Antonie van Leeuwenhoek

, Volume 108, Issue 6, pp 1309–1318 | Cite as

Faecalibaculum rodentium gen. nov., sp. nov., isolated from the faeces of a laboratory mouse

  • Dong-Ho Chang
  • Moon-Soo Rhee
  • Sharon Ahn
  • Byung-Ho Bang
  • Ji Eun Oh
  • Heung Kyu Lee
  • Byoung-Chan Kim
Original Paper


A novel strictly anaerobic strain, ALO17T, was isolated from mouse faeces and found to produce lactic acid as a major metabolic end product. The isolate was observed to be Gram-stain positive, non-motile, non-spore forming small rods, oxidase and catalase negative, and to form cream-coloured colonies on DSM 104 agar plates. The NaCl range for growth was determined to be 0–2 % (w/v). The isolate was found to grow optimally at 37 °C, with 0.5 % (w/v) NaCl and at pH 7. The cell wall hydrolysates were found to contain ribose as a major sugar. The genomic DNA G+C content was determined to be 52.3 mol%. A phylogenetic analysis of the 16S rRNA gene sequence revealed that Holdemanella biformis DSM 3989T, Faecalicoccus pleomorphus ATCC 29734T, Faecalitalea cylindroides ATCC 27803T, and Allobaculumstercoricanis DSM 13633T are closely related to the isolate (87.4, 87.3, 86.9 and 86.9 % sequence similarity), respectively. The major cellular fatty acids (>10 %) of the isolate were identified as C18:1 cis 9 FAME (36.9 %), C16:0 FAME (33.7 %) and C18:0 FAME (13.2 %). In contrast to the tested reference strains, C20:0 FAME (4.0 %) was detected only in strain ALO17T whilst C16:0 DMA was absent. The isolate also differed in its substrate oxidation profiles from the reference strains by being positive for d-melibiose and stachyose but negative for N-acetyl-d-galactosamine and 3-methyl-d-glucose. On the basis of polyphasic taxonomic evidence from this study, the isolate is concluded to belong to a novel genus within the family Erysipelothricaceae. We propose the name Faecalibaculum rodentium gen. nov., sp. nov. to accommodate strain ALO17T (=KCTC 15484T = JCM 30274T) as the type strain.


Faecalibaculum Rodentium Polyphasic approaches Mouse Faeces 



Fatty acid methyl ester




Dimethyl acetal



This work was supported by the Research Program for Agricultural Science & Technology Development (Project No. PJ010168) and was partially supported by grants from the National Research Foundation of Korea (NRF) (2008-2004721 & NRF-2013M3A9A5076601), the KRIBB Research Initiative Programs (KGS4121551) and by a grant from of the Korea Health Technology R&D Project (HI14C0368).

Supplementary material

10482_2015_583_MOESM1_ESM.docx (768 kb)
Supplementary material 1 (DOCX 767 kb)


