Published papers

We characterized the N-glycosylation profiles of anhydrobiotic tardigrades, Ramazzottius varieornatus and Hypsibius exemplaris, identifying high-mannose, paucimannose, and complex-type oligosaccharides, while hybrid-type glycans were undetectable. Notably, paucimannose-type oligosaccharides accounted for 39% of the N-glycans in R. varieornatus and 17% in H. exemplaris, with a substantial proportion of them exhibiting fucosylation of the innermost GlcNAc via an α1,6-linkage. This core fucosylation pattern, common to all animals, was observed alongside a distinctive glycosylation signature prominently observed in tardigrades: complex-type glycans lacking galactosylation but containing α1,3-fucosylated GlcNAc at non-reducing termini. This structure was more prevalent in H. exemplaris, with 22 out of 87 identified glycoproteins expressing the Fucα1,3-GlcNAc motif, including eight induced during anhydrobiosis. Key glycoproteins such as Cu/Zn-superoxide dismutase and papilin, implicated in oxidative stress protection and extracellular matrix remodeling, were among those modified. Comparative analyses reveal that non-reducing terminal α1,3-fucosylation in tardigrades is distinct from the mammalian Lewis X antigen and similar structures found in invertebrates, suggesting a unique substrate specificity of fucosyltransferases in these species. Genomic analysis identified homologs of FUT9 and FucTC, indicating potential candidates responsible for this glycosylation pattern. Our findings provide new insights into the molecular mechanisms of glycosylation in tardigrades and their relevance to their extreme stress tolerance.

Spider silk is a natural fiber with remarkable strength, toughness, and elasticity that is attracting attention as a biomaterial of the future. Golden orb-weaving spiders (Trichonephila clavata) construct large, strong webs using golden threads. To characterize the pigment of golden T. clavata dragline silk, we used liquid chromatography and mass spectrometric analysis. We found that the major pigment in the golden dragline silk of T. clavata was xanthurenic acid. To investigate the possible function of the pigment, we tested the effect of xanthurenic acid on bacterial growth using gram-negative Escherichia coli and gram-positive Bacillus subtilis. We found that xanthurenic acid had a slight antibacterial effect. Furthermore, to investigate the UV tolerance of the T. clavata threads bleached of their golden color, we conducted tensile deformation tests and scanning electron microscope observations. However, in these experiments, no significant effect was observed. We therefore speculate that golden orb-weaving spiders use the pigment for other purposes, such as to attract their prey in the sunlight.

Spider silks are among the toughest known materials and thus provide models for renewable, biodegradable, and sustainable biopolymers. However, the entirety of their diversity still remains elusive, and silks that exceed the performance limits of industrial fibers are constantly being found. We obtained transcriptome assemblies from 1098 species of spiders to comprehensively catalog silk gene sequences and measured the mechanical, thermal, structural, and hydration properties of the dragline silks of 446 species. The combination of these silk protein genotype-phenotype data revealed essential contributions of multicomponent structures with major ampullate spidroin 1 to 3 paralogs in high-performance dragline silks and numerous amino acid motifs contributing to each of the measured properties. We hope that our global sampling, comprehensive testing, integrated analysis, and open data will provide a solid starting point for future biomaterial designs.

The high-throughput long-read sequencing has become affordable enough for any molecular biology lab to utilize genome sequencing in their research. Complete genome sequencing and assembly of bacterial genomes is one such application which is powerful yet simple enough for anyone without advanced molecular biology or bioinformatics skills to conduct on his/her own. High-throughput sequencing will eventually become a basic routine tool in molecular biology labs just like polymerase chain reaction and electrophoresis in a near future. To assist the use of such nanopore sequencing technologies, we designed a graduate school course to learn both the experimental and bioinformatic skills of complete bacterial genome sequencing and assembly.

Aims/Introduction: Obesity is a known risk factor for several chronic diseases, including type 2 diabetes mellitus, which results from increased insulin resistance and impaired insulin secretion. However, the association between obesity and insulin resistance in Asian populations has not yet been fully elucidated. Therefore, we aimed to investigate the causal relationship between body mass index (BMI) and glycemic traits using Mendelian randomization (MR). Materials and Methods: We performed individual-level MR analyses using genetic risk scores based on BMI-related variants in 3,745 individuals without diabetes mellitus from a Japanese cohort. We examined heterogeneity through subgroup analyses based on potential modifiers and determined the shape of the causal relationship using nonlinear MR analyses to further assess the impact of BMI on the homeostasis model assessment of insulin resistance (HOMA-IR). Results: MR analyses revealed a significant positive association between BMI and HOMA-IR (β = 0.077; 95% confidence interval, 0.014–0.141; P = 0.016; outcome variable was log-transformed and standardized). Additional analyses revealed heterogeneity among subgroups differentiated by age, sex, lifestyle habits, and cardiometabolic traits. Nonlinear MR analyses suggested a potential J-shaped causal relationship between BMI and HOMA-IR. Conclusions: Our findings demonstrated that obesity and low BMI may contribute to increased insulin resistance. Furthermore, the impact of BMI on insulin resistance could vary owing to effect modification. Managing BMI is crucial in individuals at high risk of increased insulin resistance and may have important implications for preventing type 2 diabetes, especially given the low insulin secretory capacity observed in East Asian populations.

