Streptococcus danieliae sp. nov., a novel bacterium isolated from the caecum of a mouse

Archives of Microbiology

Volumn 195, Issue 1, 2013, Pages 43-49

  Clavel, Thomas ^a   Charrier, Cédric ^b   Haller, Dirk ^a  

^a TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^b NOVABIOTICS LTD   (United Kingdom)

Author keywords

Bacterial culture; Crohn's disease like ileitis; Intestinal microbiota; Streptococcus; TNFdeltaARE mice

Indexed keywords

ACETOIN; ALPHA GALACTOSIDASE; BETA GLUCOSIDASE; ESCULIN; RNA 16S; STARCH; TREHALOSE; UREASE;

ANIMAL EXPERIMENT; ANTIGEN ANTIBODY REACTION; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATE; CECUM; DNA DNA HYBRIDIZATION; GENE SEQUENCE; GENOTYPE PHENOTYPE CORRELATION; HEAT TREATMENT; HYDROLYSIS; MALE; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; STREPTOCOCCUS; STREPTOCOCCUS ALACTOLYTICUS; STREPTOCOCCUS DANIELIAE; STREPTOCOCCUS GORDONII; STREPTOCOCCUS INTERMEDIUS; STREPTOCOCCUS SANGUINIS;

ALPHA-GALACTOSIDASE; ANIMALS; BASE SEQUENCE; CECUM; DNA, BACTERIAL; GENOTYPE; MALE; MICE; MICE, INBRED C57BL; MICROSCOPY, PHASE-CONTRAST; MOLECULAR SEQUENCE DATA; NUCLEIC ACID HYBRIDIZATION; PHYLOGENY; RNA, RIBOSOMAL, 16S; SPECIES SPECIFICITY; STREPTOCOCCUS; UREASE;

BACTERIA (MICROORGANISMS); MUS; STREPTOCOCCUS; STREPTOCOCCUS ALACTOLYTICUS; STREPTOCOCCUS GORDONII; STREPTOCOCCUS INTERMEDIUS; STREPTOCOCCUS SANGUINIS;

EID: 84872268984     PISSN: 03028933     EISSN: 1432072X     Source Type: Journal    
DOI: 10.1007/s00203-012-0846-6     Document Type: Article