  1. Bang BH, Rhee MS, Chang DH, Park DS, Kim BC (2015) Erysipelothrix larvae sp. nov., isolated from the larval gut of the rhinoceros beetle, Trypoxylus dichotomus (Coleoptera: Scarabaeidae). Antonie Van Leeuwenhoek 107:443–451CrossRefPubMedGoogle Scholar
  2. Barnes EM, Impey CS, Stevens BJH, Peel JL (1997) Streptococcus pleomorphus sp. nov. : an anaerobic Streptococcus isolated mainly from the caeca of birds. J Gen Microbiol 102:45–53CrossRefGoogle Scholar
  3. Becker B, Lechevalier MP, Lechevalier HA (1965) Chemical composition of cell-wall preparations from strains of various form-genera of aerobic actinomycetes. Appl Microbiol 13:236–243PubMedPubMedCentralGoogle Scholar
  4. Benson D, Lipman DJ, Ostell J (1993) GenBank. Nucleic Acids Res 21:2963–2965CrossRefPubMedPubMedCentralGoogle Scholar
  5. Bosshard PP, Zbinden R, Altwegg M (2002) Turicibacter sanguinis gen. nov., sp. nov., a novel anaerobic, Gram-positive bacterium. Int J Syst Evol Microbiol 52:1263–1266PubMedGoogle Scholar
  6. Cato EP, Salmon CW, Holdeman LV (1974) Eubacterium cylindroides (Rocchi) Holdeman and Moore: emended description and designation of neotype strain. Int J Syst Bacteriol 24:256–259CrossRefGoogle Scholar
  7. Cho JC, Giovannoni SJ (2003) Parvularcula bermudensis gen. nov., sp. nov., a marine bacterium that forms a deep branch in the α-Proteobacteria. Int J Syst Evol Microbiol 53:1031–1036CrossRefPubMedGoogle Scholar
  8. De Maesschalck C, Van Immerseel F, Eeckhaut V, De Baere S, Cnockaert M, Croubels S, Haesebrouck F, Ducatelle R, Vandamme P et al (2014) Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae. Int J Syst Evol Microbiol 64:3877–3884CrossRefPubMedGoogle Scholar
  9. Downes J, Olsvik B, Hiom SJ, Spratt DA, Cheeseman SL, Olsen I, Weightman AJ, Wade WG (2000) Bulleidia extructa gen. nov., sp. nov., isolated from human oral cavities. Int J Syst Evol Microbiol 50:979–983CrossRefPubMedGoogle Scholar
  10. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376CrossRefPubMedGoogle Scholar
  11. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefPubMedGoogle Scholar
  12. Fritz JV, Desai MS, Shah P, Schneider JG, Wilmes P (2013) From meta-omics to causality: experimental models for human microbiome research. Microbiome 1:14CrossRefPubMedPubMedCentralGoogle Scholar
  13. Gerhardt P, Murray RGE, Wood WA, Krieg NR (1994) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DCGoogle Scholar
  14. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE (2006) Metagenomic analysis of the human distal gut microbiome. Science 312:1355–1359CrossRefPubMedPubMedCentralGoogle Scholar
  15. Greetham HL, Gibson GR, Giffard C, Hippe H, Merkhoffer B, Steiner U, Falsen E, Collins MD (2004) Allobaculum stercoricanis gen. nov., sp. nov., isolated from canine feces. Anaerobe 10:301–307CrossRefPubMedGoogle Scholar
  16. Greiner T, Bäckhed F (2011) Effects of the gut microbiota on obesity and glucose homeostasis. Trends Endocrinol Metab 22:117–123CrossRefPubMedGoogle Scholar
  17. Guarner F, Malagelada JR (2003) Gut flora in health and disease. Lancet 361:512–519CrossRefPubMedGoogle Scholar
  18. Han I, Congeevaram S, Ki DW, Oh BT, Park J (2011) Bacterial community analysis of swine manure treated with autothermal thermophilic aerobic digestion. Appl Microbiol Biotechnol 89:835–842CrossRefPubMedGoogle Scholar
  19. Kageyama A, Benno Y (2000a) Catenibacterium mitsuokai gen. nov., sp. nov., a gram-positive anaerobic bacterium isolated from human faeces. Int J Syst Evol Microbiol 50(4):1595–1599CrossRefPubMedGoogle Scholar
  20. Kageyama A, Benno Y (2000b) Coprobacillus catenaformis gen. nov., sp. nov., a new genus and species isolated from human feces. Microbiol Immunol 44:23–28CrossRefPubMedGoogle Scholar
  21. Kageyama A, Benno Y (2000c) Phylogenic and phenotypic characterization of some Eubacterium-like isolates from human feces: description of Solobacterium moorei Gen. Nov., Sp. Nov. Microbiol Immunol 44:223–227CrossRefPubMedGoogle Scholar
  22. Kanno M, Katayama T, Morita N, Tamaki H, Hanada S, Kamagata Y (2015) Catenisphaera adipataccumulans gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from an anaerobic digester. Int J Syst Evol Microbiol 65:805–810CrossRefPubMedGoogle Scholar
  23. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA Gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721CrossRefPubMedGoogle Scholar
  24. Kostic AD, Howitt MR, Garrett WS (2013) Exploring host-microbiota interactions in animal models and humans. Genes Dev 27:701–718CrossRefPubMedPubMedCentralGoogle Scholar
  25. Lagier JC, Million M, Hugon P, Armougom F, Raoult D (2012) Human gut microbiota: repertoire and variations. Front Cell Infect Microbiol 2:136CrossRefPubMedPubMedCentralGoogle Scholar
  26. Lagier JC, Hugon P, Khelaifia S, Fournier PE, La Scola B, Raoult D (2015) The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 28:237–264CrossRefPubMedPubMedCentralGoogle Scholar
  27. Langille MG, Meehan CJ, Koenig JE, Dhanani AS, Rose RA, Howlett SE, Beiko RG (2014) Microbial shifts in the aging mouse gut. Microbiome 2:50CrossRefPubMedPubMedCentralGoogle Scholar
  28. Lee JY, Hwang BK (2002) Diversity of antifungal actinomycetes in various vegetative soils of Korea. Can J Microbiol 48:407–417CrossRefPubMedGoogle Scholar
