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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.
Alternative σ factors regulate the activity of RNA polymerases under specific conditions and are regulated through various mechanisms, most of which depend on anti-σ factors to regulate their on/off status. This study reports a new mode of σ factor regulation that does not require an anti-σ factor, but instead σ factor phosphorylation in response to the presence of an antibiotic.
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.
The autophagy proteins Beclin 1 and FIP200, but not other essential autophagy components, such as ATG5, ATG16L1 or ATG7, regulate quiescence of tissue-resident macrophages, thereby modulating immune activation and resistance to Listeria monocytogenes infection.
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.
In an interesting demonstration of how bacterial subcellular organization influences physiology, polar accumulation of PopZ protein in a membraneless microdomain is found to drive asymmetric phosphorylation of CtrA-P, which creates a gradient that is responsible for asymmetric cell division in Caulobacter.
The use of an in vitro system in which key proteins involved in cell division are attached to supported lipid bilayers reveals that membrane-bound cytosolic peptides of FtsN and FtsQ co-migrate with treadmilling FtsZ–FtsA filaments via a diffusion-and-capture mechanism, elucidating how FtsZ dynamics regulate the distribution of peptidoglycan synthases.
This study tracks emergent ciprofloxacin-resistant Shigella sonnei in Vietnam, showing displacement of sensitive strains by others that acquired beta-lactam-antibiotic-resistance plasmids from commensal E. coli in infected individuals.
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.
Bacterial cell wall amidases typically hydrolyse crosslinked peptidoglycan between daughter cells so they can separate. An amidase that cleaves uncrosslinked peptidoglycan and its regulator are identified here and shown to regulate cell growth, rather than separation. This enzyme regulates the density of peptidoglycan assembly sites, ensuring coordination between cell expansion and cell division.