Lacticaseibacillus paracasei completely utilizes fructooligosacchrides in the human gut through ß-fructosidase (FosE).

The fecal microbiota of two healthy adults was cultivated in a medium containing commercial fructooligosaccharides [FOS; 1-kestose (GF2), nystose (GF3), and 1F-fructofuranosylnystose (GF4)]. Initially, the proportions of lactobacilli in the two feces samples were only 0.42% and 0.17%; however, they significantly increased to 7.2% and 4.8%, respectively, after cultivation on FOS. Most FOS-utilizing isolates could utilize only GF2; however, Lacticaseibacillus paracasei strain Lp02 could fully consume GF3 and GF4 too. The FOS operon (fosRABCDXE) was present in Lc. paracasei Lp02 and another Lc. paracasei strain, KCTC 3510T, but fosE was only partially present in the non-FOS-degrading strain KCTC 3510T. In addition, the top six upregulated genes in the presence of FOS were fosABCDXE, particularly fosE. FosE is a ß-fructosidase that hydrolyzes both sucrose and all three FOS. Finally, a genome-based analysis suggested that fosE is mainly observed in Lc. paracasei, and only 13.5% (61/452) of their reported genomes were confirmed to include it. In conclusion, FosE allows the utilization of FOS, including GF3 and GF4 as well as GF2, by some Lc. paracasei strains, suggesting that this species plays a pivotal role in FOS utilization in the human gut.

Bacteroides faecium sp. nov. isolated from human faeces.

A novel bacterial strain, CBA7301T, was isolated from human faeces and was characterised using a polyphasic taxonomic approach. A phylogenetic analysis based on 16S rRNA gene sequences revealed that CBA7301T represented a member of the genus Bacteroides, in the family Bacteroidaceae. The similarity between the 16S rRNA gene sequence of CBA7301T and that of its most closely related species, Bacteroides faecichinchillae JCM 17102T, was 96.2 %, and the average nucleotide identity between these two strains was 77.9 %. The genome size was 6 782 182 bp, and the DNA G+C content was 42.5 mol%. Cells of CBA7301T were Gram-stain-negative, strictly anaerobic and rod-shaped. The optimal growth of this organism occurred at 30-35 °C, pH 7.0 and 0.5 % (w/v) NaCl. The respiratory quinone was menaquinone 10. The predominant polar lipids were phosphatidylethanolamine, phospholipids and aminophospholipids. The major cellular fatty acid was anteiso-C15 : 0. According to the results of the polyphasic taxonomic analysis, CBA7301T represents a novel species of the genus Bacteroides, which we named Bacteroides faecium sp. nov. The type strain is CBA7301T (=KCCM 43355T=ATCC TSD-227T).

Genome analysis of 1-deoxynojirimycin (1-DNJ)-producing Bacillus velezensis K26 and distribution of Bacillus sp. harboring a 1-DNJ biosynthetic gene cluster.

1-Deoxynojirumycin (1-DNJ) is a representative iminosugar with α-glucosidase inhibition (AGI) activity. In this study, the full genome sequencing of 1-DNJ-producing Bacillus velezensis K26 was performed. The genome consists of a circular chromosome (4,047,350 bps) with two types of putative virulence factors, five antibiotic resistance genes, and seven secondary metabolite biosynthetic gene clusters. Genomic analysis of a wide range of Bacillus species revealed that a 1-DNJ biosynthetic gene cluster was commonly present in four Bacillus species (B. velezensis, B. pseudomycoides, B. amyloliquefaciens, and B. atrophaeus). In vitro experiments revealed that the increased mRNA expression levels of the three 1-DNJ biosynthetic genes were closely related to increased AGI activity. Genomic comparison and alignment of multiple gene sequences indicated the conservation of the 1-DNJ biosynthetic gene cluster in each Bacillus species. This genomic analysis of Bacillus species having a 1-DNJ biosynthetic gene cluster could provide a basis for further research on 1-DNJ-producing bacteria.

Genome Analysis of Enterococcus mundtii Pe103, a Human Gut-Originated Pectinolytic Bacterium.

