1887

Abstract

Two recently reported bacterial strains that were identified as the dominant caproate-producing bacteria in pit clay, were further characterized to determine their phylogeny and taxonomy. The two strains, designated as LBM19010 and JNU-WLY1368, were short rod-shaped, Gram-stain-positive, non-motile and strictly anaerobic. Analysis of the 16S rRNA gene sequences revealed that strains LBM19010 and JNU-WLY1368 shared a 16S rRNA gene sequence similarity of 99.93 % and belonged to a recent proposed genus in the family . The proposed type strain, LBM19010, showed the highest 16S rRNA gene sequence similarity to LBM18003 (96.34%), followed by JCM 30532 (94.14 %). The pairwise average nucleotide identity and average amino acid identity values between strains LBM19010 and LBM18003 were 74.84 and 76.18 %, respectively. Growth of strain LBM19010 occurred at pH 4.5–7.5 (optimum, pH 5.0–5.5), 20–40 °C (optimum, 35 °C) and with 0–1 % (w/v) NaCl (optimum, 0 %). Strains LBM19010 and JNU-WLY1368 were both able to ferment several hexoses, disaccharides, starch and lactate but not pentoses. Caproate and butyrate were the major end-products from glucose. The predominant cellular fatty acids (>10 %) of strain LBM19010 were C (56.3 %), C DMA (19.5 %) and C (14.9 %). The identified polar lipids of strain LBM19010 were diphosphatidylglycerol, phosphatidylglycerol, three unidentified phospholipids and nine unidentified glycolipids. Based on phylogenetic, phenotypic and chemotaxonomic evidence, strains LBM19010 and JNU-WLY1368 belong to a novel species of the genus , for which the name sp. nov. is proposed. The type strain is LBM19010 (=GDMCC 1.1627=JCM 33782).

Funding
This study was supported by the:
  • Postgraduate Research & Practice Innovation Program of Jiangsu Province (Award KYCX18_1795)
    • Principle Award Recipient: HuilinWang
  • National Natural Science Foundation of China (Award 31530055)
    • Principle Award Recipient: YanXu
  • National Natural Science Foundation of China (Award 21706097)
    • Principle Award Recipient: CongRen
  • Open Foundation from the Key Light-industry Laboratory of Solid-state Fermentation for Strong Aroma-type Liquor (Award 2017JJ019)
    • Principle Award Recipient: CongRen
  • Chinese Baijiu Industrial Technology Innovation Strategic Alliance project (Award 2018-3)
    • Principle Award Recipient: YanXu
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.005206
2022-01-27
2024-05-06
Loading full text...

Full text loading...

