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Mashup Score: 2
Ostreid herpesvirus 1 (OsHV-1), a member of the family Malacoherpesviridae (order Herpesvirales), is a major pathogen of bivalves. However, the molecular details of the malacoherpesvirus infection cycle and its overall similarity to the replication of mammalian herpesviruses (family Orthoherpesviridae) remain obscure. Here, to gain insights into the OsHV-1 biology, we performed long read sequencing of infected blood clams, Anadara broughtonii, which yielded over one million OsHV-1 long reads. This data enabled the annotation of the viral genome with 78 gene units and 274 transcripts, of which 67 were polycistronic mRNAs, 35 ncRNAs and 20 natural antisense transcripts (NATs). Transcriptomics and proteomics data indicate preferential transcription and independent translation of the capsid scaffold protein as an OsHV-1 capsid maturation protease isoform. The conservation of this transcriptional architecture across Herpesvirales likely indicates its functional importance and ancient origin
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Mashup Score: 3
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 cellulolytic Cononympha protists in the hindgut of the Formosan 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 greatly 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; ‘Ca. Methanobrevibacter cononymphae’ is facultati
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Mashup Score: 3Exploring the genome-wide expression level of the bacterial strain belonging to Bacillus safensis (MM19) against Phomopsis viticola - 1 day(s) ago
Introduction: Rhizobacteria has the suppression ability to compete with pathogenic microorganisms and help for plant immunity and defense mechanism. Their growth and survival in rhizosphere ensure biological balance in favor of the host plant. Methods: In our study, with agar diffusion assays, we found a rhizobacterium species belonging to Bacillus safensis , which can significantly suppress Phomopsis viticola . To elucidate the antagonistic mechanism, genome-wide gene expression profiling of B. safensis (strain MM19) was performed in the presence and absence of P. viticola . We used RNA-seq analysis to obtain a comprehensive overview of the responsive B. safensis whole gene expression classified according to biological and metabolic process to P. viticola concomitant growth in liquid culture. Results: The differential gene expression profiles of B. safensis (MM19) revealed significantly increased expression of prominent genes related to thiamine biosynthesis involving various metaboli
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Mashup Score: 2Plasmids from a complex biome exist as communities - 1 day(s) ago
Plasmids play a crucial role in the spread of antimicrobial resistance genes (ARGs) across One Health due to their ability to transfer a wide range of ARGs within and across bacterial species and biomes. We sequenced 173 circularised plasmids transferred from wastewater treatment plant (WWTP) effluent into Escherichia coli and subsequently characterised their genetic content. Multiple multidrug resistant plasmids were identified with a significant number of mega plasmids (>100Kb). Plasmids existing in isolation were rare and almost all existed with other plasmids. Our results suggest that positive epistasis promotes plasmid persistence in WWTP populations in a similar manner to that identified in vitro via infectious transmission, varying properties against plasmid community backgrounds, interactions with a range of other plasmids, source-sink spill-over transmission within the plasmid community rather than the host bacteria and compensatory mutations. We have demonstrated that the pla
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Mashup Score: 2Molecular characterisation of Streptococcus pyogenes (StrepA) non-invasive isolates during the 2022-23 UK upsurge - 1 day(s) ago
At the end of 2022 into early 2023 the UK Health Security Agency reported unusually high levels of scarlet fever and invasive disease caused by Streptococcus pyogenes (StrepA or group A Streptococcus). During this time, we collected and genome sequenced 341 non-invasive throat and skin S. pyogenes isolates identified during routine clinical diagnostic testing in Sheffield, a large UK city. We compared the data with that obtained from a similar collection of 165 isolates from 2016-17. Numbers of throat-associated isolates collected peaked in early December 2022, reflecting the national scarlet fever upsurge, while skin infections peaked later in December. The most common emm-types in 2022-23 were emm1 (28.7%), emm12 (24.9%), and emm22 (7.7%) in throat; and emm1 (22%), emm12 (10%), emm76 (18%), and emm49 (7%) in skin. Whilst all emm1 isolates were the M1UK lineage, comparison with 2016-17 revealed diverse lineages in other emm-types, including emm12, and emergent lineages within other ty
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Mashup Score: 0
Switchgrass (Panicum virgatum L.) is considered a sustainable biofuel feedstock, given its fast-growth, low input requirements, and high biomass yields. Improvements in bioenergy conversion efficiency of switchgrass could be made by reducing its lignin content. Engineered switchgrass that expresses a bacterial 3-dehydroshikimate dehydratase (QsuB) has reduced lignin content and improved biomass saccharification due to the rerouting of the shikimate pathway towards the simple aromatic protocatechuate at the expense of lignin biosynthesis. However, the impacts of this QsuB trait on switchgrass microbiome structure and function remains unclear. To address this, wildtype and QsuB engineered switchgrass were grown in switchgrass field soils and samples were collected from inflorescences, leaves, roots, rhizospheres, and bulk soils for microbiome analysis. We investigated how QsuB expression influenced switchgrass-associated fungal and bacterial communities using high-throughput Illumina MiS
