1887

Abstract

Two strains of Gram-negative, anaerobic, rod-shaped bacteria, from an abundant but uncharacterized rumen bacterial group of the order ‘, were phylogenetically and phenotypically characterized. These strains, designated R-7 and WTE2008, shared 98.6–99.0 % sequence identity between their 16S rRNA gene sequences. R-7 and WTE2008 clustered together on a distinct branch from other strains and had <88.1 % sequence identity to the closest type-strain sequence from NSJ-44. The genome sequences of R-7 and WTE2008 had 83.6 % average nucleotide identity to each other, and taxonomic assignment using the Genome Taxonomy Database indicates these are separate species within a novel family of the order ‘’. Cells of R-7 and WTE2008 lacked any obvious appendages and their cell wall ultra-structures were characteristic of Gram-negative bacteria. The five most abundant cellular fatty acids of both strains were C, C iso, C anteiso, C and C anteiso. The strains used a wide range of the 23 soluble carbon sources tested, and grew best on cellobiose, but not on sugar-alcohols. Xylan and pectin were fermented by both strains, but not cellulose. Acetate, hydrogen, ethanol and lactate were the major fermentation end products. R-7 produced considerably more hydrogen than WTE2008, which produced more lactate. Based on these analyses, fam. nov. and gen. nov., with type species sp. nov., are proposed. Strains R-7 (=DSM 112795=JCM 34733) and WTE2008 (=DSM 112788=JCM 34734) are the proposed type strains for sp. nov. and sp. nov., respectively.

Funding
This study was supported by the:
  • Ministry for Business Innovation and Employment (Award C10X1702)
    • Principle Award Recipient: NotApplicable
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005831
2023-05-12
2024-05-03
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/73/5/ijsem005831.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.005831&mimeType=html&fmt=ahah

