Commissioned obituaries should be abandoned

Craig, Donna

doi:10.1136/bmj.310.6980.660a

Cited by 7 publications

(12 citation statements)

References 1 publication

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“…We first examined tailocin production and sensitivity in 12 Pseudomonas strains isolated from groundwater. These strains are classified into ten species under the genus “Pseudomonas_E” according to the Genome Taxonomy Database (GTDB) [ 23 ] (see Supplementary Table S1 for all strain information). To aid discussion, we will describe these 12 strains using codenames (“Pse##”) defined in Supplementary Table S1 .…”

Section: Resultsmentioning

confidence: 99%

Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins

et al. 2021

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Tailocins are bactericidal protein complexes produced by a wide variety of bacteria that kill closely related strains and may play a role in microbial community structure. Thanks to their high specificity, tailocins have been proposed as precision antibacterial agents for therapeutic applications. Compared to tailed phages, with whom they share an evolutionary and morphological relationship, bacterially produced tailocins kill their host upon production but producing strains display resistance to self-intoxication. Though lipopolysaccharide (LPS) has been shown to act as a receptor for tailocins, the breadth of factors involved in tailocin sensitivity, and the mechanisms behind resistance to self-intoxication, remain unclear. Here, we employed genome-wide screens in four non-model pseudomonads to identify mutants with altered fitness in the presence of tailocins produced by closely related pseudomonads. Our mutant screens identified O-antigen composition and display as most important in defining sensitivity to our tailocins. In addition, the screens suggest LPS thinning as a mechanism by which resistant strains can become more sensitive to tailocins. We validate many of these novel findings, and extend these observations of tailocin sensitivity to 130 genome-sequenced pseudomonads. This work offers insights into tailocin–bacteria interactions, informing the potential use of tailocins in microbiome manipulation and antibacterial therapy.

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Section: Resultsmentioning

confidence: 99%

Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins

et al. 2021

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“…5 ; iTOL 113 v4). Finer taxonomic assignations of the resulting 317 MAGs were estimated against the Genome Taxonomy Database (release r89) using GTDB-Tk 114 (v1.0.2; classify_wf) (Supplementary Data 9 ). Briefly, the annotation relies on both taxonomic placement in a backbone tree (using marker genes) and average nucleotide identity (ANI) comparison based on ~150,000 genomes, spanning isolates, MAGs as well as SAGs.…”

Section: Methodsmentioning

confidence: 99%

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

et al. 2021

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The deep sea, the largest ocean’s compartment, drives planetary-scale biogeochemical cycling. Yet, the functional exploration of its microbial communities lags far behind other environments. Here we analyze 58 metagenomes from tropical and subtropical deep oceans to generate the Malaspina Gene Database. Free-living or particle-attached lifestyles drive functional differences in bathypelagic prokaryotic communities, regardless of their biogeography. Ammonia and CO oxidation pathways are enriched in the free-living microbial communities and dissimilatory nitrate reduction to ammonium and H2 oxidation pathways in the particle-attached, while the Calvin Benson-Bassham cycle is the most prevalent inorganic carbon fixation pathway in both size fractions. Reconstruction of the Malaspina Deep Metagenome-Assembled Genomes reveals unique non-cyanobacterial diazotrophic bacteria and chemolithoautotrophic prokaryotes. The widespread potential to grow both autotrophically and heterotrophically suggests that mixotrophy is an ecologically relevant trait in the deep ocean. These results expand our understanding of the functional microbial structure and metabolic capabilities of the largest Earth aquatic ecosystem.

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“…It does not perform assignment of accessory genes to strains. It will additionally perform taxonomic assignment of MAGs using GTDB [ 11 ] and generate phylogenetic trees for strains within MAGs and if evaluation genomes are available generate metrics of strain quality.…”

Section: Resultsmentioning

confidence: 99%

“…The most abundant MAG, Bin_72, had an aggregate short read coverage depth of 2364.25, across all the samples. This MAG was assigned to the phylum Cloacimonadota using the GTDB taxonomy [ 11 ]. Interestingly, this is an example of a MAG which changes significantly in abundance, decreasing over time, (adjusted p =4.9 e −05) but where the proportions of the three strains predicted varied less dramatically ( R 2 = 0.35 adjusted p =0.089 - Additional file 1 : Figure S4).…”

Section: Resultsmentioning

confidence: 99%

STRONG: metagenomics strain resolution on assembly graphs

et al. 2021

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We introduce STrain Resolution ON assembly Graphs (STRONG), which identifies strains de novo, from multiple metagenome samples. STRONG performs coassembly, and binning into metagenome assembled genomes (MAGs), and stores the coassembly graph prior to variant simplification. This enables the subgraphs and their unitig per-sample coverages, for individual single-copy core genes (SCGs) in each MAG, to be extracted. A Bayesian algorithm, BayesPaths, determines the number of strains present, their haplotypes or sequences on the SCGs, and abundances. STRONG is validated using synthetic communities and for a real anaerobic digestor time series generates haplotypes that match those observed from long Nanopore reads.

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Commissioned obituaries should be abandoned

Cited by 7 publications

References 1 publication

Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins

Systematic discovery of pseudomonad genetic factors involved in sensitivity to tailocins

Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities

STRONG: metagenomics strain resolution on assembly graphs

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