1887

Abstract

A Gram-stain-negative, non˗spore-forming, rod˗shaped, obligately anaerobic bacterium, designated strain BP5G, was isolated from the hindgut of a silver drummer () fish collected from the Hauraki Gulf, New Zealand. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate belonged to the family in the phylum and was most closely related to with 94.06 % sequence identity. Isolate BP5G grew on agar medium containing mannitol and fish gut fluid as carbon sources. Clear colonies of approximately 1 mm diameter of the isolate grew within a week at 20–28 °C (optimum, 28 °C) and pH 7.6–8.5 (optimum, pH 8.5). Strain BP5G was very sensitive to NaCl and the optimal concentration for growth was 0.045 % (w/v). Acetate and propionate were the major fermentation products. The major cellular fatty acids were C, C, C and C. The genome sequence of the isolate was determined. Its G+C content was 38.41 mol% and the 71.41 % average nucleotide identity of the BP5G genome to its closest neighbour with a sequenced genome ( DSM 1682) indicated low genomic relatedness. Based on the phenotypic and taxonomic characteristics observed in this study, a novel genus and species named gen. nov., sp. nov. is proposed for isolate BP5G (=ICMP 24687=JCM 35769).

Funding
This study was supported by the:
  • Ministry of Business, Innovation and Employment (Award UOAX1608, UOAX1808-CR-2)
    • Principle Award Recipient: KendallD Clements
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-10-26
2024-10-04
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References

  1. Vacca M, Celano G, Calabrese FM, Portincasa P, Gobbetti M et al. The controversial role of human gut Lachnospiraceae. Microorganisms 2020; 8:573 [View Article] [PubMed]
    [Google Scholar]
  2. Vos P, Garrity G, Jones D, Krieg NR, Ludwig W et al. Lachnospiraceae fam. nov. Bergey’s Manual of Systematic Bacteriology Springer; 2009 pp 921–968
    [Google Scholar]
  3. Bryant MP, Small N. Characteristics of two new genera of anaerobic curved rods isolated from the rumen of cattle. J Bacteriol 1956; 72:22–26 [View Article] [PubMed]
    [Google Scholar]
  4. Keshavarzian A, Engen P, Bonvegna S, Cilia R. The gut microbiome in Parkinson’s disease: A culprit or a bystander?. Prog Brain Res 2020; 252:357–450 [View Article] [PubMed]
    [Google Scholar]
  5. Sorbara MT, Littmann ER, Fontana E, Moody TU, Kohout CE et al. Functional and genomic variation between human-derived isolates of Lachnospiraceae reveals inter- and intra-species diversity. Cell Host Microbe 2020; 28:134–146 [View Article] [PubMed]
    [Google Scholar]
  6. Pardesi B, Roberton AM, Lee KC, Angert ER, Rosendale DI et al. Distinct microbiota composition and fermentation products indicate functional compartmentalization in the hindgut of a marine herbivorous fish. Mol Ecol 2022; 31:2494–2509 [View Article] [PubMed]
    [Google Scholar]
  7. Sparagon WJ, Gentry EC, Minich JJ, Vollbrecht L, Laurens LML et al. Fine scale transitions of the microbiota and metabolome along the gastrointestinal tract of herbivorous fishes. Anim Microbiome 2022; 4:33 [View Article] [PubMed]
    [Google Scholar]
  8. Clever F, Sourisse JM, Preziosi RF, Eisen JA, Guerra ECR et al. The gut microbiome variability of a butterflyfish increases on severely degraded Caribbean reefs. Commun Biol 2022; 5:770 [View Article] [PubMed]
    [Google Scholar]
  9. Angert ER. Epulopiscium spp. Trends Microbiol 2022; 30:97–98 [View Article] [PubMed]
    [Google Scholar]
  10. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  11. Clements KD, Angert ER, Montgomery WL, Choat JH. Intestinal microbiota in fishes: what’s known and what’s not. Mol Ecol 2014; 23:1891–1898 [View Article] [PubMed]
    [Google Scholar]
  12. Clements KD, Gleeson VP, Slaytor M. Short-chain fatty acid metabolism in temperate marine herbivorous fish. J Comp Physiol B 1994; 164:372–377 [View Article]
    [Google Scholar]
  13. Mountfort DO, Campbell J, Clements KD. Hindgut fermentation in three species of marine herbivorous fish. Appl Environ Microbiol 2002; 68:1374–1380 [View Article] [PubMed]
    [Google Scholar]
  14. Pardesi B, Roberton AM, Wollmuth EM, Angert ER, Rosendale DI et al. Tannockella kyphosi gen. nov., sp. nov., a member of the family Erysipelotrichaceae, isolated from the hindgut of the marine herbivorous fish Kyphosus sydneyanus. Int J Syst Evol Microbiol 2022; 72: [View Article]
    [Google Scholar]
  15. Clements KD, Choat JH. Comparison of herbivory in the closely-related marine fish genera Girella and Kyphosus. Mar Biol 1997; 127:579–586 [View Article]
    [Google Scholar]
  16. Moran D, Clements KD. Diet and endogenous carbohydrases in the temperate marine herbivorous fish Kyphosus sydneyanus. J Fish Biol 2002; 60:1190–1203 [View Article]
    [Google Scholar]
  17. Johnson KS, Clements KD. Histology and ultrastructure of the gastrointestinal tract in four temperate marine herbivorous fishes. J Morphol 2022; 283:16–34 [View Article] [PubMed]
    [Google Scholar]
  18. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  19. Guindon S, Dufayard J-F, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010; 59:307–321 [View Article] [PubMed]
    [Google Scholar]
  20. Posada D, Crandall KA. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998; 14:817–818 [View Article] [PubMed]
    [Google Scholar]
  21. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
    [Google Scholar]
  22. Tavaré S. eds Some Probabilistic and Statistical Problems in the Analysis of DNA Sequences Lectures on Mathematics in the Life Sciences; 1986
    [Google Scholar]
  23. 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] [PubMed]
    [Google Scholar]
  24. Parkar S, Blatchford P, Kim C, Rosendale D, Ansell J. New and tailored prebiotics: established applications. In Probiotics and Prebiotics: Current Research and Future Trends Academic Press; 2015 pp 289–314 [View Article]
    [Google Scholar]
  25. 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]
  26. Sambrook J, Russell DW. Purification of nucleic acids by extraction with phenol:chloroform. CSH Protoc 2006; 2006:pdb.prot4455 [View Article] [PubMed]
    [Google Scholar]
  27. Martin JH, Savage DC. Degradation of DNA in cells and extracts of the obligately anaerobic bacterium Roseburia cecicola upon exposure to air. Appl Environ Microbiol 1988; 54:1619–1621 [View Article] [PubMed]
    [Google Scholar]
  28. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article] [PubMed]
    [Google Scholar]
  29. Chen I-M, Chu K, Palaniappan K, Pillay M, Ratner A et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res 2019; 47:D666–D677 [View Article] [PubMed]
    [Google Scholar]
  30. Yoon S-H, Ha S-M, 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]
  31. 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 2021; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]
  32. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  33. Lepage G, Roy CC. Direct transesterification of all classes of lipids in a one-step reaction. J Lipid Res 1986; 27:114–120 [PubMed]
    [Google Scholar]
  34. Cardon BP, Barker HA. Two new amino-acid-fermenting bacteria, Clostridium propionicum and Diplococcus glycinophilus. J Bacteriol 1946; 52:629–634 [View Article] [PubMed]
    [Google Scholar]
  35. Ueki A, Goto K, Ohtaki Y, Kaku N, Ueki K. Description of Anaerotignum aminivorans gen. nov., sp. nov., a strictly anaerobic, amino-acid-decomposing bacterium isolated from a methanogenic reactor, and reclassification of Clostridium propionicum, Clostridium neopropionicum and Clostridium lactatifermentans as species of the genus Anaerotignum. Int J Syst Evol Microbiol 2017; 67:4146–4153 [View Article] [PubMed]
    [Google Scholar]
  36. Choi S-H, Kim J-S, Park J-E, Lee KC, Eom MK et al. Anaerotignum faecicola sp. nov., isolated from human faeces. J Microbiol 2019; 57:1073–1078 [View Article] [PubMed]
    [Google Scholar]
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