Pectin exists in significant amounts in vegetables and fruits as a component of the plant cell wall. In human diet, pectin is not degraded by the human digestive enzymes due to its complex structure; only gut bacteria degrade pectin in the large intestine. To date, although pectin is one of the most important sources of dietary fiber in human diet, there have been only few reports on human gut-originated pectinolytic bacteria. In this study, the strain Enterococcus mundtii Pe103, a bacterium with pectin-degrading activity, was isolated from the feces of a healthy Korean adult female. Culture experiments revealed that it could grow on pectin as the sole carbon source by degrading pectin to approximately 35% within 13 h. We report the complete genome data of human gut E. mundtii Pe103. It consists of a circular chromosome (3,084,146 bps) and two plasmids (63,713 and 56,223 bps). Genomic analysis suggested that at least nine putative enzymes related to pectin degradation are present in E. mundtii Pe103. These enzymes may be involved in the degradation of pectin. The whole genome information of E. mundtii Pe103 could improve the understanding of the mechanism underlying the degradation of pectin by human gut microbiota.

Elucidating the triplicated ancestral genome structure of radish based on chromosome-level comparison with the Brassica genomes.

KEYMESSAGE: This study presents a chromosome-scale draft genome sequence of radish that is assembled into nine chromosomal pseudomolecules. A comprehensive comparative genome analysis with the Brassica genomes provides genomic evidences on the evolution of the mesohexaploid radish genome. Radish (Raphanus sativus L.) is an agronomically important root vegetable crop and its origin and phylogenetic position in the tribe Brassiceae is controversial. Here we present a comprehensive analysis of the radish genome based on the chromosome sequences of R. sativus cv. WK10039. The radish genome was sequenced and assembled into 426.2 Mb spanning >98 % of the gene space, of which 344.0 Mb were integrated into nine chromosome pseudomolecules. Approximately 36 % of the genome was repetitive sequences and 46,514 protein-coding genes were predicted and annotated. Comparative mapping of the tPCK-like ancestral genome revealed that the radish genome has intermediate characteristics between the Brassica A/C and B genomes in the triplicated segments, suggesting an internal origin from the genus Brassica. The evolutionary characteristics shared between radish and other Brassica species provided genomic evidences that the current form of nine chromosomes in radish was rearranged from the chromosomes of hexaploid progenitor. Overall, this study provides a chromosome-scale draft genome sequence of radish as well as novel insight into evolution of the mesohexaploid genomes in the tribe Brassiceae.

A genome-wide scan for signatures of directional selection in domesticated pigs.

BACKGROUND: Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. RESULTS: Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an F ST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness. CONCLUSIONS: We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs.

Construction of a reference genetic map of Raphanus sativus based on genotyping by whole-genome resequencing.

KEY MESSAGE: This manuscript provides a genetic map of Raphanus sativus that has been used as a reference genetic map for an ongoing genome sequencing project. The map was constructed based on genotyping by whole-genome resequencing of mapping parents and F 2 population. Raphanus sativus is an annual vegetable crop species of the Brassicaceae family and is one of the key plants in the seed industry, especially in East Asia. Assessment of the R. sativus genome provides fundamental resources for crop improvement as well as the study of crop genome structure and evolution. With the goal of anchoring genome sequence assemblies of R. sativus cv. WK10039 whose genome has been sequenced onto the chromosomes, we developed a reference genetic map based on genotyping of two parents (maternal WK10039 and paternal WK10024) and 93 individuals of the F2 mapping population by whole-genome resequencing. To develop high-confidence genetic markers, ~83 Gb of parental lines and ~591 Gb of mapping population data were generated as Illumina 100 bp paired-end reads. High stringent sequence analysis of the reads mapped to the 344 Mb of genome sequence scaffolds identified a total of 16,282 SNPs and 150 PCR-based markers. Using a subset of the markers, a high-density genetic map was constructed from the analysis of 2,637 markers spanning 1,538 cM with 1,000 unique framework loci. The genetic markers integrated 295 Mb of genome sequences to the cytogenetically defined chromosome arms. Comparative analysis of the chromosome-anchored sequences with Arabidopsis thaliana and Brassica rapa revealed that the R. sativus genome has evident triplicated sub-genome blocks and the structure of gene space is highly similar to that of B. rapa. The genetic map developed in this study will serve as fundamental genomic resources for the study of R. sativus.

Construction of a genetic map based on high-throughput SNP genotyping and genetic mapping of a TuMV resistance locus in Brassica rapa.

