Volume 7 Issue 1, January 2022

Interactive annotation and commenting tools provide a means to ground animations in experimental evidence and to support scientific discourse and progress.

Training in visualization should be a part of every scientist’s journey.

Crystallizing biological complexity into animation has been Arkitek Scientific’s mission for the past 25 years. Co-founder Beth Anderson explains how she got started in science animation and why it remains her passion.

Advances in CRISPR–Cas tools coupled with innovative screening and bioinformatic pipelines make it possible to conduct strain-specific and site-specific genome editing within a microbial community without the need for prior culturing or engineering.

Construction of a global catalogue of human gut archaeal genomes and their viruses provides insights into the structure, composition and function of the human gut archaeome.

Immunologic recognition of bacterial products during skin infection triggers a cytokine and chemokine response that facilitates neutrophil recruitment to the site of infection. Staphylococcus aureus phenol-soluble modulins can function as early chemoattractants to directly recruit neutrophils and alert the host to infection.

Cooperative interaction between low-abundance gut bacteria is required to convert l-carnitine to TMAO via a multi-step pathway, which leads to an increased risk of cardiovascular disease.

A statistical framework that integrates data from a fine-scale targeted testing scheme and regular randomized surveillance surveys provides unbiased and fine-grained estimates of key SARS-CoV-2 epidemiological parameters that are critical for real-time policy decision-making.

The development of the infant gut microbiota into an adult configuration is heavily influenced by lifestyle. A large study of children from The Gambia reveals how the microbiota assembles in children with a non-industrial lifestyle.

Shigella uses the OspC3 type III secretion system effector to catalyze ADP riboxanation of caspases-4 and 11, preventing lipopolysaccharide recognition and pyroptotic death of the infected cell.

Gut microbiome development in full-term infants has important implications for health and disease, but less is known for preterm infants. Here the authors summarize current knowledge in preterm infants, compare this to what is known for full-term babies, and discuss potential diagnostics and interventions to improve outcomes for preterm infants.

A suite of methods enables programmable species- and locus-specific editing of bacteria in communities.

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.

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.

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.

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.

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.

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.

(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.

Analysis of gut microbiomes from Gambian infants reveals bacterial trophic networks based around Prevotella species, which are typically enriched in non-industrialized populations.

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.

Vaccinia virus protein F14 mimics the transactivation domain of the p65 subunit of NF-κB to evade host immunity.

Cultivation and metagenomic assembly of the skin microbiome genome catalogue paves the way to establishing a multi-kingdom map of microorganisms that pattern human skin.