Shinichi Sunagawa

The paper identifies genomically discrete and ecologically cohesive subspecies in the global ocean microbiome, showing they are biologically meaningful units driven by environmental factors.

The paper introduces the Ocean Microbiomics Database (OMDB) to analyze microbial thermal niches and predict their response to ocean warming, showing richness declines faster than abundance.

The paper develops a high-resolution mass spectrometry method to quantify nitrogen-containing compounds across diverse systems, revealing microbiome impacts on nitrogen distribution in mice.

The paper catalogs diazotroph genomes and analyzes their distribution across environments, identifying freshwater and sedimentary ecosystems as key nitrogen-fixation reservoirs.

The paper develops a mathematical framework to predict microbial community assembly using monoculture growth kinetics and inferred species interactions, revealing biphasic community development driven by competition and cross-feeding.

The paper identifies a diverse microbial reservoir in the ultrasmall ocean fraction, including nitrogen-fixing diazotrophs, with implications for global biogeochemical cycles.

The paper demonstrates that satellite DNA barcodes facilitate meiotic pairing in Drosophila by showing that repeat mismatches disrupt pairing and that pairing defects correlate with oocyte death.

The paper examines latitudinal diversity gradients in the ocean microbiome, finding they are not universal but vary by taxa and environmental factors.

The paper characterizes the eukaryotic diversity in coral reef environments, revealing high diversity and identifying environmental drivers shaping these communities.

The paper identifies conserved bacterial genes responsible for thallusin biosynthesis, a morphogen that influences algal development across marine and terrestrial environments.

This study assesses the microbial biosynthetic potential of reef-building corals using genome-resolved metagenomics, revealing host-specific microbiomes with high biotechnological value.

The paper develops CRISPR-PAMdb and CICERO to uncover PAM diversity in Cas9 proteins, enabling better CRISPR tool design.

This study shows that algal glycine betaine stimulates bacterial cobalamin production, creating a feedback loop that influences marine microbial interactions and productivity.

The paper uses multimutant Salmonella strains to identify SPI-2 effector functions in gut inflammation and systemic colonization, finding SopD2 and GtgE critical for mucosal pathology.

The paper shows that the gfr operon in Salmonella Typhimurium provides a fitness advantage during gut colonization by utilizing dietary Amadori compounds like fructoselysine.

The paper introduces a transcriptomic marker gene-based classifier to predict bacterial growth states across species in microbial communities.

The paper introduces the JEDI marker as a universal biodiversity measure, demonstrating its applicability across ecological scales and providing an automated bioinformatic workflow for standardized analysis.

The paper maps E. coli capsule serotypes using genomic data, identifies novel K-types, and develops an in silico serotyping tool applicable to diverse E. coli genomes.

The paper develops a target capture sequencing method to detect low-abundance chemoreceptor genes in diverse environments, revealing novel microbial chemosensory biodiversity.

This study analyzes diatom diversity and abundance in the global ocean using Tara Oceans data, identifying key environmental drivers and community patterns.

The paper introduces a biochemical method to detect and analyze capsular polysaccharides in bacteria, improving upon traditional serotyping assays.

The paper examines environmental controls on dark CO2 fixation pathways in estuarine wetlands using multi-omics approaches, finding that different pathways are favored under varying environmental conditions.

The paper examines microbial lifestyles on suspended and sinking particles in the Elbe estuary, finding distinct gene expression patterns linked to carbon cycling and methane production.

The paper discovers a new group of DNA viruses, egoviruses, found in the digestive systems of humans and animals, closely related to poxviruses and suggesting an evolutionary link between gut-infecting viruses and animal pathogens.

mBARq simplifies the analysis of DNA barcode data from transposon libraries and isogenic strains through a user-friendly tool and web app integration.

This study investigates the seasonal dynamics of aerobic anoxygenic phototrophic bacteria in a freshwater lake, revealing their role in organic matter recycling and ecological dynamics.

The paper analyzes genetic divergence in three coral species across a Pacific environmental gradient, showing species-specific evolutionary patterns despite similar environments.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

This study shows that rearing environment significantly affects the phenotype of genetically identical mice, influencing gut microbiota, body weight, behavior, and epigenetic patterns.

The paper introduces mOTUs3, a tool for reference genome-independent taxonomic profiling of metagenomes, improving accuracy and coverage for underexplored microbiomes.