Biology subjects

Omori, T.

Publications and source records attributed to Omori, T..

4 recordsLinked to original sources

bioRxiv2024

Genotype dependence of virulence-associated genes in ESBL-producing Escherichia coli isolated from the blood of patients with urinary tract infections

Approximately 80% of urinary tract infections (UTIs) are caused by uropathogenic Escherichia coli (UPEC). The prevalence of extended-spectrum {beta}-lactamase (ESBL)- producing E. coli in UPEC isolates belonging to specific multilocus sequence-type clones is a global concern. Relations between the pathogenicity of UPEC virulence factors and genotype have been discussed. However, the specific virulence factors and genotypes associated with a higher likelihood of causing UTIs remain unclear. This study analyzed the genotypes and virulence-associated genes of 46 ESBL-producing strains isolated from the blood of patients with UTIs who visited the Department of Emergency Medicine from 2017 to 2022 to elucidate the characteristics of UPEC strains associated with severe infections. Most phylogroups of clinical isolates were B2, except for D, found in three strains. The dominant multilocus sequence typing (MLST) was ST131, followed by ST73, ST95, and ST38, frequently observed in UPEC strains. ST131 strains were more resistant to levofloxacin (87.5%) than non-ST131 strains (50.0%) and caused fewer sepsis cases than non-ST131 strains. Based on in silico analysis, of 23 clinical isolates, the genes detected in all clinical strains could have important role in invasive UTIs. Clustering analysis highlighted the genotype MLST dependence of UPEC-specific virulence-associated genes. The absence of several UPEC-specific gene loci or the presence of ST38-specific indicated atypical repertories of virulence-associated genes in ST38 strains. Genes encoding secretion systems, which were found in enteropathogenic E. coli, were less detected in ST131 strains. These results suggested that the correlation of MLST and repertories should be considered to understand UPEC virulence. IMPORTANCE STATEMENTSeveral virulence genes, their diverse repertories depending on the strains, and various pathological indications complicate the pathogenicity of uropathogenic Escherichia coli (UPEC). The genes detected in all clinical isolates in this study would play a crucial role in UPEC pathogenicity. In contrast, depending on the genotype, the distribution of UPEC- specific genes and other pathogenic E. coli virulence genes in some genotype strains varied. Secretion system genes related to the pathogenicity of enteropathogenic E. coli (EPEC) were less in the strains of the most prevalent genotype, ST131; this was relevant to the number of sepsis cases. These results clearly indicated genotype dependencies on virulence-associated gene repertories and ambiguity in UPEC and EPEC. This study proposed that analyzing genotype-specific virulence factors and sharing virulence genes with EPEC will bring new insights into UPEC pathogenicity.

microbiology↗

bioRxiv2024

Facultative endosymbiosis between cellulolytic protists and methanogenic archaea in the gut of the Formosan termite Coptotermes formosanus

Anaerobic protists frequently harbour methanogenic archaea, which apparently contribute to the hosts fermentative metabolism by consuming excess H2. However, the ecological properties of endosymbiotic methanogens remain elusive in many cases. Here we investigated the ecology and genome of the endosymbiotic methanogen of the Cononympha protists in the hindgut of the termite Coptotermes formosanus. Microscopic and 16S rRNA amplicon sequencing analyses revealed that a single species, designated here Candidatus Methanobrevibacter cononymphae, is associated with both Cononympha leidyi and Cononympha koidzumii and that its infection rate in Cononympha cells varied from 0.0 to 99.8% among termite colonies. Fine-scale network analysis indicated that multiple 16S rRNA sequence variants coexisted within a single host cell and that identical variants were present in both Cononympha species and also on the gut wall. Thus, Ca. Methanobrevibacter cononymphae is a facultative endosymbiont, transmitted vertically with frequent exchanges with the gut environment. Indeed, transmission electron microscopy showed escape or uptake of methanogens from/by a Cononympha cell. The genome of Ca. Methanobrevibacter cononymphae showed features consistent with its facultative lifestyle: i.e., the genome size (2.7 Mbp) comparable to those of free-living relatives; the pseudogenization of the formate dehydrogenase gene fdhA, unnecessary within the non-formate-producing host cell; the dependence on abundant acetate in the host cell as an essential carbon source; and the presence of a catalase gene, required for colonization on the microoxic gut wall. Our study revealed a versatile endosymbiosis between the methanogen and protists, which may be a strategy responding to changing conditions in the termite gut.

microbiology↗

bioRxiv2024

The Architecture of Sponge Choanocyte Chambers Maximizes Mechanical Pumping Efficiency

Sponges, the basalmost members of the animal kingdom, exhibit a range of complex architectures in which microfluidic channels connect multitudes of spherical chambers lined with choanocytes, flagellated filter-feeding cells. Choanocyte chambers can possess scores or even hundreds of such cells, which drive complex flows entering through porous walls and exiting into the sponge channels. One of the mysteries of the choanocyte chamber is its spherical shape, as it seems inappropriate for inducing directional transport since many choanocyte flagella beat in opposition to such a flow. Here we combine direct imaging of choanocyte chambers in living sponges with computational studies of many-flagella models to understand the connection between chamber architecture and directional flow. We find that those flagella that beat against the flow play a key role in raising the pressure inside the choanocyte chamber, with the result that the mechanical pumping efficiency, calculated from the pressure rise and flow rate, reaches a maximum at a small outlet opening angle. Comparison between experimental observations and the results of numerical simulations reveal that the chamber diameter, flagellar wave number and the outlet opening angle of the freshwater sponge E. muelleri, as well as several other species, are related in a manner that maximizes the mechanical pumping efficiency. These results indicate the subtle balances at play during morphogenesis of choanocyte chambers, and give insights into the physiology and body design of sponges.

biophysics↗

bioRxiv2022

Immotile cilia of the mouse node sense a fluid flow-induced mechanical force for left-right symmetry breaking

Immotile cilia of crown cells at the node of mouse embryos are required for sensing of a leftward fluid flow1 that gives rise to the breaking of left-right (L-R) symmetry2. The flow-sensing mechanism has long remained elusive, however, with both mechanosensing and chemosensing models having been proposed1, 3-5. Here we show that immotile cilia at the mouse node respond to mechanical force. In the presence of a leftward flow, immotile cilia on the left side of the node bend toward the ventral side whereas those on the right side bend toward the dorsal side. Application of mechanical stimuli to immotile cilia along the dorsoventral axis by optical tweezers induced Ca2+ transients and degradation of Dand5 mRNA--the first known L-R asymmetric molecular events--in the targeted cells. The Pkd2 channel protein was found to be preferentially localized to the dorsal side of immotile cilia on both left and right sides of the node, and the observed induction of Ca2+ transients preferentially by mechanical stimuli directed toward the ventral side could explain the differential response of immotile cilia to the directional flow. Our results thus suggest that immotile cilia at the node sense the direction of fluid flow in a manner dependent on a flow-generated mechanical force.

developmental biology↗