Brassica rapa is a member of the Brassicaceae family and includes vegetables and oil crops that are cultivated worldwide. The introduction of durable resistance against turnip mosaic virus (TuMV) into agronomically important cultivars has been a significant challenge for genetic and horticultural breeding studies of B. rapa. Based on our previous genome-wide analysis of DNA polymorphisms between the TuMV-resistant doubled haploid (DH) line VC40 and the TuMV-susceptible DH line SR5, we constructed a core genetic map of the VCS-13M DH population, which is composed of 83 individuals derived from microspore cultures of a F1 cross between VC40 and SR5, by analyzing the segregation of 314 sequence-characterized genetic markers. The genetic markers correspond to 221 SNPs and 31 InDels of genes as well as 62 SSRs, covering 1,115.9 cM with an average distance of 3.6 cM between the adjacent marker loci. The alignment and orientation of the constructed map showed good agreement with the draft genome sequence of Chiifu, thus providing an efficient strategy to map genic sequences. Using the genetic map, a novel dominant TuMV resistance locus (TuMV-R) in the VCS-13M DH population was identified as a 0.34 Mb region in the short arm of chromosome A6 in which four CC-NBS-LRR resistance genes and two pathogenesis-related-1 genes reside. The genetic map developed in this study can play an important role in the genetic study of TuMV resistance and the molecular breeding of B. rapa.

Comparative analysis of the radish genome based on a conserved ortholog set (COS) of Brassica.

KEY MESSAGE: This manuscript provides a Brassica conserved ortholog set (COS) that can be used as diagnostic cross-species markers as well as tools for genetic mapping and genome comparison of the Brassicaceae. A conserved ortholog set (COS) is a collection of genes that are conserved in both sequence and copy number between closely related genomes. COS is a useful resource for developing gene-based markers and is suitable for comparative genome mapping. We developed a COS for Brassica based on proteome comparisons of Arabidopsis thaliana, B. rapa, and B. oleracea to establish a basis for comparative genome analysis of crop species in the Brassicaceae. A total of 1,194 conserved orthologous single-copy genes were identified from the genomes based on whole-genome BLASTP analysis. Gene ontology analysis showed that most of them encoded proteins with unknown function and chloroplast-related genes were enriched. In addition, 152 Brassica COS primer sets were applied to 16 crop and wild species of the Brassicaceae and 57.9-92.8 % of them were successfully amplified across the species representing that a Brassica COS can be used as diagnostic cross-species markers of diverse Brassica species. We constructed a genetic map of Raphanus sativus by analyzing the segregation of 322 COS genes in an F2 population (93 individuals) of Korean cultivars (WK10039 × WK10024). Comparative genome analysis based on the COS genes showed conserved genome structures between R. sativus and B. rapa with lineage-specific rearrangement and fractionation of triplicated subgenome blocks indicating close evolutionary relationship and differentiation of the genomes. The Brassica COS developed in this study will play an important role in genetic, genomic, and breeding studies of crop Brassicaceae species.

Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity.

BACKGROUND: Hanwoo (Korean cattle), which originated from natural crossbreeding between taurine and zebu cattle, migrated to the Korean peninsula through North China. Hanwoo were raised as draft animals until the 1970s without the introduction of foreign germplasm. Since 1979, Hanwoo has been bred as beef cattle. Genetic variation was analyzed by whole-genome deep resequencing of a Hanwoo bull. The Hanwoo genome was compared to that of two other breeds, Black Angus and Holstein, and genes within regions of homozygosity were investigated to elucidate the genetic and genomic characteristics of Hanwoo. RESULTS: The Hanwoo bull genome was sequenced to 45.6-fold coverage using the ABI SOLiD system. In total, 4.7 million single-nucleotide polymorphisms and 0.4 million small indels were identified by comparison with the Btau4.0 reference assembly. Of the total number of SNPs and indels, 58% and 87%, respectively, were novel. The overall genotype concordance between the SNPs and BovineSNP50 BeadChip data was 96.4%. Of 1.6 million genetic differences in Hanwoo, approximately 25,000 non-synonymous SNPs, splice-site variants, and coding indels (NS/SS/Is) were detected in 8,360 genes. Among 1,045 genes containing reliable specific NS/SS/Is in Hanwoo, 109 genes contained more than one novel damaging NS/SS/I. Of the genes containing NS/SS/Is, 610 genes were assigned as trait-associated genes. Moreover, 16, 78, and 51 regions of homozygosity (ROHs) were detected in Hanwoo, Black Angus, and Holstein, respectively. 'Regulation of actin filament length' was revealed as a significant gene ontology term and 25 trait-associated genes for meat quality and disease resistance were found in 753 genes that resided in the ROHs of Hanwoo. In Hanwoo, 43 genes were located in common ROHs between whole-genome resequencing and SNP chips in BTA2, 10, and 13 coincided with quantitative trait loci for meat fat traits. In addition, the common ROHs in BTA2 and 16 were in agreement between Hanwoo and Black Angus. CONCLUSIONS: We identified 4.7 million SNPs and 0.4 million small indels by whole-genome resequencing of a Hanwoo bull. Approximately 25,000 non-synonymous SNPs, splice-site variants, and coding indels (NS/SS/Is) were detected in 8,360 genes. Additionally, we found 25 trait-associated genes for meat quality and disease resistance among 753 genes that resided in the ROHs of Hanwoo. These findings will provide useful genomic information for identifying genes or casual mutations associated with economically important traits in cattle.

