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Analysis of gut microbiomes from Gambian infants reveals bacterial trophic networks based around Prevotella species, which are typically enriched in non-industrialized populations.
A causal debiasing framework provides accurate estimates of local prevalence and effective reproduction number for surveillance of SARS-CoV-2 cases using data from randomized testing schemes to model ascertainment bias in targeted subpopulation data.
Recovery of 1,167 nonredundant archaeal genomes from the human gut microbiomes reveals previously undescribed genera, associations with sociodemographic factors and the presence of an archaeal virome.
Quantitative metagenomic analyses of gut microbiomes reveals kinship, together with current cohabitation, as drivers of microbial community transmission and persistence between family members over three to five generations.
(Meta)genomic mining, bioinformatic prediction and chemical synthesis reveal biosynthetic gene clusters encoding structurally new menaquinone-binding antibiotics that are active against multidrug-resistant Staphylococcus aureus in vivo and Mycobacterium tuberculosis in vitro.
The gbu gene cluster, present in the human gut microbiota member Emergencia timonensis, converts γ-butyrobetaine (γBB) to trimethylamine in the conversion of dietary l-carnitine, which is found in red meat, to the proatherosclerotic metabolite trimethylamine-N-oxide. Individuals with high plasma γBB levels had increased risk of cardiovascular events.
An amplicon-based sequencing protocol that includes synthetic DNA spike-ins improves the quality and efficiency of SARS-CoV-2 high-throughput sequencing and detects common errors in genomic data.
Arbitrium, a peptide signal used by phages to communicate among themselves and control the lysis–lysogeny transition, is shown here to also regulate phage induction (the lysogeny–lysis transition). Arbitrium signalling represses DNA-damage-dependent phage induction, enabling prophages to sense the abundance of lysogens in the population so they can time the lytic transition for when uninfected hosts are available.
Staphylococcus aureus phenol-soluble modulin toxins trigger a fast immune response that involves recruitment of leucocytes to the site of infection via the transcription factor EGR1.
By combining the use of a small anti-CRISPR protein, AcrIIA23, with direct integration into the host cell’s CRISPR locus, the lysogenic phage ΦAP1.1 neutralizes CRISPR-mediated anti-phage immunity in Streptococcus pyogenes.
Systematic analysis of bacterial phyllosphere isolates and their ability to protect Arabidopsis thaliana plants against infection, with the model pathogen Pseudomonas syringae pv. tomato DC3000, identified protective isolates such as Rhizobium Leaf202, whose activity involves direct interaction with the pathogen.
Global syphilis prevalence has been increasing. Sequencing and analysis of a global collection of 726 Treponema pallidum samples reveal globally circulating lineages linked to a rapid expansion occurring since the end of the twentieth century.
The de novo genome assembly and analysis of 300 Aspergillus fumigatus genomes from environmental and clinical isolates provides insight into the pan-genome of this important human fungal pathogen. Genome-wide association studies identify genomic variation associated with human infection and triazole resistance, and reveal potential therapeutic antifungal targets.
Wolbachia cifB expression in Anopheles gambiae males is sufficient to induce cytoplasmic incompatibility that is sensitive to the expression level of the factors involved.
Using genome-resolved metagenomics for 41 Arctic seawater samples, this ecogenomic analysis of 530 metagenome-assembled genomes (MAGs) from the polar Arctic Ocean reveals uncultured Arctic bacterial and archaeal MAGs, their gene expression patterns, habitat preferences and metabolic potential.
Analysis of the fungal and bacterial components of the intestinal microbiota of patients undergoing allogeneic haematopoietic cell transplantation identifies an association between fungal dysbiosis, an expansion of Candida parapsilosis complex species and worse patient outcomes.