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

Volume 76, Issue 1

gen. nov., sp. nov., a novel member of the family isolated from pit clay for strong aroma-type liquor production No Access

Abstract

A novel, strictly anaerobic, Gram-positive, rod-shaped bacterium, designated strain LBM23126, was isolated from the pit clay of strong aroma-type liquor-making, exhibiting high temperature tolerance and lacking motility. LBM23126 had a genome size of 2,416,380 bp and a G+C content of 52.5 mol%. The major fatty acid was C (16.46%). The polar lipids of strain LBM23126 were composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, three glycolipids, nine phospholipids, two aminolipids, two aminophospholipids and six unidentified lipids. LBM23126 thrived in a pH range from 6.0 to 8.5 (optimum, pH 7.0–8.0), a temperature from 30 °C to 40 °C (optimum, 35–40 °C) and a salt tolerance of 0–2 % (w/v) sodium chloride (optimum, 0%). Notably, this bacterium was unable to utilize common sugars like glucose, maltose and sucrose, making it unique within the family . LBM23126 can use pyruvate as the carbon source to produce acetic acid as the primary metabolic product. LBM23126 grew well with yeast extract, beef extract and tryptone. Comparing the 16S rRNA gene sequence identities of LBM23126 with other members, LBM23126 showed the closest relationship with SRB-521-5-I (91.94%) and followed by GD2 (91.22%). The average nucleotide identity (ANIb) based on values for strain LBM23126 with SRB-521-5-I and GD2 were 74.05 and 74.07 %, respectively. The average amino acid identity (AAI) values for strain LBM23126 with SRB-521-5-I and GD2 were 53.63 and 53.31 %, respectively, while the percentage of conserved proteins (POCP) was 35 and 34 %, respectively. The AAI and POCP values were all lower than the thresholds required for classifying a new genus. Based on morphology, physiology, biochemistry, genotypic characteristics and phylogenetic analysis, strain LBM23126 represents a novel species of a novel genus of the family , for which the name gen. nov., sp. nov. is proposed. The type strain is LBM23126 (=GDMCC 1.4723=JCM 37290).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Oscillospiraceae , pit clay and short-chain fatty acid
Funding
This study was supported by the:
  • National First-Class Discipline Program of Light Industry Technology and Engineering (Award QGJC20230301)
    • Principal Award Recipient: YanXu
  • National Natural Science Foundation of China (Award 32172177)
    • Principal Award Recipient: CongRen
© 2026 The Authors
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2026-01-07
2026-01-20

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References

  1. Hu X, Du H, Ren C, Xu Y. Illuminating anaerobic microbial community and cooccurrence patterns across a quality gradient in Chinese liquor fermentation pit muds. Appl Environ Microbiol 2016; 82:2506–2515 [View Article]
     [Google Scholar]
  2. Fu JX, Chen L, Yang SZ, Li YZ, Jin L et al. Metagenome and analysis of metabolic potential of the microbial community in pit mud used for Chinese strong-flavor liquor production. Food Res Int 2021; 143:110294 [View Article] [PubMed]
     [Google Scholar]
  3. Wang XS, Du H, Xu Y. Source tracking of prokaryotic communities in fermented grain of Chinese strong-flavor liquor. Int J Food Microbiol 2017; 244:27–35 [View Article]
     [Google Scholar]
  4. Fan WL, Qian MC. Characterization of aroma compounds of Chinese “Wuliangye” and “Jiannanchun” liquors by aroma extract dilution analysis. J Agric Food Chem 2006; 54:2695–2704 [View Article]
     [Google Scholar]
  5. Chai L-J, Qian W, Zhong X-Z, Zhang X-J, Lu Z-M et al. Mining the factors driving the evolution of the pit mud microbiome under the impact of long-term production of strong-flavor baijiu. Appl Environ Microbiol 2021; 87: [View Article]
     [Google Scholar]
  6. Gao JJ, Liu GY, Li AJ, Liang CC, Ren C et al. Domination of pit mud microbes in the formation of diverse flavour compounds during Chinese strong aroma-type baijiu fermentation. LWT 2021; 137:110442 [View Article]
     [Google Scholar]
