Lactobacillus buchneri Subsp. silagei Subsp. Nov., Isolated From Rice Grain Silage

Int J Syst Evol Microbiol. 2020 May;70(5):3111-3116. doi: 10.1099/ijsem.0.004138. Epub 2020 Apr 6.

Abstract

Two Gram-stain-positive, rod-shaped, non-motile, non-spore-forming, catalase-negative bacteria, designated strains SG162T and NK01, were isolated from Japanese rice grain silage and total mixed ration silage, respectively. They were initially identified as Lactobacillus buchneri based on the 16S rRNA gene sequence similarities. However, the two strains were separated into a distinct clade from L. buchneri DSM 20057T (=JCM 1115T) through whole-genome sequence-based characterization, forming an infraspecific subgroup together with strains CD034 and S42, whose genomic sequences were available in the public sequence database. Strains within the subgroup shared 99.4-99.7 % average nucleotide identity (ANI) and 97.5-99.0 % digital DNA-DNA hybridization (dDDH) with each other, albeit 96.9-97.0 % ANI and 76.0-76.6 % dDDH against DSM 20057T. Strains SG162T and NK01 could utilize more substrates as sole carbon sources than DSM 20057T, potentially owing to the abundance of genes involved in carbon metabolism, especially the Entner-Doudoroff pathway. The inability of γ-aminobutyric acid (GABA) production was evidenced by the lack of glutamate decarboxylase and glutamate/GABA antiporter genes in the new subgroup strains. Strain SG162T grew at 10-45 °C (optimum, 30 °C), pH 3.5-8.0, and 0-8 % (w/v) NaCl. Its genomic DNA G+C content was 44.1 mol%. The predominant fatty acids were C16 : 0, C19 : 0 cyclo ω8c, and summed feature 8. On the basis of the polyphasic characterization findings, strains SG162T and NK01 represent a novel subspecies of L. buchneri, for which the name Lactobacillus buchneri subsp. silagei subsp. nov. is proposed. The type strain is SG162T (=JCM 32599T=DSM 107969T), and strains CD034 and S42 are also transferred to L. buchneri subsp. silagei.

Keywords: Lactobacillus buchneri; firmicutes; lactic acid bacteria; rice grain silage.

MeSH terms

  • Bacterial Typing Techniques
  • Base Composition
  • DNA, Bacterial / genetics
  • Edible Grain / microbiology
  • Fatty Acids / chemistry
  • Genes, Bacterial
  • Japan
  • Lactobacillus / classification*
  • Lactobacillus / isolation & purification
  • Nucleic Acid Hybridization
  • Oryza / microbiology*
  • Phylogeny*
  • RNA, Ribosomal, 16S / genetics
  • Sequence Analysis, DNA
  • Silage / microbiology*

Substances

  • DNA, Bacterial
  • Fatty Acids
  • RNA, Ribosomal, 16S

Supplementary concepts

  • Lactobacillus buchneri