Analysis of the canine brain transcriptome with an emphasis on the hypothalamus and cerebral cortex.

The diversity of dog breeds make the domestic dog a valuable model for identifying genes responsible for many phenotypic and behavioral traits. The brain, in particular, is a region of interest for the analysis of molecular changes that are involved in dog-specific behavioral phenotypes. However, such studies are handicapped due to incomplete annotation of the dog genome. We present a high-coverage transcriptome of the dog brain using RNA-Seq. Two areas of the brain, hypothalamus and cerebral cortex, were selected for their roles in cognition, emotion, and neuroendocrine functions. We detected many novel features of the dog transcriptome, including 13,799 novel exons, 51,357 exons with unique 5' or 3' modifications, and many novel alternative splicing events. We provide some examples of novel features in genes that are related to domestication, including ADCY8, SMOC2, and PRNP. We also found 247 novel protein-coding genes and 328 noncoding RNAs, including 57 long noncoding RNAs that represent the first empirical evidence for a large fraction of noncoding RNAs in the dog. In addition, we analyze both gene expression and alternative splicing differences between the hypothalamus and cerebral cortex and find that there is very little overlap between genes that are differentially alternatively spliced and genes that are differentially expressed. We thereby suggest that researchers who want to pinpoint the genetic causes for dog breed-specific traits and diseases should not confine their studies to gene expression alone, but should consider other factors such as alternative splicing and changes in untranslated regions.

Dynamic genetic features of chromosomes revealed by comparison of soybean genetic and sequence-based physical maps.

Despite the intensive soybean [Glycine max (L.) Merrill] genome studies, the high chromosome number (20) of the soybean plant relative to many other major crops has hindered the development of a high-resolution genomewide genetic map derived from a single population. Here, we report such a map, which was constructed in an F15 population derived from a cross between G. max and G. soja lines using indel polymorphisms detected via a G. soja genome resequencing. By targeting novel indel markers to marker-poor regions, all marker intervals were reduced to under 6 cM on a genome scale. Comparison of the Williams 82 soybean reference genome sequence and our genetic map indicated that marker orders of 26 regions were discrepant with each other. In addition, our comparison showed seven misplaced and two absent markers in the current Williams 82 assembly and six markers placed on the scaffolds that were not incorporated into the pseudomolecules. Then, we showed that, by determining the missing sequences located at the presumed beginning points of the five major discordant segments, these observed discordant regions are mostly errors in the Williams 82 assembly. Distributions of the recombination rates along the chromosomes were similar to those of other organisms. Genotyping of indel markers and genome resequencing of the two parental lines suggested that some marker-poor chromosomal regions may represent introgression regions, which appear to be prevalent in soybean. Given the even and dense distribution of markers, our genetic map can serve as a bridge between genomics research and breeding programs.

Draft genome sequence of Staphylococcus vitulinus F1028, a strain isolated from a block of fermented soybean.

Staphylococcus vitulinus is a coagulase-negative staphylococcus in the family Staphylococcaceae. This report describes the draft genome sequence of S. vitulinus F1028, which was isolated from a traditional Korean soybean food (meju). This 2.56-Mbp genome sequence is the first S. vitulinus genome of a strain isolated from a fermented soybean product.

Genome sequence of Staphylococcus lentus F1142, a strain isolated from Korean soybean paste.

This report describes the draft genome sequence of Staphylococcus lentus F1142, which was isolated from a Korean fermented soybean paste (doenjang). The draft genome sequence contained 2.79 Mbp with a G+C content of 31.8%; this is the first S. lentus genome to be reported.

Human gut commensal bacterium Ruminococcus species FMB-CY1 completely degrades the granules of resistant starch.

