gen. nov., sp. nov., a -arabinose-utilizing bacterium isolated from faeces of C57BL/6J mice that is a close relative of species ASF 502 Free

Abstract

The use of gnotobiotics has attracted wide interest in recent years due to technological advances that have revealed the importance of host-associated microbiomes for host physiology and health. One of the oldest and most important gnotobiotic mouse model, the altered Schaedler flora (ASF) has been used for several decades. ASF comprises eight different bacterial strains, which have been characterized to different extent, but only a few are available through public strain collections. Here, the isolation of a close relative of one of the less-studied ASF strains, species ASF 502, from faeces of C57BL/6J mice is reported. Isolate TLL-A1 shares 99.5 % 16S rRNA gene sequence identity with species ASF 502 and phylogenetic analyses indicate that both strains belong to the uncultured so-called ‘Lachnospiraceae UCG 006’ clade. The rare sugar -arabinose was used as a sole carbon source in the anaerobic isolation medium. Results of growth experiments with TLL-A1 on different carbon sources and analysis of its ~6.5 Gb indicate that TLL-A1 harbours a large gene repertoire that enables it to utilize a variety of carbohydrates for growth. Comparative genome analyses of TLL-A1 and species ASF 502 reveal differences in genome content between the two strains, in particular with regards to carbohydrate-activating enzymes. Based on genomic, molecular and phenotypic differences, we propose to classify strain TLL-A1 (DSM 106076T=KCTC 15657T) as a representative of a new genus and a new species, for which we propose the name gen. nov., sp. nov.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003671
2019-11-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/11/3616.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003671&mimeType=html&fmt=ahah

