Lentibacillus amyloliquefaciens sp. nov., a halophilic bacterium isolated from saline sediment sample

The spatio-temporal diversity and succession of microbial community and its environment driving factors during stacking fermentation of Maotai-flavor baijiu

Stacking fermentation is an important stage of microbial expansion and enrichment in the brewing process of Maotai-flavor baijiu and has an important impact on quality. However, the structure and succession of microbial communities at different spatial points of fermented grains, as well as the key environmental factors driving community assembly, remain unclear. Here, we analyzed spatio-temporal similarities and differences in the microbial community structure and succession during 1-6 rounds of stacking fermentation of Maotai-flavor baijiu. The microbial diversity and richness in the pile center were higher than those at the pile surface. The dominant bacterial genus changed from Lactobacillus to Acetobacter, while the dominant fungal genus Pichia was gradually replaced by Candida, however, some microorganisms (Acetobacter, Thermoascus) could not occupy community dominance in both the pile surface and the pile center of fermented grains. Most of the biomarkers (Kroppenstedtia, Thermomyces, etc.) of the pile surface showed thermostable or thermophilic characteristics, while most biomarkers (Aspergillus, Hyphopicia, etc.) of the pile center were functional microorganisms. Furthermore, pH and moisture were the main environmental driving factors of community construction at the pile surface and the pile center, respectively, with starch and reducing sugars having a greater impact on the microbial community assembly of the pile center than that of the pile surface. The main differences in the metabolic pathways of the dominant bacterial genera of the pile surface and the pile center were concentrated around cell growth and death, amino acids, leading to enrichment and growth of microbial communities at the pile surface and nitrogen utilization at the pile center, respectively. This study reveals the spatio-temporal differences in microbial community structure, succession and corresponding environmental driving factors during stacking fermentation, which will provide guidance for regulating the microbial community diversity to produce high-quality Maotai-flavor baijiu.

Lentibacillus saliphilus. sp. nov., a moderately halophilic bacterium isolated from a saltern in Korea

A novel moderately halophilic bacterial strain, designated YIM 93176^T, was isolated from a saltern in Korea and subjected to a polyphasic taxonomic study. This isolate YIM 93176^T was observed to grow in the presence of 0-22% (w/v) NaCl and at pH 6.0-10.0 and 10-45 °C; optimum growth was observed with 5-10% (w/v) NaCl and at pH 7.0-9.0 and 28-37 °C. Based on 16S rRNA gene sequences analysis, the nearest relatives were Lentibacillus alimentarius M2024^T (96.5% similarity), followed by Virgibacillus carmonensis LMG 20964^T (96.0%) and the other type strains of the family Bacillaceae, but phylogenetic analysis indicated that strain YIM 93176^T belonged to the cluster comprising type species of the genus Lentibacillus. Genome sequencing of strain YIM 93176^T revealed a genome size of 3.2 Mb and a DNA G + C content of 40.5 mol%. The major fatty acids were anteiso-C_15:0 (40.7%) and iso-C_15:0 (26.4%), while the predominant respiratory quinone was menaquinone 7. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. These genotypic and chemotaxonomic characteristics supported affiliation of strain YIM 93176^T to the genus Lentibacillus. In addition, phenotypic characteristics could distinguish strain YIM 93176^T from its closely related species in genus Lentibacillus. Based on the cumulative evidences from the polyphasic taxonomic study, strain YIM 93176^T represents a novel species of the genus Lentibacillus, for which name Lentibacillus saliphilus sp. nov. (type strain YIM 93176^T = CCTCC AB 208139^T = DSM 21375^T) is proposed.

Lentibacillus cibarius sp. nov., isolated from kimchi, a Korean fermented food

Two bacterial strains designated NKC220-2^T and NKC851-2 were isolated from commercial kimchi from different areas in Korea. The strains were Gram-positive, aerobic, oxidaseand catalase-positive, rod-shaped, spore-forming, non-motile, and halophilic bacteria. Both strains grew without NaCl, unlike type species in the genus Lentibacillus. The optimal pH for growth was 8.0, higher than that of the type species in the genus Lentibacillus, although growth was observed at pH 5.5-9.0. 16S rRNA gene sequence-based phylogenetic analysis indicated that the two strains (99.3-99.9% similarity) are grouped within the genus Lentibacillus and most closely related to Lentibacillus juripiscarius IS40-3^T (97.4-97.6% similarity) isolated from fish sauce in Thailand. OrthoANI value between two novel strains and Lentibacillus lipolyticus SSKP1-9^T (79.5-79.6% similarity) was far lower than the species demarcation threshold. Comparative genomic analysis displayed differences between the two strains as well as among other strains belonging to Lentibacillus. Furthermore, each isolate had strain-specific groups of orthologous genes based on pangenome analysis. Genomic G + C contents of strains NKC-220-2^T and NKC851-2 were 41.9 and 42.2 mol%, respectively. The strains contained meso-diaminopimelic acid in their cell walls, and the major menaquinone was menaquinone-7. Phosphatidylglycerol, diphosphatidylglycerol, and an unidentified glycolipid, aminophospholipid, and phospholipid were the major polar lipid components of both strains. The major cellular fatty acids of the strains were anteiso-C_15:0 and anteiso-C_17:0. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic features, strains NKC220-2^T and NKC851-2 represent novel species of the genus Lentibacillus, for which the name Lentibacillus cibarius sp. nov. is proposed. The type strain is NKC220-2^T (= KACC 21232^T = JCM 33390^T).