  29. Lee GH, Rhee MS, Chang DH, Lee J, Kim S, Yoon MH, Kim BC (2013a) Oscillibacter ruminantium sp. nov., isolated from the rumen of Korean native cattle. Int J Syst Evol Microbiol 63:1942–1946CrossRefPubMedGoogle Scholar
  30. Lee JH, Kumar S, Lee GH, Chang DH, Rhee MS, Yoon MH, Kim BC (2013b) Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle. Int J Syst Evol Microbiol 63:4196–4201CrossRefPubMedGoogle Scholar
  31. Lee GH, Rhee MS, Chang DH, Kwon KK, Bae KS, Yang SH, Kim BC (2014) Bacillus solimangrovi sp. nov., isolated from mangrove soil. Int J Syst Evol Microbiol 64:1622–1628CrossRefPubMedGoogle Scholar
  32. Louis P, Young P, Holtrop G, Flint HJ (2010) Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene. Environ Microbiol 12:304–314CrossRefPubMedGoogle Scholar
  33. Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vázquez-Baeza Y, Jansson JK, Gordon JI, Knight R (2013) Meta-analyses of studies of the human microbiota. Genome Res 23:1704–1714CrossRefPubMedPubMedCentralGoogle Scholar
  34. Ludwig W, Schleifer K-H, Whitman WB (2009) Class III. Erysipelotrichia class nov. In: Vos PD, Garrity GM, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer K-H, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 3, 2nd edn. Springer, New York, p 1298Google Scholar
  35. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by highperformance liquid chromatography. Int J Syst Bacteriol 39:159–167CrossRefGoogle Scholar
  36. Ramasamy D, Lagier JC, Nguyen TT, Raoult D, Fournier PE (2013) Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the family Erysipelotrichaceae. Stand Genomic Sci 8:336–351CrossRefPubMedPubMedCentralGoogle Scholar
  37. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol 4:406–425Google Scholar
  38. Salvetti E, Felis GE, Dellaglio F, Castioni A, Torriani S, Lawson PA et al (2011) Reclassification of Lactobacillus catenaformis (Eggerth 1935) Moore and Holdeman 1970 and Lactobacillus vitulinus Sharpe et al 1973 as Eggerthia catenaformis gen. nov., comb. nov. and Kandleria vitulina gen. nov., comb. nov., respectively. Int J Syst Evol Microbiol 61:2520–2524CrossRefPubMedGoogle Scholar
  39. Skerman VBD, McGowan V, Sneath PHA (1980) Approved lists of bacterial names. Int J Syst Bacteriol 30:225–420CrossRefGoogle Scholar
  40. Stackebrandt E (2009) Family 1. Erysipelotrichaceae. In: Vos PD, Garrity GM, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer K-H, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 3, 2nd edn. Springer, New York, pp 1299–1317Google Scholar
  41. Takahashi T, Fujisawa T, Benno Y, Tamura Y, Sawada T, Suzuki S, Muramatsu M, Mitsuoka T (1987) Erysipelothrix tonsillarum sp. nov., isolated from tonsils of apparently healthy pigs. Int J Syst Bacteriol 37:166–168CrossRefGoogle Scholar
  42. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729CrossRefPubMedPubMedCentralGoogle Scholar
  43. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882CrossRefPubMedPubMedCentralGoogle Scholar
  44. Verbarg S, Rheims H, Emus S, Frühling A, Kroppenstedt RM, Stackebrandt E, Schumann P (2004) Erysipelothrix inopinata sp. nov., isolated in the course of sterile filtration of vegetable peptone broth, and description of Erysipelotrichaceae fam. nov. Int J Syst Evol Microbiol 54:221–225CrossRefPubMedGoogle Scholar
  45. Wade WG (2009) Genus I. Eubacterium Prévot 1938, 294AL. In: Vos PD, Garrity GM, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer K-H, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 3, 2nd edn. Springer, New York, pp 865–891Google Scholar
  46. Willems A, Moore WE, Weiss N, Collins MD (1997) Phenotypic and phylogenetic characterization of some Eubacterium-like isolates containing a novel type B wall murein from human feces: description of Holdemania filiformis gen. nov., sp. nov. Int J Syst Bacteriol 47:1201–1204CrossRefPubMedGoogle Scholar
  47. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W, Schleifer KH, Whitman WB, Euzéby J, Amann R, Rosselló-Móra R (2014) Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 12:635–645CrossRefPubMedGoogle Scholar
  48. Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, Knight R, Gordon JI (2012) Human gut microbiome viewed across age and geography. Nature 486:222–227PubMedPubMedCentralGoogle Scholar
  49. Zillig W, Holz I, Janekovic D, Klenk H-P, Imsel E, Trent J, Wunderl S, Forjaz VH, Coutinho R, Ferreira T (1990) Hyperthermus butylicus, a hyperthermophilic sulfur-reducing archaebacterium that ferments peptides. J Bacteriol 172:3959–3965CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Dong-Ho Chang
    • 1
  • Moon-Soo Rhee
    • 1
  • Sharon Ahn
    • 1
  • Byung-Ho Bang
    • 2
  • Ji Eun Oh
    • 3
  • Heung Kyu Lee
    • 3
  • Byoung-Chan Kim
    • 1
  1. 1.Korean Collection for Type Cultures (KCTC), Biological Resource Center (BRC)Korea Research Institute of Bioscience and Biotechnology (KRIBB)DaejeonRepublic of Korea
  2. 2.Department of Food and Nutrition ScienceEulji UniversitySeongnam-siRepublic of Korea
  3. 3.Graduate School of Medical Science and EngineeringKorea Advanced Institute of Science and Technology (KAIST)DaejeonRepublic of Korea

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