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Complete Genome Sequence of Clostridium kluyveri JZZ Applied in Chinese Strong-Flavor Liquor Production

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Abstract

Chinese strong-flavor liquor (CSFL), accounting for more than 70% of both Chinese liquor production and sales, was produced by complex fermentation with pit mud. Clostridium kluyveri, an important species coexisted with other microorganisms in fermentation pit mud (FPM), could produce caproic acid, which was subsequently converted to the key CSFL flavor substance ethyl caproate. In this study, we present the first complete genome sequence of C. kluyveri isolated from FPM. Clostridium kluyveri JZZ contains one circular chromosome and one circular plasmid with length of 4,454,353 and 58,581 bp, respectively. 4158 protein-coding genes were predicted and 2792 genes could be assigned with COG categories. It possesses the pathway predicted for biosynthesis of caproic acid with ethanol. Compared to other two C. kluyveri genomes, JZZ consists of longer chromosome with multiple gene rearrangements, and contains more genes involved in defense mechanisms, as well as DNA replication, recombination, and repair. Meanwhile, JZZ contains fewer genes involved in secondary metabolites biosynthesis, transport, and catabolism, including genes encoding Polyketide Synthases/Non-ribosomal Peptide Synthetases. Additionally, JZZ possesses 960 unique genes with relatively aggregating in defense mechanisms and transcription. Our study will be available for further research about C. kluyveri isolated from FPM, and will also facilitate the genetic engineering to increase biofuel production and improve fragrance flavor of CSFL.

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References

  1. Barker HA (1937) The production of caproic and butyric acids by the methane fermentation of ethyl alcohol. Arch Mikrobiol 8(1):415–421

    Article  CAS  Google Scholar 

  2. Barker HA, Taha SM (1942) Clostridium kluyverii, an organism concerned in the formation of caproic acid from ethyl alcohol. J Bacteriol 43(3):347–363

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Cheon Y, Kim JS, Park JB, Heo P, Lim JH, Jung GY, Seo JH, Park JH, Koo HM, Cho KM, Park JB, Ha SJ, Kweon DH (2014) A biosynthetic pathway for hexanoic acid production in Kluyveromyces marxianus. J Biotechnol 182:30–36

    Article  Google Scholar 

  4. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J (2013) Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10(6):563–569

    Article  CAS  Google Scholar 

  5. Darling ACE, Mau B, Blattner FR, Perna NT (2004) Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 14(7):1394–1403

    Article  CAS  Google Scholar 

  6. Darling AE, Mau B, Perna NT (2010) progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5(6):e11147

    Article  Google Scholar 

  7. Gildemyn S, Molitor B, Usack JG, Nguyen M, Rabaey K, Angenent LT (2017) Upgrading syngas fermentation effluent using Clostridium kluyveri in a continuous fermentation. Biotechnol Biofuels 10:83

    Article  Google Scholar 

  8. Grant JR, Stothard P (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36:W181–W184

    Article  CAS  Google Scholar 

  9. Hu X, Du H, Ren C, Xu Y, Björkroth J (2016) Illuminating anaerobic microbial community and cooccurrence patterns across a quality gradient in chinese liquor fermentation pit muds. Appl Environ Microbiol 82(8):2506–2515

    Article  CAS  Google Scholar 

  10. Hu XL, Du H, Xu Y (2015) 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 214:116–122

    Article  CAS  Google Scholar 

  11. Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35(9):3100–3108

    Article  CAS  Google Scholar 

  12. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9(4):357–359

    Article  CAS  Google Scholar 

  13. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Proc GPD (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25(16):2078–2079

    Article  Google Scholar 

  14. Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu SN, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Marchler GH, Song JS, Thanki N, Wang ZX, Yamashita RA, Zhang DC, Zheng CJ, Bryant SH (2015) CDD: NCBI’s conserved domain database. Nucleic Acids Res 43(D1):D222–D226

    Article  CAS  Google Scholar 

  15. Peng B, Zhu X, Li Z, Zhang B, Cheng W, Chen X, Xie G, Yang L, Huang X, Zhang B (2016) Isolation and identification of the strains with high caproic acid yield from pit mud and optimization of cultural conditions. China Brewing 35(5):43–46

    Google Scholar 

  16. Richter H, Molitor B, Diender M, Sousa DZ, Angenent LT (2016) A narrow pH range supports butanol, hexanol, and octanol production from syngas in a continuous co-culture of Clostridium ljungdahlii and Clostridium kluyveri with in-line product extraction. Front Microbiol 7:1773