Lentibacillus lipolyticus sp. nov., a moderately halophilic bacterium isolated from shrimp paste (Ka-pi)

A Gram-stain-positive, aerobic, spore-forming, moderately halophilic bacterium, SSKP1-9^T, was isolated from traditional salted shrimp paste (Ka-pi) produced in Samut Sakhon Province, Thailand. This strain grew optimally at 37-40 °C, pH 7.0 and in the presence of 8-16 % (w/v) NaCl. The 16S rRNA gene sequence similarity values between strain SSKP1-9^T and Lentibacillus juripiscarius TISTR 1535^T and Lentibacillus halophilus TISTR 1549^T were 98.7 and 97.2 %, respectively. Based on 16S rRNA gene sequence similarity, strain SSKP1-9^T represents a distinct novel species, as shown by phenotypic traits, DNA-DNA hybridization and average nucleotide identity values. In addition, the whole-cell protein profile confirmed the novelty of the taxon. The genomic DNA G+C content was 44.6 mol%. The major isoprenoid quinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. Polar lipid analysis revealed the presence of phosphatidylglycerol, diphosphatidylglycerol, four unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The major cellular fatty acids were anteiso-C_15 : 0, anteiso-C_17 : 0 and iso-C_16 : 0. The results of phenotypic and chemotaxonomic characteristics and whole-genome analysis support that strain SSKP1-9^T represents a novel species of Lentibacillus, for which the name Lentibacilluslipolyticus sp. nov. is proposed. The type strain is SSKP1-9^T (=JCM 32625^T=TISTR 2597^T).

Genome Sequence of the Moderately Halophilic Yellow Sea Bacterium Lentibacillus salicampi ATCC BAA-719 T

Lentibacillus salicampi SF-20^T (=ATCC BAA-719^T) was first isolated from a Yellow Sea salt field in Korea in 2002. Here, we report that the L. salicampi ATCC BAA-719^T genome sequence has a predicted length of 3,897,716 bp, containing 3,945 total genes and a CRISPR array, with a G+C content of 43.0%.

Lentibacillus salicampi SF-20^T (=ATCC BAA-719^T) was first isolated from a Yellow Sea salt field in Korea in 2002. Here, we report that the L. salicampi ATCC BAA-719^T genome sequence has a predicted length of 3,897,716 bp, containing 3,945 total genes and a CRISPR array, with a G+C content of 43.0%.

Acinetobacter larvae sp. nov., isolated from the larval gut of Omphisa fuscidentalis

A Gram-stain-negative, non-spore-forming, non-motile and aerobic coccobacilli-shaped strain, designated BRTC-1T, was isolated from the gut of Omphisa fuscidentalis Hampson, which is a larva of a moth and was collected from Xishuangbanna Dai Autonomous Prefecture in China. The isolate was found to grow at NaCl concentrations of 0-5 % (w/v) (optimum: 0 %), 10-45 °C (optimum: 30-35 °C) and pH 5.0-9.0 (optimum: pH 6.0) on tryptic soy agar. Analysis of the 16S rRNA gene sequence indicated that the isolate belonged to the genus Acinetobacter and was most closely related to Acinetobacter rudis LMG 26107T, Acinetobacter guillouiae LMG 988T and Acinetobacter bereziniae LMG 1003T with 96.4, 96.3 and 96.3 % sequence similarity, respectively. The comparative sequence analyses of the rpoB and gyrB genes showed that BRTC-1T is distant from the species of the genus Acinetobacter with validly published names (≤84.0 and ≤82.0 % similarity, respectively). The average nucleotide identity and digital DNA-DNA hybridization values (≤77.0 and ≤22.8 %, respectively) between the whole-genome sequence of BRTC-1T and those of the known taxa were far below the thresholds used to discriminate bacterial species. The major fatty acids were determined to be C16 : 0, C18 : 1ω9c and C16 : 1ω7c/iso-C15 : 0 2-OH. The respiratory quinone was Q-9. The polar lipids were found to be diphosphatidyglycerol, phosphatidylglycerol, phosphatidylethanolamine, five phospholipids and one phosphatidylcholine. Based on its phenotypic and chemotaxonomic characteristics from this study, the isolate is concluded to represent a novel species of the genus Acinetobacter, for which the name Acinetobacter larvae sp. nov. is proposed. The type strain is BRTC-1T (=ACCC 19936T=JCM 31367T).

Enzyme Annotation and Metabolic Reconstruction Using KEGG

KEGG is an integrated database resource for linking sequences to biological functions from molecular to higher levels. Knowledge on molecular functions is stored in the KO (KEGG Orthology) database, while cellular- and organism-level functions are represented in the PATHWAY and MODULE databases. Genes in the complete genomes, which are stored in the GENES database, are given KO identifiers by the internal annotation procedure, enabling reconstruction of KEGG pathways and modules for interpretation of higher-level functions. This is possible because all the KEGG pathways and modules are represented as networks of KO nodes. Here we present knowledge-based prediction methods for functional characterization of amino acid sequences using the KEGG resource. Specifically we show how the tools available at the KEGG website including BlastKOALA and KEGG Mapper can be utilized for enzyme annotation and metabolic reconstruction.