  7. Wang Q, Liu K, Liu L, Zheng J, Chen T et al. Correlation analysis between aroma components and microbial communities in Wuliangye-flavor raw liquor based on HS-SPME/LLME-GC-MS and PLFA. Food Res Int 2021; 140:109995 [View Article] [PubMed]
     [Google Scholar]
  8. Zeng Y, Zhong X, Chai L, Zhang X, Lu Z et al. Prokaryotic evolution shapes specialized communities in long term engineered pit mud ecosystem. NPJ Biofilms Microbiomes 2025; 11:186 [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:e01203–21 [View Article]
     [Google Scholar]
  10. Wu C, Liu X, Dong X. Syntrophomonas cellicola sp. nov., a spore-forming syntrophic bacterium isolated from a distilled-spirit-fermenting cellar, and assignment of Syntrophospora bryantii to Syntrophomonas bryantii comb. nov. Int J Syst Evol Microbiol 2006; 56:2331–2335 [View Article] [PubMed]
     [Google Scholar]
  11. Liu C, Huang D, Liu L, Zhang J, Deng Y et al. Clostridium swellfunianum sp. nov., a novel anaerobic bacterium isolated from the pit mud of Chinese luzhou-flavor liquor production. Antonie Van Leeuwenhoek 2014; 106:817–825 [View Article] [PubMed]
     [Google Scholar]
  12. Chen X-R, Shao C-B, Wang Y-W, He M-X, Ma K-D et al. Paenibacillus vini sp. nov., isolated from alcohol fermentation pit mud in Sichuan Province, China. Antonie Van Leeuwenhoek 2015; 107:1429–1436 [View Article] [PubMed]
     [Google Scholar]
  13. Wang Q, Wang C-D, Li C-H, Li J-G, Chen Q et al. Clostridium luticellarii sp. nov., isolated from a mud cellar used for producing strong aromatic liquors. Int J Syst Evol Microbiol 2015; 65:4730–4733 [View Article] [PubMed]
     [Google Scholar]
  14. Liu C, Huang D, Zhang W. Combining culture‐dependent and culture‐independent molecular methods for the isolation and purification of a potentially novel anaerobic species from pit mud in a Chinese liquor distillery. J Inst Brew 2016; 122:754–762 [View Article]
     [Google Scholar]
  15. Yin Q, Tao Y, Zhu X, Zhou Y, He X et al. Clostridium liquoris sp. nov., isolated from a fermentation pit used for the production of Chinese strong-flavoured liquor. Int J Syst Evol Microbiol 2016; 66:749–754 [View Article] [PubMed]
     [Google Scholar]
  16. Xu P-X, Chai L-J, Qiu T, Zhang X-J, Lu Z-M et al. Clostridium fermenticellae sp. nov., isolated from the mud in a fermentation cellar for the production of the Chinese liquor, baijiu. Int J Syst Evol Microbiol 2019; 69:859–865 [View Article] [PubMed]
     [Google Scholar]
  17. Chai L-J, Fang G-Y, Xu P-X, Zhang X-J, Lu Z-M et al. Novisyntrophococcus fermenticellae gen. nov., sp. nov., isolated from an anaerobic fermentation cellar of Chinese strong-flavour baijiu. Int J Syst Evol Microbiol 2021; 71: [View Article]
     [Google Scholar]
  18. 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: [View Article] [PubMed]
     [Google Scholar]
  19. Lu L-F, Yang Y, Chai L-J, Lu Z-M, Zhang L-Q et al. Blautia liquoris sp. nov., isolated from the mud in a fermentation cellar used for the production of Chinese strong-flavour liquor. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  20. Wei Z, Ma S, Chen R, Wu W, Fan H et al. Aminipila luticellarii sp. nov., an anaerobic bacterium isolated from the pit mud of strong aromatic Chinese liquor, and emended description of the genus Aminipila. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  21. Liu Q, Zheng H, Wang H, Zhou W, Zhao D et al. Proteiniphilum propionicum sp. nov., a novel member of the phylum Bacteroidota isolated from pit clay used to produce Chinese liquor. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  22. Wang HL, Gu Y, Zhao D, Qiao ZW, Zheng J et al. Caproicibacterium lactatifermentans sp. nov., isolated from pit clay used for the production of Chinese strong aroma-type liquor. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  23. Xu Y, Wu M, Niu J, Huang H, Nie Z et al. Clostridium btbubcensis BJN0001, a potentially new species isolated from the cellar mud of Chinese strong-flavor baijiu, produces ethanol, acetic acid and butyric acid from glucose. 3 Biotech 2022; 12:203 [View Article]
     [Google Scholar]
