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Hybrid selection RNA sequencing of Bacteroides fragilis from colonic lumen, mucus and epithelial tissue samples, typically enriched with host reads, revealed the spatial transcriptome of this commensal throughout the murine colon and allowed the identification of putative colonization factors.
The microrchidia (MORC) protein from Toxoplasma gondii is a transcriptional repressor that regulates parasite development and sexual commitment, and its conditional depletion paves the way to develop improved in vitro systems to investigate parasite sexual development.
Defence against type six secretion system (T6SS) effectors is thought to be mostly mediated by dedicated immunity proteins that antagonize specific effector proteins. Here, two envelope stress-response pathways, Rcs and BaeSR, are shown to regulate protection against the T6SS effector TseH by modulating the integrity of the bacterial envelope in a manner independent of immunity proteins.
This study describes the development of an approach to rapidly screen lineage B betacoronaviruses, such as SARS-CoV and the recently emerged SARS-CoV-2, for receptor usage and their ability to infect cell types from different species. Using it, they confirm human ACE2 as the receptor for SARs-CoV-2 and show that host protease processing during viral entry is a significant barrier for viral entry.
An observational human clinical trial using a bacteriophage preparation showed that it was well tolerated without major adverse events in human patients with Staphylococcus aureus septicaemia.
Gastrointestinal disturbances, such as non-antibiotic-induced diarrhoea, promote susceptibility to colonization by Clostridium difficile, providing additional insights into antibiotic-independent triggers for this infection.
Genomic neighbour typing can be used to infer the antimicrobial susceptibility and resistance of a bacterial sample based on the genomes of closest relatives. Combined with MinION sequencing, it can rapidly determine microbial resistance for clinical samples within 4 h.
This work combines mass spectrometry imaging at high resolution with FISH for the visualization and identification of microorganisms. The authors develop a sample preparation and imaging pipeline called metaFISH to colocalize metabolite patterns with community members and apply it to a host–microbe symbiosis (mussel and its symbionts) to identify symbiosis-specific metabolites.
This study reports a novel function for the N6-methyladenosine RNA modification in allowing RIG-I to discriminate self from non-self RNA and shows that human metapneumovirus induces this modification of its RNA to evade recognition in vivo.
A comparison of DNA methylation patterns between conventionally raised and germ-free mice shows that the presence of a commensal microbiota induces methylation changes at regulatory elements in a subset of genes that are important for intestinal homeostasis.
Here the authors have developed a framework to predict which Streptococcus pneumoniae serotypes would be best targeted by vaccination, of children and adults, to prevent the post-vaccine emergence of similarly virulent strains, thereby minimizing the pneumococcal disease burden.
The murine gut commensal Faecalibaculum rodentium and its human homologue, Holdemanella biformis, are under-represented in tumour development and can reduce tumour progression via short-chain fatty acid production, providing insights into a protective microbial candidate.
This study reports transposon sequencing analyses to identify genes required for Legionella pneumophila survival in amoeba hosts, showing that unique sets of genes are required for virulence in different amoebae. This enables the accumulation of virulence genes that collectively allow replication in macrophages and, in some cases, lead to redundancy in this host cell type.
Inflammatory bowel diseases (IBD) are associated with increased faecal N-acylethanolamines (NAEs), which are primarily host-produced signalling lipids, in patients and a mouse model of colitis. These metabolites can enhance the growth of bacterial species enriched in IBD faecal samples and are associated with the expression of respiratory chain genes necessary for microbial metabolism of NAEs.
Co-housing mice is shown to induce resistance against enterobacterial infection after antibiotic treatment through the ability to retain or share Klebsiella michiganensis, which is necessary and sufficient to prevent infection through competition for nutrients.
The PLate Coverage Algorithm (PLCA) determines the culture plates required for culture-enriched metagenomics and enables the recovery of greater taxonomic diversity, better quality metagenome-assembled genomes and improved functional annotations compared to metagenomics alone, indicating its utility for other microbiomes, especially those dominated by host DNA.
This study describes a new method that improves the sensitivity of viral detection compared with next-generation sequencing and enables the detection of emerging flaviviruses not specifically targeted a priori. Metagenomic sequencing with spiked primer enrichment is simple, low cost, fast and deployable on either benchtop or portable nanopore sequencers, making it applicable for diagnostic laboratory and field use.
Commensal-colonization-factor-producing Bacteroidetes protect against Klebsiella pneumoniae colonization and infection in the gut via IL-36 signalling and macrophages, and these commensals can limit transmission between hosts, whereas Proteobacteria are important for colonization resistance in the upper airway.