Deep Shotgun metagenomic and 16S rRNA analysis revealed the microbial diversity of lactic acid bacteria in traditional fermented foods of eastern Hainan, China

The eastern part of Hainan, China, has a flat terrain and a suitable climate with abundant sunshine and rain. This unique environment makes the tropical microbial resources of natural fermented food unique and rich. Therefore, we combined Shotgun metagenomic sequencing, 16S rRNA sequencing and pure culture technology to analyze the microbial diversity, microbiota composition, species differences and correlation of 30 traditional fermented food samples collected from Wenchang, Qionghai, Wanning and Lingshui in the eastern part of Hainan province, and isolated, identified and preserved the microorganisms in them. The results showed that the microbial community structure differs significantly between samples from different regions and between different substrates. The alpha diversity of microorganisms in traditional fermented foods in the Wanning area was higher than those of the other three areas. The beta diversity indicated that the microbiota structural difference between Wanning and Qionghai was smaller. This is consistent with the fact that the precipitation in the Wanning area is the highest and similar to that of Qionghai. The alpha diversity of microorganisms was the highest in fermented vegetables, followed by fermented grains, and the lowest in fermented seafood. Beta diversity showed that the microbiota composition of fermented grains and fermented vegetables is very similar, but that of fermented seafood is significantly different. The results of microbiota structural analysis showed that firmicutes and proteobacteria are the dominant bacterial phyla, and Lactobacillus plantarum and Lactobacillus fermentum are the dominant species in traditional fermented foods in eastern Hainan. Lactic acid bacteria are the dominant species in traditional fermented foods from the eastern Hainan region of China, regardless of the substrate used in fermentation. According to the microbial functional characteristics, the microbial metabolism and biosynthesis pathways in traditional fermented foods in Hainan tend to be active. In addition, combined with pure culture technology, we isolated, identified and preserved 342 lactic acid bacteria strains from traditional fermented food in eastern Hainan province. This study helped us understand the different characteristics of microbial communities in tropical southern China and supplement the Lactobacillus species resource pool in tropical southern China. Moreover, it provided new insights and directions for the development and utilization of fermented foods.

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms. Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae. The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).

Lactobacillus terrae sp. nov., a novel species isolated from soil samples in the Republic of Korea

A novel strain, designated NIBRBAC000499792^T, was isolated from a soil sample collected at Jukgye, Dongnam, Cheonan, Republic of Korea. Cells were Gram-positive, non-motile, non-spore-forming, rod-shaped, oxidase-negative and catalase-negative. Colonies grown on de Man, Rogosa and Sharpe agar were white, circular, raised and entire. Analysis of the 16S rRNA gene sequence analysis revealed that strain NIBRBAC000499792^T belongs to the genus Lactobacillus (family Lactobacillaceae) and is most closely related to Lactobacillus nodensis DSM 19682^T (96.1 % similarity) and Lactobacillus tucceti KCTC 21005^T (96.7 %). The results of DNA-DNA hybridization experiments demonstrated that strain NIBRBAC000499792^T represents a novel species. Major fatty acids are C18 : 1ω9c, C16 : 0 and unidentified 18.846 and/or C19 : 1ω6c and/or C19 : 0cyclo. The predominant respiratory quinones are menaquinone-8 and menaquinone-9. The major polar lipids are phosphatidylglycerol and diphosphatidylglycerol. The minor polar lipids are one unidentified aminophospholipid, one unidentified phospholipid, and four unidentified lipids. Next-generation sequencing analysis of strain NIBRBAC000499792^T indicated that the total genome size was 1 548 794 bp with a G+C content of 33.1 mol%, 1586 coding sequences, 50 tRNAs and nine rRNAs. The most closely related genomes belonged to Lactobacillus species. Most metabolic pathways were related to carbon metabolism and carbon fixation. Based on this polyphasic analysis, strain NIBRBAC000499792^T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus terrae sp. nov. is proposed, with the type strain NIBRBAC000499792^T (=KCTC 21093^T=JCM 32269^T).

Lactobacillus allii sp. nov. isolated from scallion kimchi

A novel strain of lactic acid bacteria, WiKim39^T, was isolated from a scallion kimchi sample consisting of fermented chili peppers and vegetables. The isolate was a Gram-positive, rod-shaped, non-motile, catalase-negative and facultatively anaerobic lactic acid bacterium. Phylogenetic analysis of the 16S rRNA gene sequence showed that strain WiKim39^T belonged to the genus Lactobacillus, and shared 97.1–98.2 % pair-wise sequence similarities with related type strains, Lactobacillus nodensis, Lactobacillus insicii, Lactobacillus versmoldensis, Lactobacillus tucceti and Lactobacillus furfuricola. The G+C content of the strain based on its genome sequence was 35.3 mol%. The ANI values between WiKim39^T and the closest relatives were lower than 80 %. Based on the phenotypic, biochemical, and phylogenetic analyses, strain WiKim39^T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus allii sp. nov. is proposed. The type strain is WiKim39^T (=KCTC 21077^T=JCM 31938^T).

Lactobacillus gorillae sp. nov., isolated from the faeces of captive and wild western lowland gorillas (Gorilla gorilla gorilla)

Four strains of Gram-staining-positive, anaerobic rods were isolated from the faeces of western lowland gorillas (Gorilla gorilla gorilla). Three strains, KZ01T, KZ02 and KZ03, were isolated at the Kyoto City Zoo, Japan, and one strain, GG02, was isolated in the Moukalaba-Doudou National Park, Gabon. These strains were investigated taxonomically. These strains belonged to the Lactobacillus reuteri phylogenetic group according to phylogenetic analysis based on 16S rRNA gene sequences and specific phenotypic characteristics. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strains KZ01T, KZ02, KZ03 and GG02 formed a single monophyletic cluster and had a distinct line of descent. Based on sequence similarity of the 16S rRNA gene, Lactobacillus fermentum JCM 1173T (96.6 %) was the closest neighbour to these novel strains, although it was clear that these strains belonged to a different species. Partial pheS sequences also supported these relationships. DNA–DNA relatedness between strain KZ01T and L. fermentum JCM 1173T was less than 22 % and the DNA G+C content of strain KZ01T was 50.7 mol%. The cell-wall peptidoglycan type was A4β (l-Orn–d-Asp) and the major fatty acids were C16 : 0, C18 : 1ω9c and C19 : 1 cyclo 9,10. Therefore, based on phylogenetic, phenotypic and physiological evidence, these strains represent a novel species of the genus Lactobacillus , for which the name Lactobacillus gorillae sp. nov. is proposed. The type strain is KZ01T ( = JCM 19575T = DSM 28356T).