    Article  Google Scholar 

  17. Richter M, Rossello-Mora R (2009) Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106(45):19126–19131

    Article  CAS  Google Scholar 

  18. Schattner P, Brooks AN, Lowe TM (2005) The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs. Nucleic Acids Res 33:W686–W689

    Article  CAS  Google Scholar 

  19. Seedorf H, Fricke WF, Veith B, Bruggemann H, Liesegang H, Strittimatter A, Miethke M, Buckel W, Hinderberger J, Li FL, Hagemeier C, Thauer RK, Gottschalk G (2008) The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc Natl Acad Sci USA 105(6):2128–2133

    Article  CAS  Google Scholar 

  20. Tao Y, Li J, Rui J, Xu Z, Zhou Y, Hu X, Wang X, Liu M, Li D, Li X (2014) Prokaryotic communities in pit mud from different-aged cellars used for the production of Chinese strong-flavored liquor. Appl Environ Microbiol 80(7):2254–2260

    Article  Google Scholar 

  21. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44(14):6614–6624

    Article  CAS  Google Scholar 

  22. Tejerizo GT, Kim YS, Maus I, Wibberg D, Winkler A, Off S, Pühler A, Scherer P, Schlüter A (2017) Genome sequence of Methanobacterium congolense strain Buetzberg, a hydrogenotrophic, methanogenic archaeon, isolated from a mesophilic industrial-scale biogas plant utilizing bio-waste. J Biotechnol 247:1–5

    Article  CAS  Google Scholar 

  23. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Muller R, Wohlleben W, Breitling R, Takano E, Medema MH (2015) antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43(W1):W237–W243

    Article  CAS  Google Scholar 

  24. Weimer PJ, Nerdahl M, Brandl DJ (2015) Production of medium-chain volatile fatty acids by mixed ruminal microorganisms is enhanced by ethanol in co-culture with Clostridium kluyveri. Bioresour Technol 175:97–101

    Article  CAS  Google Scholar 

  25. Weimer PJ, Stevenson DM (2012) Isolation, characterization, and quantification of Clostridium kluyveri from the bovine rumen. Appl Microbiol Biotechnol 94(2):461–466

    Article  CAS  Google Scholar 

  26. Wu JH, Zheng Y, Sun BG, Sun XT, Sun JY, Zheng FP, Huang MQ (2015) The occurrence of propyl lactate in Chinese baijius (Chinese liquors) detected by direct injection coupled with gas chromatography-mass spectrometry. Molecules 20(10):19002–19013

    Article  CAS  Google Scholar 

  27. Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J (2012) PGAP: pan-genomes analysis pipeline. Bioinformatics 28(3):416–418

    Article  CAS  Google Scholar 

  28. Zheng J, Liang R, Zhang LQ, Wu CD, Zhou RQ, Liao XP (2013) Characterization of microbial communities in strong aromatic liquor fermentation pit muds of different ages assessed by combined DGGE and PLFA analyses. Food Res Int 54(1):660–666

    Article  CAS  Google Scholar 

  29. Zhou C, Ma Q, Mao X, Liu B, Yin Y, Xu Y (2014) New insights into clostridia through comparative analyses of their 40 genomes. Bioenerg Res 7(4):1481–1492

    Article  Google Scholar 

Download references

Acknowledgements

We are grateful to Dr. Hang Wu from Anhui University for critical editing of the manuscript. This work was supported by Golden Seed Winery Co. Ltd in Anhui Province of China, and the Initial Foundation of Doctoral Scientific Research in Anhui University (J01001935).

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Authors and Affiliations

  1. Institute of Physical Science and Information Technology, School of Life Sciences, School of Chemistry & Chemical Engineering, Anhui University, Hefei, 230601, China

    Yansheng Wang, Bin Li, Hong Dong, Xunduan Huang, Ruiyu Chen, Changrun Li, Junfeng Xia & Buchang Zhang

  2. Golden Seed Winery Co., Ltd, Fuyang, 236023, China

    Yansheng Wang, Xingjie Chen, Laoji Yang, Bing Peng, Guopai Xie, Wei Cheng & Biao Hao

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  1. Yansheng Wang
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  2. Bin Li
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  3. Hong Dong
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  14. Buchang Zhang
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Correspondence to Buchang Zhang.

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Wang, Y., Li, B., Dong, H. et al. Complete Genome Sequence of Clostridium kluyveri JZZ Applied in Chinese Strong-Flavor Liquor Production. Curr Microbiol 75, 1429–1433 (2018). https://doi.org/10.1007/s00284-018-1539-4

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  • DOI: https://doi.org/10.1007/s00284-018-1539-4

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