Resistant starch (RS) in the diet reaches the large intestine and is fermented by the gut microbiota, providing beneficial effects on human health. The human gut bacterium FMB-CY1 was isolated and identified as a new species closest to Ruminococcus bromii. Ruminococcus sp. FMB-CY1 completely degraded RS including commercial RS types 2, 3, and 4, and generated glucose and maltose; however, it did not assimilate glucose. Genome analysis revealed 15 amylolytic enzymes (Amy) present in FMB-CY1. The evolutionary trees revealed that the Amys were well divided each other. All Amys (4, 9, 10, 12, and 16) containing cohesin and/or dockerin and scaffolding proteins known to be involved in constituting the amylosome, were identified. A new species of Ruminococcus, strain FMB-CY1, was considered to have the ability to form amylosomes for the degradation of RS. This new RS-degrading Ruminococcus species provides insights into the mechanism(s) underlying RS degradation in the human gut. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-021-01027-2.

Brachybacterium kimchii sp. nov. and Brachybacterium halotolerans subsp. kimchii subsp. nov., isolated from the Korean fermented vegetables, kimchi, and description of Brachybacterium halotolerans subsp. halotolerans subsp. nov.

Two Gram-stain-positive, oxidase-negative, catalase-positive, and coccus-shaped bacterial strains, designated CBA3104T and CBA3105T, were isolated from kimchi. Strain CBA3104T and CBA3105T grew at 10-35°C (optimum, 25°C and 30°C, respectively), at pH 6.0-8.5 (optimum, pH 6.5), and in the presence of 0-15% (w/v) NaCl (optimum, 5%). A phylogenetic analysis based on 16S rRNA gene sequences revealed that strain CBA3104T formed a distinct phylogenetic lineage within the genus Brachybacterium whereas strain CBA3105T was closely positioned with Brachybacterium halotolerans MASK1Z-5T. The 16S rRNA gene sequence similarity between strains CBA3104T and CBA3105T was 99.9%, but ANI and dDDH values between strains CBA3104T and CBA3105T were 93.61% and 51.5%, respectively. Strain CBA3104T showed lower ANI and dDDH values than species delineation against three closely related strains and type species of the genus Brachybacterium, however, strain CBA3105T showed 96.63% ANI value and 69.6% dDDH value with Brachybacterium halotolerans MASK1Z-5T. Among biochemical analysis results, strain CBA3104T could uniquely utilize bromo-succinic acid whereas only strain CBA3105T was positive for alkaline phosphatase and α-fucosidase among two novel strains, closely related strains, and type species of the genus Brachybacterium. Compared with strain CBA3105T and Brachybacterium halotolerans JCM 34339T, strain CBA3105T was differentially positive for acid production of D-arabinose, D-adonitol, and potassium 5-ketogluconate and enzyme activity of ß-glucuronidase. Both strains contained menaquinone-7 as the dominant quinone. The cell-wall peptidoglycan of two novel strains contained meso-diaminopimelic acid. The major fatty acids of strains CBA3104T and CBA3105T were anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The major polar lipids of both strains were phosphatidylglycerol and diphosphatidylglycerol. Strain CBA3104T possessed a uniquely higher abundance of tRNA (97 tRNAs) than four Brachybacterium strains used for comparative taxonomic analysis (54-62 tRNAs). Both the CBA3104T and CBA3105T strain harbored various oxidoreductase, transferase, hydrolase, and lyase as strain-specific functional genes compared to closely related strains and Brachybacterium type species. The results of biochemical/physiological, chemotaxonomic, and genomic analyses demonstrated that strains CBA3104T and CBA3105T represent a novel species of the genus Brachybacterium and a novel subspecies of B. halotolerans, respectively, for which the names Brachybacterium kimchii sp. nov. and B. halotolerans subsp. kimchii subsp. nov. are proposed. The type strains of the novel species and the novel subspecies are CBA3104T (= KCCM 43417T = JCM 34759T) and CBA3105T (= KCCM 43418T =JCM 34760T), respectively.

Genome-Wide Assessment of a Korean Composite Pig Breed, Woori-Heukdon.