  24. Zhao Q, Yang S, Bao G, Wang W, Miao L et al. Lentilactobacillus laojiaonis sp. nov., isolated from the mud in a fermentation cellar for the production of Chinese liquor. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
     [Google Scholar]
  25. Guo C, Wang H, Liu X, Guo Y, He S et al. Pontibacter liquoris sp. nov. and Pontibacter vulgaris sp. nov., two novel bacteria isolated from the pit mud of Chinese liquor. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
     [Google Scholar]
  26. Luo Q, Zheng J, Zhao D, Liu D. Clostridium aromativorans sp. nov., isolated from pit mud used for producing Wuliangye baijiu. Antonie Van Leeuwenhoek 2023; 116:739–748 [View Article] [PubMed]
     [Google Scholar]
  27. Zeng C, Zeng X, Xia S, Ye G. Caproicibacterium argilliputei sp. nov., a novel caproic acid producing anaerobic bacterium isolated from pit clay. Int J Syst Evol Microbiol 2024; 74: [View Article] [PubMed]
     [Google Scholar]
  28. Fan H, Li JR, Wu WQ, Chen R, Yang M et al. Description of a moderately acidotolerant and aerotolerant anaerobic bacterium Acidilutibacter cellobiosedens gen. nov., sp. nov. within the family Acidilutibacteraceae fam. nov., and proposal of Sporanaerobacteraceae fam. nov. and Tepidimicrobiaceae fam. nov. Syst Appl Microbiol 2023; 46:126376 [View Article] [PubMed]
     [Google Scholar]
  29. Lambrecht J, Cichocki N, Schattenberg F, Kleinsteuber S, Harms H et al. Key sub-community dynamics of medium-chain carboxylate production. Microb Cell Fact 2019; 18: [View Article]
     [Google Scholar]
  30. Xing B-S, Han Y, Wang XC, Wen J, Cao S et al. Persistent action of cow rumen microorganisms in enhancing biodegradation of wheat straw by rumen fermentation. Sci Total Environ 2020; 715:136529 [View Article] [PubMed]
     [Google Scholar]
  31. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
     [Google Scholar]
  32. Parks DH, Chuvochina M, Rinke C, Mussig AJ, Chaumeil P-A et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Res 2022; 50:D785–D794 [View Article] [PubMed]
     [Google Scholar]
  33. McInerney MJ, Bryant MP, Pfennig N. Anaerobic bacterium that degrades fatty acids in syntrophic association with methanogens. Arch Microbiol 1979; 122:129–135 [View Article]
     [Google Scholar]
  34. Lu M, Zhou W, Ji F, Wu J, Nie Y et al. Profiling prokaryotic community in pit mud of Chinese strong-aroma type liquor by using oligotrophic culturing. Int J Food Microbiol 2021; 337:108951 [View Article] [PubMed]
     [Google Scholar]
  35. Hirsch A, Grinsted E. 543. Methods for the growth and enumeration of anaerobic spore-formers from cheese, with observations on the effect of nisin. J Dairy Res 1954; 21:101–110 [View Article]
     [Google Scholar]
  36. Hu X-L, 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]
  37. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2011; 39:D38–51 [View Article] [PubMed]
     [Google Scholar]
  38. 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]
  39. 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]
  40. Kim M, Oh H-S, Park S-C, 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]
  41. Lemoine F, Correia D, Lefort V, Doppelt-Azeroual O, Mareuil F et al. NGPhylogeny.fr: new generation phylogenetic services for non-specialists. Nucleic Acids Res 2019; 47:W260–W265 [View Article] [PubMed]
     [Google Scholar]
  42. Lefort V, Longueville J-E, Gascuel O. SMS: Smart Model Selection in PhyML. Mol Biol Evol 2017; 34:2422–2424 [View Article] [PubMed]
     [Google Scholar]
  43. 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]
  44. Letunic I, Bork P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res 2024; 52:W78–W82 [View Article] [PubMed]
     [Google Scholar]
  45. 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]
  46. 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]
  47. Vaser R, Sović I, Nagarajan N, Šikić M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 2017; 27:737–746 [View Article] [PubMed]
     [Google Scholar]
  48. Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W et al. The medaka draft genome and insights into vertebrate genome evolution. Nature 2007; 447:714–719 [View Article] [PubMed]
     [Google Scholar]
