Deciphering gut microbiome patterns from host preferences and microbial interactions in healthy Korean individuals.

Background: The gut microbiome is crucial for human health maintenance and disease development, yet limited understanding of its structure and maintenance hinders effective microbiome-based health improvement strategies. We investigated gut microbiome compositional patterns in healthy Koreans (n = 890), identifying six clusters (I-VI) with unique compositions and host preferences.

Results: Each cluster had a distinct topological structure within the microbial interaction network, underscoring its diverse roles in maintaining microbial communities.

Detection of Copy Number Variations in Woori-Heukdon Populations with the Illumina PorcineSNP60 Bead-Chip Array.

This study investigated copy number variations (CNVs) in 2112 pigs from five populations: Korean Duroc (DUC), Korean Native Pig (KNP), and their crossbred offspring (F, F, and WRH). CNVs were detected using PennCNV and QuantiSNP, with CNVRuler identifying 698 CNV regions (CNVRs), covering 109 Mb (4.83%) of the porcine genome.

Clade-specific extracellular vesicles from Akkermansia muciniphila mediate competitive colonization via direct inhibition and immune stimulation.

Akkermansia muciniphila, a promising candidate for next-generation probiotics, exhibits significant genomic diversity, classified into several distinct clades (AmI to AmIV). Notably, a single Akkermansia clade tends to predominate within individual hosts, with co-occurrence of different clades being rare. The mechanisms driving such clade-specific exclusion remain unclear.

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

The fecal microbiota of two healthy adults was cultivated in a medium containing commercial fructooligosaccharides [FOS; 1-kestose (GF), nystose (GF), and 1-fructofuranosylnystose (GF)]. Initially, the proportions of lactobacilli in the two feces samples were only 0.42% and 0.

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 (, , , , and ) within same metagenomic DNA samples through qRT-PCR assay in parallel.

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

Unlabelled: 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 . sp.

Effect of Supplementation on the Gut Microbial Composition of Healthy Korean Adults: A Single-Group Pilot Study.

is a type of meal-replacement product or dietary supplement comprising an uncooked and dried plant-based food mixture with various health-promoting properties, such as antidiabetic, anti-dyslipidemic, antioxidant, and anticancer properties. Although these properties are considered attributable to the various bioactive components absorbed through the intestine and its remolding effect on intestinal microorganisms, the effect of supplementation on gut microbiota profiles has not yet been studied. In this study, we investigated the effect of administration on the composition of gut microbiota.

Amelioration of Hepatic Steatosis in Mice through CBA7346-Mediated Regulation of High-Fat Diet-Induced Insulin Resistance and Lipogenesis.

Dietary habits and gut microbiota play an essential role in non-alcoholic fatty liver disease (NAFLD) and related factors such as insulin resistance and de novo lipogenesis. In this study, we investigated the protective effects of CBA7346, isolated from the gut of healthy Koreans, on mice with high-fat diet (HFD)-induced NAFLD. Administration of CBA7346 reduced body and liver weight gain, serum alanine aminotransferase and aspartate aminotransferase levels, liver steatosis, and liver triglyceride levels in mice on an HFD; the strain also decreased homeostatic model assessment for insulin resistance values, as well as serum cholesterol, triglyceride, lipopolysaccharide, leptin, and adiponectin levels in mice on an HFD.

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 effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology.

Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S).

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.

Beneficial Effects of Newly Isolated Strains from the Human Gut on Obesity and Metabolic Dysregulation.

The identification of new probiotics with anti-obesity properties has attracted considerable interest. In the present study, the anti-obesity activities of () strains isolated from human stool samples and their relationship with the gut microbiota were evaluated using a high fat-diet (HFD)-fed mice model. Three strains of were chosen from 27 isolates selected based on their anti-lipogenic activity in 3T3-L1 cells.

The presence of resistant starch-degrading amylases in Bifidobacterium adolescentis of the human gut.

Resistant starch (RS) is a complex prebiotic carbohydrate beneficial to the human gut. In the present study, four genes encoding for putative amylolytic enzymes, likely to be responsible for RS-degradation, were identified in the genome of Bifidobacterium adolescentis P2P3 by comparative genomic analysis. Our results showed that only three enzymes (RSD1, RSD2, and RSD3) exhibited non-gelatinized high amylose corn starch (HACS)-degrading activity in addition to typical α-amylase activity.

Complete genome sequence of P2P3, a human gut bacterium possessing strong resistant starch-degrading activity.

Resistant starch (RS) is an important food source from which gut bacteria produce short chain fatty acids, which have beneficial effects for human health. The P2P3, a human gut bacterium possessing a strong RS-degrading activity, was isolated from a healthy Korean adult male. In vitro experiments showed that this bacterium could utilize approximately 63% of high amylose corn starch after forming RS granule clusters.

Whole-genome resequencing analysis of 20 Micro-pigs.

Background: Miniature pigs have been increasingly used as mammalian model animals for biomedical research because of their similarity to human beings in terms of their metabolic features and proportional organ sizes. However, despite their importance, there is a severe lack of genome-wide studies on miniature pigs.

Objective: In this study, we performed whole-genome sequencing analysis of 20 Micro-pigs obtained from Medi Kinetics to elucidate their genomic characteristics.

Whole genome sequencing analysis of horse populations inhabiting the Korean Peninsula and Przewalski's horse.

Background: The Jeju horse is an indigenous horse breed in Korea. However, there is a severe lack of genomic studies on Korean horse breeds.

Objective: The objective of this study was to report genomic characteristics of domestic horse populations that inhabit South Korea (Jeju, Jeju crossbred, and Thoroughbred) and a wild horse breed (Przewalski's horse).

Complete genome sequence of acetate-producing L5-2 isolated from infant feces.

Acetate is an important metabolite in infants as it can affect metabolism as well as immune and inflammatory responses. However, there have been no studies on acetate production by isolated from infant feces. In this study, we isolated a strain, L5-2, from infant feces, and we found it produces acetate.

The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces.

High-quality and high-throughput sequencing technologies are required for therapeutic and diagnostic analyses of human gut microbiota. Here, we evaluated the advantages and disadvantages of the various commercial sequencing platforms for studying human gut microbiota. We generated fecal bacterial sequences from 170 Korean subjects using the GS FLX+ (V1-4), Illumina MiSeq (V1-3, V3-4 and V4), and PacBio (V1-9) systems.