References

  1. Cavalcante W de A, Leitão RC, Gehring TA, Angenent LT, Santaella ST. Anaerobic fermentation for n-caproic acid production: A review. Process Biochemistry 2017; 54:106–119 [View Article]
    [Google Scholar]
  2. Candry P, Ganigué R. Chain elongators, friends, and foes. Curr Opin Biotechnol 2021; 67:99–110 [View Article]
    [Google Scholar]
  3. Gu Y, Zhu X, Lin F, Shen C, Li Y et al. Caproicibacterium amylolyticum gen. nov., sp. nov., a novel member of the family oscillospiraceae isolated from pit clay used for making chinese strong aroma-type liquor. Int J Syst Evol Microbiol 2021; 71:004789 [View Article]
    [Google Scholar]
  4. Kim B-C, Seung Jeon B, Kim S, Kim H, Um Y et al. Caproiciproducens galactitolivorans gen. nov., sp. nov., a bacterium capable of producing caproic acid from galactitol, isolated from a wastewater treatment plant. Int J Syst Evol Microbiol 2015; 65:4902–4908 [View Article]
    [Google Scholar]
  5. Flaiz M, Baur T, Brahner S, Poehlein A, Daniel R et al. Caproicibacter fermentans gen. nov., sp. nov., a new caproate-producing bacterium and emended description of the genus Caproiciproducens. Int J Syst Evol Microbiol 2020; 70:4269–4279 [View Article]
    [Google Scholar]
  6. Esquivel-Elizondo S, Bağcı C, Temovska M, Jeon BS, Bessarab I et al. The isolate Caproiciproducens sp. 7D4C2 produces n-caproate at mildly acidic conditions from hexoses: genome and rBOX comparison with related strains and chain-elongating bacteria. Front Microbiol 2020; 11:18 [View Article] [PubMed]
    [Google Scholar]
  7. Zhu X, Zhou Y, Wang Y, Wu T, Li X et al. Production of high-concentration n-caproic acid from lactate through fermentation using a newly isolated Ruminococcaceae bacterium CPB6. Biotechnol Biofuels 2017; 10:1–12 [View Article] [PubMed]
    [Google Scholar]
  8. Liu B, Popp D, Müller N, Sträuber H, Harms H et al. Three novel Clostridia isolates produce n-caproate and iso-butyrate from lactate: comparative genomics of chain-elongating bacteria. Microorganisms 2020; 8:23 [View Article] [PubMed]
    [Google Scholar]
  9. Wang H, Gu Y, Zhou W, Zhao D, Qiao Z et al. Adaptability of a caproate-producing bacterium contributes to its dominance in an anaerobic fermentation system. Appl Environ Microbiol 2021; 87:e01203–01221 [View Article] [PubMed]
    [Google Scholar]
  10. Hu XL, Du H, Xu Y. Identification and quantification of the caproic acid-producing bacterium Clostridium kluyveri in the fermentation of pit mud used for Chinese strong-aroma type liquor production. Int J Food Microbiol 2015; 214:116–122 [View Article] [PubMed]
    [Google Scholar]
  11. Sayers EW, Beck J, Bolton EE, Bourexis D, Brister JR et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2021; 49:D10–D17 [View Article] [PubMed]
    [Google Scholar]
  12. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
    [Google Scholar]
  13. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  14. Sourdis J, Nei M. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol Biol Evol 1988; 5:298–311 [View Article] [PubMed]
    [Google Scholar]
  15. Huelsenbeck JP, Crandall KA. Phylogeny estimation and hypothesis testing using maximum likelihood. Annu Rev Ecol Syst 1997; 28:437–466 [View Article]
    [Google Scholar]
  16. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  18. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
    [Google Scholar]
  19. Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol 2015; 16:1–14 [View Article] [PubMed]
    [Google Scholar]
  20. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
    [Google Scholar]
  21. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
    [Google Scholar]
  22. Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Bioinformatics 1992; 8:275–282 [View Article]
    [Google Scholar]
  23. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  24. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article] [PubMed]
    [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. Zhou J, Bruns MA, Tiedje JM. DNA recovery from soils of diverse composition. Appl Environ Microbiol 1996; 62:316–322 [View Article] [PubMed]
    [Google Scholar]
  27. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
    [Google Scholar]
  28. 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]
  29. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  30. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70:4432–4450 [View Article] [PubMed]
    [Google Scholar]
  31. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
    [Google Scholar]
  32. Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH et al. A genus definition for bacteria and archaea based on a standard genome relatedness index. mBio 2020; 11:e02475-19 [View Article] [PubMed]
    [Google Scholar]
  33. Seedorf H, Fricke WF, Veith B, Brüggemann H, Liesegang H et al. The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc Natl Acad Sci USA 2008; 105:2128–2133 [View Article] [PubMed]
    [Google Scholar]
  34. Servinsky MD, Kiel JT, Dupuy NF, Sund CJ. Transcriptional analysis of differential carbohydrate utilization by Clostridium acetobutylicum. Microbiology 2010; 156:3478–3491 [View Article] [PubMed]
    [Google Scholar]
  35. Weghoff MC, Bertsch J, Müller V. A novel mode of lactate metabolism in strictly anaerobic bacteria. Environ Microbiol 2015; 17:670–677 [View Article] [PubMed]
    [Google Scholar]
  36. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1988; 19:1–67 [View Article]
    [Google Scholar]
  37. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Microbiol 1979; 47:87–95 [View Article]
    [Google Scholar]
  38. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Microbiol 1980; 48:459–470 [View Article]
    [Google Scholar]
  39. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI technical note 101. Newark, DE: MIDI inc; 1990
    [Google Scholar]
  40. Lagier J-C, Bibi F, Ramasamy D, Azhar EI, Robert C et al. Non contiguous-finished genome sequence and description of Clostridium jeddahense sp. nov. Stand Genomic Sci 2014; 9:1003–1019 [View Article]
    [Google Scholar]
  41. Moore WEC, Johnson JL, Holdeman LV. Emendation of Bacteroidaceae and Butyrivibrio and descriptions of Desulfomonas gen. nov. and ten new species in the genera Desulfomonas, Butyrivibrio, Eubacterium, Clostridium, and Ruminococcus. Int J Syst Bacteriol 1976; 26:238–252 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.005206
Loading
/content/journal/ijsem/10.1099/ijsem.0.005206
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