor RB (1999) Differential induction of colitis and gastritis in HLA-B27 transgenic rats selectively colonized with Bacteroides vulgatus or Escherichia coli. Infect Immun 67:2969–2974

    CAS  PubMed  Google Scholar 

  • Reichardt N, Gniechwitz D, Steinhart H, Bunzel M, Blaut M (2009) Characterization of high molecular weight coffee fractions and their fermentation by human intestinal microbiota. Mol Nutr Food Res 53:287–299

    Article  CAS  PubMed  Google Scholar 

  • Rhuland L, Work E, Denman R, Hoare D (1955) The behavior of the isomers of alpha, epsilon-diaminopimelic acid on paper chromatograms. J Am Chem Soc 77:4844–4846

    Article  CAS  Google Scholar 

  • Rigottier-Gois L, Rochet V, Garrec N, Suau A, Dore J (2003) Enumeration of Bacteroides species in human faeces by fluorescent in situ hybridisation combined with flow cytometry using 16S rRNA probes. Syst Appl Microbiol 26:110–118

    Article  PubMed  Google Scholar 

  • Rothkotter HJ, Pabst R (1989) Lymphocyte subsets in jejunal and ileal Peyer’s patches of normal and gnotobiotic minipigs. Immunology 67:103–108

    CAS  PubMed  Google Scholar 

  • Rutgeerts P, Goboes K, Peeters M, Hiele M, Penninckx F, Aerts R, Kerremans R, Vantrappen G (1991) Effect of faecal stream diversion on recurrence of Crohn’s disease in the neoterminal ileum. Lancet 338:771–774

    Article  CAS  PubMed  Google Scholar 

  • Salzman NH, de Jong H, Paterson Y, Harmsen HJ, Welling GW, Bos NA (2002) Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria. Microbiology 148:3651–3660

    CAS  PubMed  Google Scholar 

  • Santos SR, Ochman H (2004) Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 6:754–759

    Article  CAS  PubMed  Google Scholar 

  • Shah HN, Collins MD (1983) Genus Bacteroides. A chemotaxonomical perspective. J Appl Bacteriol 55:403–416

    CAS  PubMed  Google Scholar 

  • Sokol H, Lepage P, Seksik P, Dore J, Marteau P (2006) Temperature gradient gel electrophoresis of fecal 16S rRNA reveals active Escherichia coli in the microbiota of patients with ulcerative colitis. J Clin Microbiol 44:3172–3177

    Article  CAS  PubMed  Google Scholar 

  • Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic Actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231

    CAS  PubMed  Google Scholar 

  • Stecher B, Robbiani R, Walker AW, Westendorf AM, Barthel M, Kremer M, Chaffron S, Macpherson AJ, Buer J, Parkhill J, Dougan G, von Mering C, Hardt WD (2007) Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol 5:2177–2189

    Article  CAS  PubMed  Google Scholar 

  • Tamaoka J, Komagata K (1984) Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125–128

    Article  CAS  Google Scholar 

  • Tannock GW, Savage DC (1974) Influences of dietary and environmental stress on microbial populations in the murine gastrointestinal tract. Infect Immun 9:591–598

    CAS  PubMed  Google Scholar 

  • Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, Ugarte E, Munoz-Tamayo R, Paslier DL, Nalin R, Dore J, Leclerc M (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 11:2574–2584

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  • Visuvanathan S, Moss M, Standord J, Hermon-Taylor J, McFadden J (1989) Simple enzymatic method for isolation of DNA from diverse bacteria. J Microbiol Methods 10:59–64

    Article  CAS  Google Scholar 

  • Wang RF, Cao WW, Cerniglia CE (1996) PCR detection and quantitation of predominant anaerobic bacteria in human and animal fecal samples. Appl Environ Microbiol 62:1242–1247

    CAS  PubMed  Google Scholar 

  • Whiton RS, Lau P, Morgan SL, Gilbart J, Fox A (1985) Modifications in the alditol acetate method for analysis of muramic acid and other neutral and amino sugars by capillary gas chromatography-mass spectrometry with selected ion monitoring. J Chromatogr 347:109–120

    Article  CAS  PubMed  Google Scholar 

  • Wohlgemuth S, Haller D, Blaut M, Loh G (2009) Reduced microbial diversity and high numbers of one single Escherichia coli strain in the intestine of colitic mice. Environ Microbiol 11:1562–1571

    Article  PubMed  Google Scholar 

  • Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glockner FO, Rossello-Mora R (2008) The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 31:241–250

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

The heterozygous TNFdeltaARE mouse model of ileitis was a generous gift from Dr. George Kollias (Biomedical Sciences Research Center Alexander Fleming, Vari, Greece). We thank Prof. J.P. Euzeby (Ecole Nationale Vétérinaire, Toulouse, France) for his support in creating Latin names, Dr. Sigrid Kisling (TUM, BFLM) for histological analysis, Dr. Herbert Seiler (TUM, Microbiology) for microscopic analysis and co-workers of the DSMZ and of the Culture Collection University of Göteborg (CCUG) for contributing to the description of strain A-C2-0.

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  1. Biofunctionality, ZIEL, Research Center for Nutrition and Food Science, Technische Universität München (TUM), Gregor-Mendel-Str. 2, 85350, Freising Weihenstephan, Germany

    Thomas Clavel, Anja Saalfrank & Dirk Haller

  2. NovaBiotics Ltd., Aberdeen, AB21 9TR, UK

    Cédric Charrier

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  1. Thomas Clavel
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Correspondence to Thomas Clavel.

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Communicated by Erko Stackebrandt.

The GenBank accession number for the 16S rRNA and gyrase B gene sequences of strain A-C2-0 is GQ456204 and GQ409831, respectively.

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Clavel, T., Saalfrank, A., Charrier, C. et al. Isolation of bacteria from mouse caecal samples and description of Bacteroides sartorii sp. nov. Arch Microbiol 192, 427–435 (2010). https://doi.org/10.1007/s00203-010-0568-6

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  • DOI: https://doi.org/10.1007/s00203-010-0568-6

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