References

  1. Creevey CJ, Kelly WJ, Henderson G, Leahy SC. Determining the culturability of the rumen bacterial microbiome. Microb Biotechnol 2014; 7:467–479 [View Article]
    [Google Scholar]
  2. Henderson G, Cox F, Ganesh S, Jonker A, Young W et al. Rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. Sci Rep 2015; 5:14567 [View Article] [PubMed]
    [Google Scholar]
  3. Henderson G, Yilmaz P, Kumar S, Forster RJ, Kelly WJ et al. Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework. PeerJ 2019; 7:e6496 [View Article]
    [Google Scholar]
  4. 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]
  5. Mahoney-Kurpe SC, Palevich N, Noel SJ, Kumar S, Gagic D et al. Complete genome sequences of three Clostridiales R-7 group strains isolated from the bovine rumen in New Zealand. Microbiol Resour Announc 2021; 10:e0031021 [View Article]
    [Google Scholar]
  6. Seshadri R, Leahy SC, Attwood GT, Teh KH, Lambie SC et al. Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection. Nat Biotechnol 2018; 36:359–367 [View Article]
    [Google Scholar]
  7. Bryant MP, Burkey LA. Cultural methods and some characteristics of some of the more numerous groups of bacteria in the bovine rumen. J Dairy Sci 1953; 36:205–217 [View Article]
    [Google Scholar]
  8. Minato H, Otsuka M, Shirasaka S, Itabashi H, Mitsumori M. Colonization of microorganisms in the rumen of young calves. J Gen Appl Microbiol 1992; 38:447–456 [View Article]
    [Google Scholar]
  9. Noel S. Cultivation and community composition analysis of plant-adherent rumen bacteria, PhD thesis. Palmerston North, New Zealand: Massey University; 2013
  10. Button DK, Schut F, Quang P, Martin R, Robertson BR. Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results. Appl Environ Microbiol 1993; 59:881–891 [View Article] [PubMed]
    [Google Scholar]
  11. Kenters N, Henderson G, Jeyanathan J, Kittelmann S, Janssen PH. Isolation of previously uncultured rumen bacteria by dilution to extinction using a new liquid culture medium. J Microbiol Methods 2011; 84:52–60 [View Article] [PubMed]
    [Google Scholar]
  12. Moench TT, Zeikus JG. An improved preparation method for a titanium (III) media reductant. J Microbiol Methods 1983; 1:199–202 [View Article]
    [Google Scholar]
  13. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, 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]
  14. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
    [Google Scholar]
  15. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  16. Liu C, Du M-X, Abuduaini R, Yu H-Y, Li D-H et al. Enlightening the taxonomy darkness of human gut microbiomes with a cultured biobank. Microbiome 2021; 9:119 [View Article] [PubMed]
    [Google Scholar]
  17. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–21 [View Article] [PubMed]
    [Google Scholar]
  18. Luo H, Gao F. DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids. Nucleic Acids Res 2019; 47:D74–D77 [View Article] [PubMed]
    [Google Scholar]
  19. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]
  20. Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019; 36:1925–1927 [View Article]
    [Google Scholar]
  21. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article]
    [Google Scholar]
  22. Salvetti E, Harris HMB, Felis GE, O’Toole PW. Comparative genomics of the genus Lactobacillus reveals robust phylogroups that provide the basis for reclassification. Appl Environ Microbiol 2018; 84:e00993-18 [View Article]
    [Google Scholar]
  23. Joblin KN. Methanogenic archaea. In Makkar HPS, McSweeney CS. eds Methods in Gut Microbial Ecology for Ruminants Dordrecht: Springer Netherlands; 2005 pp 47–53
    [Google Scholar]
  24. Coico R. Gram staining. Curr Protoc Microbiol 2005A.3C.1-A.3C.2 [View Article]
    [Google Scholar]
  25. Della Rosa MM, Sandoval E, Reid P, Luo D, Pacheco D et al. Substituting ryegrass-based pasture with graded levels of forage rape in the diet of lambs decreases methane emissions and increases propionate, succinate, and primary alcohols in the rumen. J Anim Sci 2022; 100:skac223 [View Article]
    [Google Scholar]
  26. Richardson AJ, Calder AG, Stewart CS, Smith A. Simultaneous determination of volatile and non-volatile acidic fermentation products of anaerobes by capillary gas chromatography. Lett Appl Microbiol 1989; 9:5–8 [View Article]
    [Google Scholar]
  27. Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 2021; 71:005056 [View Article] [PubMed]
    [Google Scholar]
  28. Lefort V, Desper R, Gascuel O. FastME 2.0: A comprehensive, accurate, and fast distance-based phylogeny inference program. Mol Biol Evol 2015; 32:2798–2800 [View Article]
    [Google Scholar]
  29. Farris JS. Estimating phylogenetic trees from distance matrices. Am Nat 1972; 106:645–668 [View Article]
    [Google Scholar]
  30. Morotomi M, Nagai F, Watanabe Y. Description of Christensenella minuta gen. nov., sp. nov., isolated from human faeces, which forms a distinct branch in the order Clostridiales, and proposal of Christensenellaceae fam. nov. Int J Syst Evol Microbiol 2012; 62:144–149 [View Article]
    [Google Scholar]
  31. Lau SKP, McNabb A, Woo GKS, Hoang L, Fung AMY et al. Catabacter hongkongensis gen. nov., sp. nov., isolated from blood cultures of patients from Hong Kong and Canada. J Clin Microbiol 2007; 45:395–401 [View Article]
    [Google Scholar]
  32. Liu X, Sutter JL, de la Cuesta-Zuluaga J, Waters JL, Youngblut ND et al. Reclassification of Catabacter hongkongensis as Christensenella hongkongensis comb. nov. based on whole genome analysis. Int J Syst Evol Microbiol 2021; 71:004774 [View Article]
    [Google Scholar]
  33. Zou Y, Xue W, Lin X, Hu T, Liu S-W et al. Taxonomic description and genome sequence of Christensenella intestinihominis sp. nov., a novel cholesterol-lowering bacterium isolated from human gut. Front Microbiol 2021; 12:632361 [View Article]
    [Google Scholar]
  34. Alonso BL, Irigoyen von Sierakowski A, Sáez Nieto JA, Rosel AB. First report of human infection by Christensenella minuta, a Gram-negative, strickly anaerobic rod that inhabits the human intestine. Anaerobe 2017; 44:124–125 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005831
Loading
/content/journal/ijsem/10.1099/ijsem.0.005831
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error