• Journal of Species Research
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• v.10 no.2
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• pp.142-153
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• 2021

Algal genomics approaches provide a massive number of genome/transcriptome sequences and reveal the evolutionary history vis-à-vis primary and serial endosymbiosis events that contributed to the biodiversity of photosynthetic eukaryotes in the eukaryote tree of life. In particular, phylogenomic methods using several hundred or thousands of genes have provided new insights into algal taxonomy and systematics. Using this method, many novel insights into algal species diversity and systematics occurred, leading to taxonomic revisions. In addition, horizontal gene transfers (HGTs) of functional genes have been identified in algal genomes that played essential roles in environmental adaptation and genomic diversification. Finally, algal genomics data can be used to address the pangenome, including core genes shared among all isolates and partially shared strain-specific genes. However, some aspects of the pangenome concept (genome variability of intraspecies level) conflict with population genomics concepts, and the issue is closely related to defining species boundaries using genome variability. This review suggests a desirable future direction to merge algal pangenomics and population genomics beyond traditional molecular phylogeny and taxonomy.

• Microbiology and Biotechnology Letters
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• v.51 no.1
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• pp.128-131
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• 2023

Here we report the draft genome sequence of Weissella koreensis strain HJ and genomic analysis of its key features. The genome consists of 1,427,571 bp with a GC content of 35.5%, and comprises 1,376 coding genes. In silico analysis revealed the absence of pathogenic factors within the genome. The genome harbors several genes that play an important role in the survival of the gastrointestinal tract. In addition, a type III polyketide synthase cluster was identified. Pangenome analysis identified 68 unique genes in W. koreensis strain HJ. The genome information of this strain provides the basis for understanding its probiotic properties.

• Microbiology and Biotechnology Letters
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• v.51 no.4
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• pp.526-530
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• 2023

Here, we report the draft genome sequence of Latilactobacillus sakei subsp. sakei FBL10 isolated from Saeujeot (salted fermented shrimp). The draft genome consists of 2,285,672 bp with a G+C content of 41.1% and contains 2,282 coding genes. Genome analysis revealed that clusters associated with bacteriocin production were identified, in addition to several probiotic properties, such as stress resistance factors and aggregation. On the other hand, antibiotic resistance genes and virulence factors were not present. Pangenome analysis for 32 genomes showed 213 unique genes for FBL10 strain. These results demonstrate the beneficial properties of strain FBL10 as a putative probiotic.

• Journal of Microbiology and Biotechnology
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• v.31 no.2
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• pp.280-289
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• 2021

Genetic markers currently used for the discrimination of Lactobacillus delbrueckii subspecies have low efficiency for identification at subspecies level. Therefore, our objective in this study was to select novel genetic markers for accurate identification and discrimination of six L. delbrueckii subspecies based on pangenome analysis. We evaluated L. delbrueckii genomes to avoid making incorrect conclusions in the process of selecting genetic markers due to mislabeled genomes. Genome analysis showed that two genomes of L. delbrueckii subspecies deposited at NCBI were misidentified. Based on these results, subspecies-specific genetic markers were selected by comparing the core and pangenomes. Genetic markers were confirmed to be specific for 59,196,562 genome sequences via in silico analysis. They were found in all strains of the same subspecies, but not in other subspecies or bacterial strains. These genetic markers also could be used to accurately identify genomes at the subspecies level for genomes known at the species level. A real-time PCR method for detecting three main subspecies (L. delbrueckii subsp. delbrueckii, lactis, and bulgaricus) was developed to cost-effectively identify them using genetic markers. Results showed 100% specificity for each subspecies. These genetic markers could differentiate each subspecies from 44 other lactic acid bacteria. This real-time PCR method was then applied to monitor 26 probiotics and dairy products. It was also used to identify 64 unknown strains isolated from raw milk samples and dairy products. Results confirmed that unknown isolates and subspecies contained in the product could be accurately identified using this real-time PCR method.

• Journal of Microbiology and Biotechnology
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• v.29 no.5
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• pp.794-808
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• 2019

Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.

• Journal of Microbiology and Biotechnology
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• v.33 no.11
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• pp.1428-1436
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• 2023

The three Gram-negative, catalase- and oxidase-positive bacterial strains RS43^T, HBC28, and HBC61^T, were isolated from fresh water and subjected to a polyphasic study. Comparison of 16S rRNA gene sequence initially indicated that strains RS43^T, HBC28, and HBC61^T were closely related to species of genus Curvibacter and shared the highest sequence similarity of 98.14%, 98.21%, and 98.76%, respectively, with Curvibacter gracilis 7-1^T. Phylogenetic analysis based on genome sequences placed all strains within the genus Curvibacter. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the three strains and related type strains supported their recognition as two novel genospecies in the genus Curvibacter. Comparative genomic analysis revealed that the genus possessed an open pangenome. Based on KEGG BlastKOALA analyses, Curvibacter species have the potential to metabolize benzoate, phenylacetate, catechol, and salicylate, indicating their potential use in the elimination of these compounds from the water systems. The results of polyphasic characterization indicated that strain RS43^T and HBC61^T represent two novel species, for which the name Curvibacter microcysteis sp. nov. (type strain RS43^T =KCTC 92793^T=LMG 32714^T) and Curvibacter cyanobacteriorum sp. nov. (type strain HBC61^T =KCTC 92794^T=LMG 32713^T) are proposed.