References

  1. Orcutt R, Gianni F, Judge R. Development of an “Altered Schaedler Flora” for NCI gnotobiotic rodents. Microecol Ther 1987; 17:
    [Google Scholar]
  2. Dewhirst FE, Chien CC, Paster BJ, Ericson RL, Orcutt RP et al. Phylogeny of the defined murine microbiota: altered Schaedler flora. Appl Environ Microbiol 1999; 65:3287–3292[PubMed]
    [Google Scholar]
  3. Collins MD, Lawson PA, Willems A, Cordoba JJ, Fernandez-Garayzabal J et al. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 1994; 44:812–826 [View Article][PubMed]
    [Google Scholar]
  4. Lawson PA, Rainey FA. Proposal to restrict the genus Clostridium Prazmowski to Clostridium butyricum and related species. Int J Syst Evol Microbiol 2016; 66:1009–1016 [View Article][PubMed]
    [Google Scholar]
  5. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article][PubMed]
    [Google Scholar]
  6. Rainey FA. Family V. Lachnospiraceae fam. nov; 2009
  7. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article][PubMed]
    [Google Scholar]
  8. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article][PubMed]
    [Google Scholar]
  9. Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 2006; 22:2688–2690 [View Article][PubMed]
    [Google Scholar]
  10. Ludwig W, Strunk O, Westram R, Richter L, Meier H et al. ARB: a software environment for sequence data. Nucleic Acids Res 2004; 32:1363–1371 [View Article][PubMed]
    [Google Scholar]
  11. Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res 2013; 41:D590–D596 [View Article][PubMed]
    [Google Scholar]
  12. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article][PubMed]
    [Google Scholar]
  13. Wannemuehler MJ, Overstreet AM, Ward DV, Phillips GJ. Draft genome sequences of the altered schaedler flora, a defined bacterial community from gnotobiotic mice. Genome Announc 2014; 2:e0028700214 [View Article][PubMed]
    [Google Scholar]
  14. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article][PubMed]
    [Google Scholar]
  15. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article][PubMed]
    [Google Scholar]
  16. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article][PubMed]
    [Google Scholar]
  17. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article][PubMed]
    [Google Scholar]
  18. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res 2017; 45:D535–D542 [View Article][PubMed]
    [Google Scholar]
  19. Zhang H, Yohe T, Huang L, Entwistle S, Wu P et al. dbCAN2: a meta server for automated carbohydrate-active enzyme annotation. Nucleic Acids Res 2018; 46:W95–W101 [View Article][PubMed]
    [Google Scholar]
  20. Lombard V, Golaconda Ramulu H, Drula E, Coutinho PM, Henrissat B. The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 2014; 42:D490–D495 [View Article][PubMed]
    [Google Scholar]
  21. Buchfink B, Xie C, Huson DH. Fast and sensitive protein alignment using DIAMOND. Nat Methods 2015; 12:59–60 [View Article][PubMed]
    [Google Scholar]
  22. Busk PK, Pilgaard B, Lezyk MJ, Meyer AS, Lange L. Homology to peptide pattern for annotation of carbohydrate-active enzymes and prediction of function. BMC Bioinformatics 2017; 18:214 [View Article][PubMed]
    [Google Scholar]
  23. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  24. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article][PubMed]
    [Google Scholar]
  25. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  26. Brown DP, Ganova-Raeva L, Green BD, Wilkinson SR, Young M et al. Characterization of spo0A homologues in diverse Bacillus and Clostridium species identifies a probable DNA-binding domain. Mol Microbiol 1994; 14:411–426 [View Article][PubMed]
    [Google Scholar]
  27. Browne HP, Forster SC, Anonye BO, Kumar N, Neville BA et al. Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation. Nature 2016; 533:543546 [View Article][PubMed]
    [Google Scholar]
  28. Kim JS, Lee KC, Suh MK, Han KI, Eom MK et al. Mediterraneibacter butyricigenes sp. nov., a butyrate-producing bacterium isolated from human faeces. J Microbiol 2019; 57:38–44 [View Article][PubMed]
    [Google Scholar]
  29. Kim MS, Roh SW, Bae JW. Ruminococcus faecis sp. nov., isolated from human faeces. J Microbiol 2011; 49:487–491 [View Article][PubMed]
    [Google Scholar]
  30. Kitahara M, Takamine F, Imamura T, Benno Y. Assignment of Eubacterium sp. VPI 12708 and related strains with high bile acid 7alpha-dehydroxylating activity to Clostridium scindens and proposal of Clostridium hylemonae sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2000; 50:971–978 [View Article][PubMed]
    [Google Scholar]
  31. Morris GN, Winter J, Cato EP, Ritchie AE, Bokkenheuser VD. Clostridium scindens sp. nov., a Human Intestinal Bacterium with Desmolytic Activity on Corticoids. Int J Syst Bacteriol 1985; 35:478–481 [View Article]
    [Google Scholar]
  32. Sakamoto M, Iino T, Ohkuma M. Faecalimonas umbilicata gen. nov., sp. nov., isolated from human faeces, and reclassification of Eubacterium contortum, Eubacterium fissicatena and Clostridium oroticum as Faecalicatena contorta gen. nov., comb. nov., Faecalicatena fissicatena comb. nov. and Faecalicatena orotica comb. nov. Int J Syst Evol Microbiol 2017; 67:1219–1227 [View Article][PubMed]
    [Google Scholar]
  33. Sakuma K, Kitahara M, Kibe R, Sakamoto M, Benno Y. Clostridium glycyrrhizinilyticum sp. nov., a glycyrrhizin-hydrolysing bacterium isolated from human faeces. Microbiol Immunol 2006; 50:481–485 [View Article][PubMed]
    [Google Scholar]
  34. Seo B, Yoo JE, Lee YM, Ko G. Merdimonas faecis gen. nov., sp. nov., isolated from human faeces. Int J Syst Evol Microbiol 2017; 67:2430–2435 [View Article][PubMed]
    [Google Scholar]
  35. Taylor MM. Eubacterium fissicatena sp.nov. isolated from the alimentary tract of the goat. J Gen Microbiol 1972; 71:457–463 [View Article][PubMed]
    [Google Scholar]
  36. Togo AH, Diop A, Bittar F, Maraninchi M, Valero R et al. Description of Mediterraneibacter massiliensis, gen. nov., sp. nov., a new genus isolated from the gut microbiota of an obese patient and reclassification of Ruminococcus faecis, Ruminococcus lactaris, Ruminococcus torques, Ruminococcus gnavus and Clostridium glycyrrhizinilyticum as Mediterraneibacter faecis comb. nov., Mediterraneibacter lactaris comb. nov., Mediterraneibacter torques comb. nov., Mediterraneibacter gnavus comb. nov. and Mediterraneibacter glycyrrhizinilyticus comb. nov. Antonie van Leeuwenhoek 2018; 111:2107–2128 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003671
Loading
/content/journal/ijsem/10.1099/ijsem.0.003671
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed