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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 74, Issue 12

gen. nov., sp. nov., a member of the family , isolated from the hindgut of the marine herbivorous fish No Access

Abstract

A Gram-stain-negative, non-spore-forming, rod-shaped, obligately anaerobic bacterium, designated strain BP47G, 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 of the isolate indicated that it belonged to the family in the phylum . The gene sequence of BP47G was most similar to with 95.23% sequence identity. Isolate BP47G grew on agar medium containing mannitol and fish gut fluid as the sole carbon sources. Clear colonies of ~1 mm diameter grew within a week at 20–28 °C (optimum 28 °C) and pH 7.1–8.5 (optimum 8.5). BP47G tolerated the addition to the medium of up to 1% NaCl. Formate and butyrate were the major fermentation products. The major cellular fatty acids were C, C, iso-C, C and C 7. Genomic analyses comparing BP47G with its closest relatives indicated low genomic relatedness based on the average nucleotide identity, average amino acid identity, percentage of conserved protein and DNA–DNA hybridization. Supported by the phenotypic and taxonomic characteristics observed in this study, a novel genus and species gen. nov., sp. nov. is proposed for isolate BP47G (=ICMP 24688=JCM 35770).

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  • Accepted:
  • Published Online:
Keyword(s): Bacillota , Firmicutes , herbivorous fish , hindgut fermentation , marine fish , Oscillospiraceae , Ruminococcaceae and seaweed
Funding
This study was supported by the:
  • Ministry for Business Innovation and Employment (Award UOAX1808-CR-2)
    • Principal Award Recipient: D. ClementsKendall
  • Ministry for Business Innovation and Employment (Award UOAX1608)
    • Principal Award Recipient: D. ClementsKendall
© 2024 The Authors
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References