References (36)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
2. 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
3. Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, Francois F, Perez-Perez G, Blaser MJ, Relman DA (2006) Molecular analysis of the bacterial microbiota in the human stomach. Proc Natl Acad Sci USA 103:732-737
4. Cartun RW, Van Kruiningen HJ, Pedersen CA, Berman MM (1993) An immunocytochemical search for infectious agents in Crohn's disease. Mod Pathol 6:212-219
5. 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
6. Clavel T, Haller D (2007) Bacteria- and host-derived mechanisms to control intestinal epithelial cell homeostasis: implications for chronic inflammation. Inflamm Bowel Dis 13:1153-1164
7. Clavel T, Lippman R, Gavini F, Dore J, Blaut M (2007) Clostridium saccharogumia sp. nov. and Lactonifactor longoviformis gen. nov., sp. nov., two novel human faecal bacteria involved in the conversion of the dietary phytoestrogen secoisolariciresinol diglucoside. Syst Appl Microbiol 30:16-26
8. deltaARE mice and description of Enterorhabdus mucosicola gen. nov., sp. nov. Int J Syst Evol Microbiol 59:1805-1812
9. Conte MP, Schippa S, Zamboni I, Penta M, Chiarini F, Seganti L, Osborn J, Falconieri P, Borrelli O, Cucchiara S (2006) Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease. Gut 55:1760-1767
10. De Ley J, Cattoir H, Reynaerts A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133-142
11. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P, Andersen GL (2006a) Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069-5072
12. DeSantis TZ Jr, Hugenholtz P, Keller K, Brodie EL, Larsen N, Piceno YM, Phan R, Andersen GL (2006b) NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res 34:W394-W399
13. Fyderek K, Strus M, Kowalska-Duplaga K, Gosiewski T, Wedrychowicz A, Jedynak-Wasowicz U, Sladek M, Pieczarkowski S, Adamski P, Kochan P, Heczko PB (2009) Mucosal bacterial microflora and mucus layer thickness in adolescents with inflammatory bowel disease. World J Gastroenterol 15:5287-5294
14. Glazunova OO, Raoult D, Roux V (2009) Partial sequence comparison of the rpoB, sodA, groEL and gyrB genes within the genus Streptococcus. Int J Syst Evol Microbiol 59:2317-2322
15. 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
16. 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
17. Hardie J, Whiley RA (2006) The genus Streptococcus - Oral. In: Dworkin M, Flakow S, Rosenberg E, Schleifer KH, Stackebrandt E (eds) Prokaryotes. Springer, Berlin, pp 76-107
18. Hong PY, Croix JA, Greenberg E, Gaskins HR, Mackie RI (2011) Pyrosequencing-based analysis of the mucosal microbiota in healthy individuals reveals ubiquitous bacterial groups and micro-heterogeneity. PLoS ONE 6:e25042
19. Hörmannsperger G, Clavel T, Haller D (2012) Gut matters: microbehost interactions in allergic diseases. J Allergy Clin Immunol 159:1452-1459
20. Huss VAR, Festl H, Schleifer KH (1983) Studies on the spectrometric determination of DNA hybridization from renaturation rates. Syst Appl Microbiol 4:184-192
21. 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
22. Kilian M, Mikkelsen L, Henrichsen J (1989) Taxonomic study of viridans streptococci: description of Streptococcus gordonii sp. nov. and emended descriptions of Streptococcus sanguis (White and Niven 1946), Streptococcus oralis (Bridge and Sneath 1982), and Streptococcus mitis (Andrewes and Horder 1906). Int J Syst Bact 39:471-484
23. 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
24. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, Sicheritz-Ponten T, Turner K, Zhu H, Yu C, Jian M, Zhou Y, Li Y, Zhang X, Qin N, Yang H, Wang J, Brunak S, Dore J, Guarner F, Kristiansen K, Pedersen O, Parkhill J, Weissenbach J, Bork P, Ehrlich SD (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59-65
25. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
26. Santos SR, Ochman H (2004) Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins. Environ Microbiol 6:754-759
27. Tamaoka J, Komagata K (1984) Determination of DNA base composition by reversed-phase high-performance liquid chromatography. FEMS Microbiol Lett 25:125-128
28. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731-2739
29. Vandamme P, Devriese LA, Haesebrouck F, Kersters K (1999) Streptococcus intestinalis Robinson et al. 1988 and Streptococcus alactolyticus Farrow et al. 1984 are phenotypically indistinguishable. Int J Syst Bacteriol 49 Pt 2:737-741
30. 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
31. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Trüper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bact 37:463-464
32. Werner T, Wagner SJ, Martinez I, Walter J, Chang JS, Clavel T, Kisling S, Schuemann K, Haller D (2011) Depletion of luminal iron alters the gut microbiota and prevents Crohn's disease-like ileitis. Gut 60:325-333
33. Whiley RA, Beighton D (1991) Emended descriptions and recognition of Streptococcus constellatus, Streptococcus intermedius, and Streptococcus anginosus as distinct species. Int J Syst Bacteriol 41:1-5
34. Wilson M (2005) Microbial inhabitants of humans: their ecology and role in health and disease. Cambridge University Press, New York
35. Yarza P, Ludwig W, Euzeby J, Amann R, Schleifer KH, Glockner FO, Rossello-Mora R (2010) Update of the all-species living tree project based on 16S and 23S rRNA sequence analyses. Syst Appl Microbiol 33:291-299
36. Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CC, Troost FJ, Bork P, Wels M, de Vos WM, Kleerebezem M (2012) The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J 6:1415-1426