  49. Wick RR, Holt KE. Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLoS Comput Biol 2022; 18:e1009802 [View Article] [PubMed]
     [Google Scholar]
  50. Linzer DA, Lewis JB. PoLCA: an r package for polytomous variable latent class analysis. J Stat Softw 2011; 42:1–29
     [Google Scholar]
  51. 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]
  52. 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]
  53. Konstantinidis KT. Sequence-discrete species for prokaryotes and other microbes: a historical perspective and pending issues. mLife 2023; 2:341–349 [View Article] [PubMed]
     [Google Scholar]
  54. Lányi B. Classical and Rapid Identification Methods for Medically Important Bacteria Budapest, Hungary: National Institute of Hygiene; 1987 pp 1–67 [View Article]
     [Google Scholar]
  55. Selby K, Lindström M, Somervuo P, Heap JT, Minton NP et al. Important role of class I heat shock genes hrcA and dnaK in the heat shock response and the response to pH and NaCl stress of group I Clostridium botulinum strain ATCC 3502. Appl Environ Microbiol 2011; 77:2823–2830 [View Article] [PubMed]
     [Google Scholar]
  56. Kanehisa M, Sato Y, Morishima K. BlastKOALA and GhostKOALA: KEGG Tools for functional characterization of genome and metagenome sequences. J Mol Biol 2016; 428:726–731 [View Article] [PubMed]
     [Google Scholar]
  57. Wang H, Zhou W, Gao J, Ren C, Xu Y. Revealing the characteristics of glucose- and lactate-based chain elongation for caproate production by Caproicibacterium lactatifermentans through transcriptomic, bioenergetic, and regulatory analyses. mSystems 2022; 7:e0053422 [View Article] [PubMed]
     [Google Scholar]
  58. Marquis B, Pillonel T, Carrara A, Bertelli C. zDB: bacterial comparative genomics made easy. mSystems 2024; 9:e0047324 [View Article] [PubMed]
     [Google Scholar]
  59. 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: [View Article]
     [Google Scholar]
  60. Van Nguyen T, Viver T, Mortier J, Liu B, Smets I et al. Isolation and characterization of a thermophilic chain elongating bacterium that produces the high commodity chemical n-caproate from polymeric carbohydrates. Bioresource Technology 2023; 367:128170 [View Article]
     [Google Scholar]
  61. Kläring K, Hanske L, Bui N, Charrier C, Blaut M et al. Intestinimonas butyriciproducens gen. nov., sp. nov., a butyrate-producing bacterium from the mouse intestine. Int J Syst Evol Microbiol 2013; 63:4606–4612 [View Article] [PubMed]
     [Google Scholar]
  62. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:1–6
     [Google Scholar]
  63. Afouda P, Durand GA, Lagier J-C, Labas N, Cadoret F et al. Noncontiguous finished genome sequence and description of Intestinimonas massiliensis sp. nov strain GD2T, the second Intestinimonas species cultured from the human gut. Microbiologyopen 2019; 8:e00621 [View Article] [PubMed]
     [Google Scholar]
  64. Sakamoto M, Iino T, Yuki M, Ohkuma M. Lawsonibacter asaccharolyticus gen. nov., sp. nov., a butyrate-producing bacterium isolated from human faeces. Int J Syst Evol Microbiol 2018; 68:2074–2081 [View Article] [PubMed]
     [Google Scholar]
  65. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of cellulomonas, oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  66. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4‐diaminobutyric Acid. J Appl Bacteriol 1980; 48:459–470 [View Article]
     [Google Scholar]
  67. 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]
  68. Carlier J-P, Marie B-F, K’Ouas G, Alauzet C, Mory F et al. Proposal to unify Clostridium orbiscindens winter et al. 1991 and Eubacterium plautii (séguin 1928) hofstad and aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov. Int J Syst Evol Micr 1991; 60:585–590
     [Google Scholar]
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Acidaminobacterium chupaoyuni gen. nov., sp. nov., a novel member of the family Oscillospiraceae isolated from pit clay for strong aroma-type liquor production
Int J Syst Evol Microbiol 76, 007015 (2026); https://doi.org/10.1099/ijsem.0.007015
/content/journal/ijsem/10.1099/ijsem.0.007015
/content/journal/ijsem/10.1099/ijsem.0.007015
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