  1. Peshkoff M. Phylogenics of new microbes Caryophanon latum and Caryophanon tenus-intermediate organisms between the Cyanophyceae and bacteria. Zh Obshch Biol 1940; 1:597–617
     [Google Scholar]
  2. Rainey FA VIII. Ruminococcaceae. In de Vos P, Garrity GM, Jones J, Krieg K, Ludwig L. eds Bergey’s Manual of Systematic Bacteriology The Firmicutes, 2nd edn. vol 3 New York: Springer; 2009 p 1016
     [Google Scholar]
  3. Tindall BJ. The names Hungateiclostridium Zhang et al. 2018, Hungateiclostridium thermocellum (Viljoen et al. 1926) Zhang et al. 2018, Hungateiclostridium cellulolyticum (Patel et al. 1980) Zhang et al. 2018, Hungateiclostridium aldrichii (Yang et al. 1990) Zhang et al. 2018, Hungateiclostridium alkalicellulosi (Zhilina et al. 2006) Zhang et al. 2018, Hungateiclostridium clariflavum (Shiratori et al. 2009) Zhang et al. 2018, Hungateiclostridium straminisolvens (Kato et al. 2004) Zhang et al. 2018 and Hungateiclostridium saccincola (Koeck et al. 2016) Zhang et al. 2018 contravene Rule 51b of the International Code of Nomenclature of Prokaryotes and require replacement names in the genus Acetivibrio Patel et al. 1980. Int J Syst Evol Microbiol 2019; 69:3927–3932 [View Article]
     [Google Scholar]
  4. Gaffney J, Embree J, Gilmore S, Embree M. Ruminococcus bovis sp. nov., a novel species of amylolytic Ruminococcus isolated from the rumen of a dairy cow. Int J Syst Evol Microbiol 2021; 71:004924 [View Article] [PubMed]
     [Google Scholar]
  5. Sakamoto M, Ikeyama N, Toyoda A, Murakami T, Mori H et al. Coprobacter secundus subsp. similis subsp. nov. and Solibaculum mannosilyticum gen. nov., sp. nov., isolated from human feces. Microbiol Immunol 2021; 65:245–256 [View Article]
     [Google Scholar]
  6. Slobodkina GB, Baslerov RV, Kostryukova NK, Bonch-Osmolovskaya EA, Slobodkin AI. Tepidibaculum saccharolyticum gen. nov., sp. nov. a moderately thermophilic, anaerobic, spore-forming bacterium isolated from a terrestrial hot spring. Extremophiles 2018761–768 [View Article]
     [Google Scholar]
  7. Hungate RE. Microorganisms in the rumen of cattle fed a constant ration. Can J Microbiol 1957; 3:289–311 [View Article] [PubMed]
     [Google Scholar]
  8. Sijpesteijn AK. Cellulose-Decomposing Bacteria from the Rumen of Cattle Leiden University: Eduard Ijdo; 1948
     [Google Scholar]
  9. 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]
  10. 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]
  11. 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; 72:005374 [View Article] [PubMed]
     [Google Scholar]
  12. Pardesi B, Roberton AM, Wollmuth EM, Angert ER, Rosendale DI et al. Chakrabartyella piscis gen. nov., sp. nov., a member of the family Lachnospiraceae, isolated from the hindgut of the marine herbivorous fish Kyphosus sydneyanus. Int J Syst Evol Microbiol 2023; 72:006100 [View Article]
     [Google Scholar]
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
     [Google Scholar]
  18. 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]
  19. Posada D, Crandall KA. MODELTEST: testing the model of DNA substitution. Bioinformatics 1998; 14:817–818 [View Article]
     [Google Scholar]
  20. 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]
  21. Chaumeil PA, 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]
  22. Parkar S, Blatchford P, Kim C, Rosendale D, Ansell J. New and Tailored Prebiotics: Established Applications 2015 pp 289–314
     [Google Scholar]
  23. Sambrook J, Russell DW. Purification of nucleic acids by extraction with phenol:chloroform. Cold Spring Harb Protoc 2006; 2006:pdb-prot4455 [View Article]
     [Google Scholar]
  24. 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]
  25. 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]
  26. Chen I-MA, 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]
  27. 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]
  28. 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]
     [Google Scholar]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. Tavaré S. eds Some Probabilistic and Statistical Problems in the Analysis of DNA Sequences 1986
     [Google Scholar]
  34. Iino T, Mori K, Tanaka K, Suzuki KI, Harayama S. Oscillibacter valericigenes gen. nov., sp. nov., a valerate-producing anaerobic bacterium isolated from the alimentary canal of a Japanese corbicula clam. Int J Syst Evol Microbiol 2007; 57:1840–1845 [View Article] [PubMed]
     [Google Scholar]
  35. Kitahara M, Shigeno Y, Shime M, Matsumoto Y, Nakamura S et al. Vescimonas gen. nov., Vescimonas coprocola sp. nov., Vescimonas fastidiosa sp. nov., Pusillimonas gen. nov. and Pusillimonas faecalis sp. nov. isolated from human faeces. Int J Syst Evol Microbiol 2021; 71:005066 [View Article]
     [Google Scholar]
  36. Kitahara M, Shigeno Y, Shime M, Matsumoto Y, Nakamura S et al. Corrigendum: Vescimonas gen. nov., Vescimonas coprocola sp. nov., Vescimonas fastidiosa sp. nov., Pusillimonas gen. nov. and Pusillimonas faecalis sp. nov. isolated from human faeces. Int J Syst Evol Microbiol 2022; 72:005317 [View Article]
     [Google Scholar]
  37. Le Roy T, Van der Smissen P, Paquot A, Delzenne N, Muccioli G. Dysosmobacter welbionis gen. nov., sp.nov., isolated from human faeces and emended description of the genus Oscillibacter. Int J Syst Evol Microbiol 2020; 70:4851–4858 [View Article]
     [Google Scholar]
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Bengtsoniella intestinalis gen. nov., sp. nov., a member of the family Oscillospiraceae, isolated from the hindgut of the marine herbivorous fish Kyphosus sydneyanus
Int J Syst Evol Microbiol 74, 006615 (2024); https://doi.org/10.1099/ijsem.0.006615
/content/journal/ijsem/10.1099/ijsem.0.006615
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