The gut microbiota is closely related to good health; thus, there have been extensive efforts dedicated to improving health by controlling the gut microbial environment. Probiotics and prebiotics are being developed to support a healthier intestinal environment. However, much work remains to be performed to provide effective solutions to overcome individual differences in the gut microbial community. This study examined the importance of nutrients, other than dietary fiber, on the survival of gut bacteria in high-health-conscious populations. We found that vitamin B1, which is an essential nutrient for humans, had a significant effect on the survival and competition of bacteria in the symbiotic gut microbiota. In particular, sufficient dietary vitamin B1 intake affects the relative abundance of Ruminococcaceae, and these bacteria have proven to require dietary vitamin B1 because they lack the de novo vitamin B1 synthetic pathway. Moreover, we demonstrated that vitamin B1 is involved in the production of butyrate, along with the amount of acetate in the intestinal environment. We established the causality of possible associations and obtained mechanical insight, through in vivo murine experiments and in silico pathway analyses. These findings serve as a reference to support the development of methods to establish optimal intestinal environment conditions for healthy lifestyles.

Wolbachia is a ubiquitous endosymbiont in arthropods that is maternally transmitted and affects host reproduction in various ways. Among these, skewing the host sex ratio towards females, either by killing males (male killing) or producing exclusively functional females (feminization or parthenogenesis), is considered advantageous for Wolbachia . In the butterfly Eurema mandarina , individuals harbouring the Wolbachia strain w Fem exclusively produce female offspring. This occurs through a two-step mechanism in which Wolbachia blocks the transmission of the Z chromosome from Z0 females and feminizes the resultant Z0 offspring. Given the unique characteristics of w Fem, understanding its genomic features is crucial to uncover the evolution and mechanisms of Wolbachia -induced reproductive manipulation. However, technical challenges in isolating w Fem from co-infecting, closely related, non-male-killing/non-feminizing w CI Wolbachia strain have hindered genomic analyses of w Fem. In this study, we established a closed circular genome of w Fem by developing a series of Wolbachia purification, cell sorting and single-cell genome sequencing techniques. w Fem genome, ~1.3 Mb in size, specifically encodes male-killing gene homologues ( Em-oscar and wmk ) and other putative virulence factors that are absent in w CI. In addition, w Fem carried prophage elements that showed high similarity to previously characterized male-killing-associated prophages in Wolbachia strains. This study highlights the shared functional genomic features between feminizing and male-killing Wolbachia in Lepidoptera and suggests a mechanistic link between these two Wolbachia -induced reproductive phenotypes.

Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogues in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.

The productivity of soybean, a globally important agricultural crop, is strongly influenced by soil- and root-associated biotic interactions, including tho