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Pontibacter beigongshangensis sp. nov., Isolated from the Mash of Wine

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Abstract

A Gram-negative, aerobic, oval-shaped, and light red pigmented bacterium, designated T6-1T, was isolated from the mash of wine collected from a wine-making laboratory simulated fermenter located in Beijing, China. The optimal growth of T6-1T occurred at 30 °C, pH 7.0 with 1% NaCl. The sole respiratory quinone was menaquinone-7 (MK-7). The principal cellular fatty acids (>5%) were iso-C15:0, iso-C17:0 3OH, C16:1 ω5c, and iso-C17:0. The major polar lipids were PE (phosphatidylethanolamine), PL (unidentified phospholipid), and L1-2 (unidentified lipids). 16S rRNA phylogenetic analysis indicated that strain T6-1T belonged to the genus Pontibacter. The 16S rRNA gene sequence of strain T6-1T was most similar to Pontibacter amylolyticus 9-2T (95.92%). The genomic DNA G+C content of strain T6-1 was 50.34 mol%. The digital DNA–DNA relatedness and average nucleotide identity value between T6-1T and 9-2T was 20.20% and 74.18%, respectively. Polyphasic taxonomy analysis indicated that strain T6-1T represents a novel species of the genus Pontibacter, for which the name Pontibacter beigongshangensis sp. nov. is proposed, with the type strain T6-1T (= CGMCC 1.17104T = KCTC 72413T).

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References

  1. Auch AF, Klenk H, Goeker M (2010) Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2(1):142–148. https://doi.org/10.4056/sigs.541628

    Article  PubMed  PubMed Central  Google Scholar 

  2. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376. https://doi.org/10.1007/BF01734359

    Article  CAS  PubMed  Google Scholar 

  3. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20(4):406–416

    Article  Google Scholar 

  4. Fluharty DM (1967) The KOH method for detecting the gram-staining potential of bacteria without staining. In: Proceedings, annual meeting of the United States Animal Health Association, vol 71, pp 473–479

  5. Gonzalez C, Gutierrez C, Ramirez C (1978) Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 24(6):710–715. https://doi.org/10.1139/m78-119

    Article  CAS  PubMed  Google Scholar 

  6. Hu HY, Lim BR, Goto N, Fujie K (2001) Analytical precision and repeatability of respiratory quinones for quantitative study of microbial community structure in environmental samples. J Microbiol Methods 47(1):17–24. https://doi.org/10.1016/S0167-7012(01)00286-X

    Article  CAS  PubMed  Google Scholar 

  7. Joung Y, Kim H, Ahn T, Joh K (2011) Pontibacter salisaro sp nov., Isolated from a clay tablet solar saltern in Korea. J Microbiol 49(2):290–293. https://doi.org/10.1007/s12275-011-0093-6

    Article  CAS  PubMed  Google Scholar 

  8. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16(2):111–120. https://doi.org/10.1007/BF01731581

    Article  CAS  PubMed  Google Scholar 

  9. Kodaka H, Armfield AY, Lombard GL, Dowell VRJ (1982) Practical procedure for demonstrating bacterial flagella. J Clin Microbiol 16(5):948–952

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24(5):713–714. https://doi.org/10.1093/bioinformatics/btn025

    Article  CAS  PubMed  Google Scholar 

  11. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K, Li S, Yang H, Wang J, Wang J (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20(2):265–272. https://doi.org/10.1101/gr.097261.109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Meier-Kolthoff JP, Auch AF, Klenk H, Goeker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14(60):1. https://doi.org/10.1186/1471-2105-14-60

    Article  Google Scholar 

  13. Nedashkovskaya OI, Kim SB, Suzuki M, Shevchenko LS, Lee MS, Lee KH, Park MS, Frolova GM, Oh HW, Bae KS, Park HY, Mikhailov VV (2005) Pontibacter actiniarum gen. nov., sp nov., a novel member of the phylum ‘Bacteroidetes’, and proposal of Reichenbachiella gen. nov as a replacement for the illegitimate prokaryotic generic name Reichenbachia Nedashkovskaya et al. 2003. Int J Syst Evolut Microbiol 55(6):2583–2588. https://doi.org/10.1099/ijs.0.63819-0

    Article  CAS  Google Scholar 

  14. Ren Q, Hou C (2017) Isolation and identification of microorganisms in Wheat Qu of Beizong Rice Wine. Food Sci 38(04):77–82. https://doi.org/10.7506/spkx1002-6630-201704013

    Article  Google Scholar 

  15. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425

    CAS  PubMed  Google Scholar 

  16. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. Vol. MIDI Technical Note 101. MIDI Inc., Newark, DE, USA

  17. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30(12):2725–2729. https://doi.org/10.1093/molbev/mst197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25(24):4876–4882. https://doi.org/10.1093/nar/25.24.4876

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Wu Y, Zhou P, Jian S, Liu Z, Wang C, Oren A, Xu X (2016) Pontibacter amylolyticus sp. nov., isolated from a deep-sea sediment hydrothermal vent field. Int J Syst Evolut Microbiol 66(4):1760–1767. https://doi.org/10.1099/ijsem.0.000944

    Article  CAS  Google Scholar 

  20. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China. Int J Syst Evolut Microbiol 55(3):1149–1153. https://doi.org/10.1099/ijs.0.63407-0

    Article  CAS  Google Scholar 

  21. Yoon S, Ha S, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evolut Microbiol 67(5):1613–1617. https://doi.org/10.1099/ijsem.0.001755

    Article  CAS  Google Scholar 

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Funding

This study was supported by Youth Funding of Beijing Technology and Business University (PXM2019_014213_000007), the Beijing Technology and Business University Graduate Research Capacity Improvement Program in 2019, the National Key Research and Development Program of China (2018YFC1603606). We would like to thank China General Microbiological Culture Collection Center (CGMCC) for their help with the predominant quinone, fatty acids, polar lipids, and Biolog GENIII analysis, Professor Yingmin Jia with preparing Biolog GEN III MicroStation System.

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Author notes

  1. Jialiang Xu and Leping Sun contributed equally to this work.

Authors and Affiliations

  1. Beijing Technology and Business University, Beijing, 100048, China

    Jialiang Xu, Leping Sun, Zhanbin Sun, Xuan Xing, Jia Li & Qing Ren

  2. Chinese Center for Disease Control and Prevention, Beijing, 102206, China

    Xin Lu & Ying Huang

Authors
  1. Jialiang Xu
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  2. Leping Sun
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  3. Zhanbin Sun
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  4. Xuan Xing
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  5. Jia Li
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  6. Xin Lu
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  7. Ying Huang
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  8. Qing Ren
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Contributions

Q.R. and J.L.X.: Methodology; L.P.S.: Writing and Original Draft Preparation; Z.B.S.: Review & Editing; X.X: Species identification; J.L.: Strain isolation; X. L.: Supervision; Y.H.: Transmission electron microscope. All authors have read and approved the manuscript.

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Correspondence to Qing Ren.

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Nucleotide Sequence Accession Number

The 16S rRNA gene sequence of strain T6-1T was submitted in GenBank to get accession number MK860107.1. The whole genome shotgun sequencing project of strain T6-1T has been deposited in GenBank to get accession number VFSD00000000. The type strain is T6-1T (= CGMCC 1.17104T = KCTC 72413T).

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Xu, J., Sun, L., Sun, Z. et al. Pontibacter beigongshangensis sp. nov., Isolated from the Mash of Wine. Curr Microbiol 76, 1525–1530 (2019). https://doi.org/10.1007/s00284-019-01782-w

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  • DOI: https://doi.org/10.1007/s00284-019-01782-w

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