A Korean synthetic pig breed, Woori-Heukdon (WRH; F3), was developed by crossing parental breeds (Korean native pig [KNP] and Korean Duroc [DUC]) with their crossbred populations (F1 and F2). This study in genome-wide assessed a total of 2,074 pigs which include the crossbred and the parental populations using the Illumina PorcineSNP60 BeadChip. After quality control of the initial datasets, we performed population structure, genetic diversity, and runs of homozygosity (ROH) analyses. Population structure analyses showed that crossbred populations were genetically influenced by the parental breeds according to their generation stage in the crossbreeding scheme. Moreover, principal component analysis showed the dispersed cluster of WRH, which might reflect introducing a new breeding group into the previous one. Expected heterozygosity values, which were used to assess genetic diversity, were .365, .349, .336, .330, and .211 for WRH, F2, F1, DUC, and KNP, respectively. The inbreeding coefficient based on ROH was the highest in KNP (.409), followed by WRH (.186), DUC (.178), F2 (.107), and F1 (.035). Moreover, the frequency of short ROH decreased according to the crossing stage (from F1 to WRH). Alternatively, the frequency of medium and long ROH increased, which indicated recent inbreeding in F2 and WRH. Furthermore, gene annotation of the ROH islands in WRH that might be inherited from their parental breeds revealed several interesting candidate genes that may be associated with adaptation, meat quality, production, and reproduction traits in pigs.

A qRT-PCR Method Capable of Quantifying Specific Microorganisms Compared to NGS-Based Metagenome Profiling Data.

Metagenome profiling research using next-generation sequencing (NGS), a technique widely used to analyze the diversity and composition of microorganisms living in the human body, especially the gastrointestinal tract, has been actively conducted, and there is a growing interest in the quantitative and diagnostic technology for specific microorganisms. According to recent trends, quantitative real-time PCR (qRT-PCR) is still a considerable technique in detecting and quantifying bacteria associated with the human oral and nasal cavities, due to the analytical cost and time burden of NGS technology. Here, based on NGS metagenome profiling data produced by utilizing 100 gut microbiota samples, we conducted a comparative analysis for the identification and quantification of five bacterial genera (Akkermansia, Bacteroides, Bifidobacterium, Phascolarctobacterium, and Roseburia) within same metagenomic DNA samples through qRT-PCR assay in parallel. Genus-specific primers, targeting the particular gene of each genus for qRT-PCR assay, allowed a statistically consistent quantification pattern with the metagenome profiling data. Furthermore, results of bacterial identification through Sanger validation demonstrated the high genus-specificity of each primer set. Therefore, our study suggests that an approach to quantifying specific microorganisms by applying the qRT-PCR method can compensate for the concerns (potential issues) of NGS while also providing efficient benefits to various microbial industries.

Draft genome sequence of the Paenibacillus polymyxa type strain (ATCC 842T), a plant growth-promoting bacterium.

Paenibacillus polymyxa is an endospore-forming Gram-positive soil bacterium that is well-known for its ability to promote plant growth. Here we report the draft genome sequence of P. polymyxa ATCC 842(T), the type strain of the species P. polymyxa, and the family Paenibacillaceae. The P. polymyxa genome contains a repertoire of biosynthetic genes for antibiotics and hydrolytic enzymes that account for its beneficial effects in the rhizosphere to the host plants it associates with.

Gut Microbiome Structure and Association with Host Factors in a Korean Population.

Characterizing the gut microbiome in the healthy population is the first step in elucidating its associations with host health conditions. Populations with different diet patterns, lifestyles, and genetic backgrounds harbor different gut microbes. In this study, we characterized the gut microbiome of 890 healthy Koreans using 16S rRNA sequencing. The Korean population harbored a relatively large fraction of the Prevotella enterotype and presented a distinctive gut microbiome, compared to that in the populations of other countries. Additionally, we determined the clusters of cooccurring microbes that were quantitatively correlated with each other. We found that microbe composition of the gut was strongly associated with age. We identified that the abundance of members of Bacteroidia and Clostridia differed with the host dietary patterns, body mass index, and stool frequency. The gut microbiome data obtained in this study would be an important resource for future studies addressing microbial contributions in health and disease. IMPORTANCE Comparing the gut microbiomes of healthy controls and disease patients showed that the composition of the gut microbiome is associated with various host health conditions. The gut microbiome in healthy Western populations is well characterized, while that of non-Western populations, with different diet patterns, lifestyles, and genetic backgrounds, is not clearly defined. In this study, we characterized the microbiome of 890 healthy Korean individuals using 16S rRNA sequencing and found that Koreans have a gut microbiome different from that in the individuals of neighboring countries. The members of Bacteroidetes and Firmicutes cooccurred and were quantitatively associated with each other. Additionally, we found that the gut microbial composition is strongly associated with the host's age. The microbiome data presented here represent the gut microbiome of a healthy Korean population and could be used to unveil gut microbiome-associated host conditions in this population.