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Mashup Score: 0Determinants of the Divergent Salmonella and Shigella Epithelial Colonization Strategies Resolved in Human Enteroids and Colonoids - 1 day(s) ago
Despite close relatedness, the major enteropathogens Salmonella and Shigella differ in infectious dose, pathogenesis, and disease kinetics. The prototype strains Salmonella enterica serovar Typhimurium (Salmonella) and Shigella flexneri (Shigella) use Type-3-secretion-systems (T3SSs) to colonize intestinal epithelial cells (IECs), but have evolved partially unique sets of T3SS effectors and accessory virulence factors. A synthesis of how these differences impact the temporal progression of infection in non-transformed human epithelia is missing. Here, we followed Salmonella and Shigella infections of human enteroids and colonoids by time-lapse imaging to pinpoint virulence factor modules that shape the divergent epithelial colonization strategies. By an apical targeting module that integrates flagella and the SPI-4-encoded adhesin system with T3SS, Salmonella accomplishes appreciable numbers of apical invasion events, promptly terminated by IEC death, and thus fostering a polyclonal it
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Mashup Score: 4Niche-aware metagenomic screening for enzyme methioninase illuminates its contribution to metabolic syntrophy - 1 day(s) ago
The single step methioninase-mediated degradation of methionine (as a sulfur containing amino acid) is a reaction at the interface of carbon, nitrogen, sulfur, and methane metabolism in microbes. This enzyme is also a therapeutic target for its role in starving auxotrophic cancer cells. Applying our refined in-silico screening pipeline on 33,469 publicly available genome assemblies and 1878 MAGs/SAGs from brackish waters of the Caspian Sea and the Fennoscandian shield deep groundwater resulted in recovering 1845 methioninases. The majority of recovered methioninases belong to representatives of phyla Proteobacteria (50%), Firmicutes (29%), and Firmicutes_A (13%). Prevalence of methioninase among anaerobic microbes and in the anoxic deep groundwater together with the relevance of its products for energy conservation in anaerobic metabolism highlights such environments as desirable targets for screening novel methioninases and resolving its contribution to microbial metabolism and intera
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Mashup Score: 1Rationally Designed Pooled CRISPRi-seq Uncovers a Novel Inhibitor of Bacterial Peptidyl-tRNA Hydrolase - 1 day(s) ago
Pooled knockdown libraries of essential genes are useful tools for elucidating the mechanisms of action of antibacterial compounds, a pivotal step in antibiotic discovery. However, achieving genomic coverage of antibacterial targets poses a challenge due to the uneven proliferation of knockdown mutants during pooled growth, leading to the unintended loss of important targets. To overcome this issue, we introduce CIMPLE (CRISPRi-mediated pooled library of essential genes), a rationally designed pooled knockdown library built in a model antibiotic-resistant bacteria, Burkholderia cenocepacia. By analysing growth parameters of clonal knockdown populations of an arrayed CRISPRi library, we predicted strain depletion levels during pooled growth and adjusted mutant relative abundance, achieving genomic coverage of antibacterial targets during antibiotic exposure. We demonstrate the utility of CIMPLE for chemogenetic profiling of known antibacterials and a previously discovered bacterial grow
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Mashup Score: 0Imaging flow cytometry enables label-free cell sorting of morphological variants from unculturable bacterial populations. - 1 day(s) ago
Bacterial populations often display remarkable morphological heterogeneity. Fluorescence activated cell sorting (FACS) is an important tool for understanding the biological significance of this morphological diversity, as it permits the separation and study of distinct morphological variants (morphotypes) from each other and their environmental milieu. In FACS, cells are first labeled with fluorescent markers such as antibodies or transgenic constructs, and then sorted based on their possession of such labels. However, since the development of fluorescent labels requires a priori knowledge of bacterial biology, it is often impossible to apply FACS to understudied and/or unculturable bacteria. This challenge has limited our capacity to investigate the role of bacterial size and shape in all but a small, largely culturable subset of bacterial taxa. Here, we present an innovative strategy that allows for label-free cell sorting of bacterial morphotypes, using an unculturable, pleiomorphic
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Long-read transcriptomics of Ostreid herpesvirus 1 uncovers a conserved expression strategy for the capsid maturation module and pinpoints a mechanism for evasion of the ADAR-based antiviral defence https://t.co/3ITRRrNiyA #bioRxiv