Comparative Genomic Insights into Pangenome Diversity and Functional Adaptation of Akkermansia and Faecalibacterium as Gut-Associated Next-Generation Probiotics: A Systematic Review

Complete genome sequence of Lacticaseibacillus rhamnosus B34-0-2 isolated from Panax ginseng in South Korea.

These genome data provide a genomic resource for future studies on functional characterization and probiotic-related properties and provide a genomic resource for future studies on functional characterization and probiotic-related properties.

Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum

This study reconstructed the first comprehensive pangenome of B. bifidum using 1,351 high-quality genomes, including metagenome-assembled genomes to identify species-specific genetic and functional features and identified significant gain-of-function events.

Automated pangenomic profiling of Pediococcus acidilactici genomes via Snakemake: uncovering genomic plasticity and specialized antimicrobial potential

Domestication reshapes the swine gut microbiome: metagenomic insights into taxonomic and functional divergence across wild and domestic populations

Background The gut microbiota constitutes a highly diverse, complex, and dynamically evolving ecosystem within the host. However, the domestication process may alter microbial community composition and function. Here, we investigate these shifts using metagenomic analysis. Methods Microbial diversity was evaluated using alpha and beta-diversity analysis. Furthermore, LEfSe and Functional analyses were employed to delineate significant disparities in microbial abundance and functional potential between wild boars (WB), Chinese domestic pigs (CDP), and Western domestic pigs (WDP). Results Our analysis revealed distinct microbial signatures across populations. WB exhibit greater diversity differentiation from WDP, while showing higher similarity to CDP. WB were significantly enriched in the genera Treponema, Oscillibacter, and Pseudoflavonifractor. In contrast, Chinese domestic breeds were characterized by Lactobacillus, Prevotella and Ruminococcus, while WDP retained high abundances of Alistipes, Bacteroides and Clostridium. Functionally, the wild boar microbiome showed significantly higher activity in pathways related to plant secondary metabolite degradation and nutrient biosynthesis. Conversely, domestic pig microbiomes showed significant enrichment in antimicrobial resistance genes and DNA damage repair pathways. Conclusions These findings indicate that domestication has influenced the swine gut microbiota, contributing to distinct compositional and functional divergences. Future research may explore the potential of reintroducing wild-derived probiotics to enhance domestic pig health.

Long-reads metagenomics reveals the effects of dulse supplementation on the poultry caecal bacteriome and its associated genetic repertoire

Introduction Dulse (Palmaria palmata) is a macroalgal feed ingredient rich in polysaccharides and bioactive compounds that offers a sustainable strategy to enhance animal health and productivity through modulation of gut microbiota. However, the impact of dulse supplementation on the taxonomic composition and genetic repertoire of the broiler chicken caecal microbiota remains poorly characterised. Methods We applied long-read shotgun metagenomic sequencing on 18 caecal samples collected from 27-day-old male Ross 308 broilers following a 7-day feeding trial with three dietary treatments — a reference diet, a soyabean meal-supplemented diet, and a diet supplemented with 30% dulse — to investigate the effects of dulse inclusion on microbial community composition, genetic diversity, and antimicrobial resistance (AMR) and virulence determinants. Results Across all dietary treatments, the Clostridia class predominated (71%), whereas primary fermenters (L. phocaeense), lactic acid bacteria (L. salivarius), and hydrogenotrophic cross-feeders (B. hydrogenotrophica) were enriched in the reference diet, dulse-supplemented and soyabean meal-supplemented groups, respectively (KW p < 0.05), contributing to potential improvements in caecal function, immune resilience, and nutrient utilisation while reducing pathogen load. The overall resistome profiles were comparable across dietary treatments and were dominated by genes conferring resistance to tetracyclines, lincosamides, and aminoglycosides. In contrast, the virulome displayed diet-associated shifts: Enterobacteriaceae were enriched in the dulse and reference diets relative to the soyabean meal diet, with an expanded functional repertoire of virulence-associated genes, particularly those involved in adhesion, iron acquisition, and secretion systems. Multidrug resistance genes, virulence determinants, and Col/IncF-type plasmid replicons were associated with E. coli reads, highlighting its potential resistance and virulence arsenal within the caecal microbiota. Discussion Our findings suggest that the benefits of dulse extend beyond its nutritional value, residing in its ability to foster ecosystem resilience; by promoting a diverse, niche-stabilised microbiota, dulse minimises the risk of opportunistic pathogen proliferation, supporting its use as a sustainable, functional feed ingredient.

Pangenome analysis of Nocardia brasiliensis reveals phylogenetic divergence, high genomic diversity and widespread distribution of biosynthetic gene clusters involved in secondary metabolite biosynthesis.

Significant genomic diversity and a wide distribution of biosynthetic clusters within the Nocardia brasiliensis pangenome are revealed, demonstrating its genomic plasticity and the variability in metabolic potential across strains.