A mesophilic bacterium Actinoplanes sichuanensis strain 03-723T was previously isolated from soil by Sun et al. Here, we present a complete and annotated genome sequence of this strain, which has a total size of 12.1 Mbp with a G + C content of 70.1%.

Adlercreutzia equolifaciens subsp. celatus DSM 18785 was isolated from the cecal contents of a rat and is an obligately anaerobic equol-producing bacterium. Here, we report the finished and annotated genome sequence of this organism, which has a genome size of 2, 929, 991 bp and a G1C content of 63.2%.

Atopobiaceae bacterium strain P1 (Actinobacteria, Coriobacteriales) was isolated from mouse feces. Here, we report the complete genome sequence of this strain, which has a total size of 2,028,478bp and a G1C content of 58.6%.

Bulleidia sp. is a non-spore-forming, obligatory anaerobic, Gram-positive bacterium isolated from the stool samples of human colon cancer patients. We report the complete genome sequence of Bulleidia sp. 10714-15, comprising a single linear chromosome of 2,218,984 bp with a G + C content of 36.6%.

We report here the complete genome sequence of Geobacter sp. strain SVR, isolated from antimony mine soil in Nakase Mine, Hyogo Prefecture, Japan. SVR strains proliferate using antimonate [Sb(V)] as an electron acceptor, providing insights into the antimony reduction mechanism.

Actinobacteria produce about two-thirds of all naturally derived antibiotics currently in clinical use. Kitasatospora aureofaciens Tü117 is a species of Actinobacteria and produces α-lipomycin. We report the complete genome sequence of K. aureofaciens, composed of a single linear chromosome of 8,717,539 Mbp with a G + C content of 72.0%.

Limnobacter thiooxidans CS-K2T is a Gram-negative bacterium first isolated from the sediment of the littoral zone of a freshwater lake in Germany. We here present the complete annotated genome sequence of this thiosulfate-oxidizing bacterium, spanning 3.54 Mb and encoding 3,192 protein-coding sequences.

We report the complete genome sequence of Mediterraneibacter gnavus strain RI1, a Gram-positive anaerobic gut microbe isolated from human feces. The complete circular genome has a genome size of 3.25 Mb, with a G+C content of 42.6%.

Marinobacter nanhaiticus D15-8W is known for its ability to metabolize polycyclic aromatic hydrocarbons. Here, we report the complete circular genome sequence of this strain to be 5,336,660 bp (G + C content, 58.6%; 4,869 protein-coding sequences) with one plasmid (69,655 bp).

Rhodopseudomonas palustris R1 is a phototrophic, purple, non-sulfur Gram-negative bacterium first isolated from the soils of rice fields, known for its polylactic acid degradability. Here, we present the complete circular genome sequence of this bacterium, spanning 5.32 Mbp and 4,949 protein-coding sequences.

Serratia plymuthica strain SWSY-3.47 is a Gram-negative, rod-shaped bacteria isolated for its high chitinolytic activity. Here, we report the complete genome of this strain comprised of a single circular chromosome of 5,636,345 bp with a G + C content of 56.0%.

We report the complete circular genome sequence (2,316,546 bp; 37.0% G + C) of Solobacterium moorei 10714-02, a gram-positive obligate anaerobe isolated from stool samples of a human colorectal cancer patient, differing from the typically linear chromosome of this species.

The genus Streptomyces is a promising source of biologically active secondary metabolites. Here, we report the complete genome sequence of Streptomyces albus strain G153. The assembled genome comprised a single linear chromosome of 6.9 Mbp with a G1C content of 73.3%.

We isolated and sequenced the complete genomes of four bacteria from the gut contents of a spiny ant (Polyrhachis lamellidens) sampled from a primeval beech forest in Yamagata Prefecture, Japan. The isolates belong to the genera Tsukamurella, Enterococcus, Lysinibacillus, and Streptomyces and provide insights into the functional roles of microbiomes of ants.

Lysobacter species produce lysobactin, a depsipeptide antibiotic that is effective against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Staphylococcus aureus. Here, we report complete genome sequences of two Lysobacter strains, which were isolated from seawater (Lysobacter caseinilyticus) and soil (Lysobacter helvus) in South Korea.