Phage Annotation Server -- phage genome annotation

Free automated phage genome annotation -- pharokka, phold and phynteny in one pipeline.

phage-annotation.org

ISME20: ISME20 News | International Society for Microbial Ecology

isme.live.ws-django.co.uk

Eximiradius proteiniborus gen. nov., sp. nov., the first cultivated representative of the “Candidatus Kapaibacteriia” (lineage OPB56) and a proposal of Eximiradiaceae fam. nov., Eximiradiales ord. nov., Eximiradiia class. nov. within the phylum Bacteroidota

A novel strictly anaerobic moderately thermophilic bacterium, strain OB-3-phT, was isolated from a fouling under the flow of thermal well water (North…

sciencedirect.com

ENVnet provides a global molecular resource of dissolved organic matter - Nature Biotechnology

A resource of dissolved organic matter illuminates carbon and microbial life in Earth’s ecosystems.

nature.com

Psychrophiles elude genomic prediction of optimal growth temperature | mSystems

Most prokaryotic taxa remain difficult to grow and study in culture, and their environmental preferences remain largely unquantified (1). As one example, we know that the optimal temperature for growth (OGT) can vary dramatically across prokaryotes, but the OGT values for most prokaryotic species found on Earth remain unknown. As OGT is an important determinant of when and where species will grow, being able to reliably infer OGT values is useful for many reasons, from identifying effective culturing strategies to predicting how the distributions of microbial taxa will shift in response to climate change (1). Because the phylogenetic coherence of this trait is weak, with even members of the same genus having variable OGTs (2), we cannot simply predict OGT values from taxonomic or phylogenetic information alone (3). Instead, given the vast quantity of genomic information now available for uncultured prokaryotes, there is broad interest in developing genome-based models to infer OGT for uncultured species. Pre-existing modeling efforts have leveraged various genomic features to infer OGT values with varying degrees of success. Examples of such models include those based on nucleotide sequences (4–10); amino acid sequences and protein annotations (8, 11–14); and a combination of features derived from DNA and protein data (15). Yet, because trait axes orthogonal to OGT also impact genome composition, composition alone is not sufficient to explain OGT differences between thermophiles and psychrophiles (16, 17).

journals.asm.org

The planktonic microbiome of the Great Barrier Reef - Nature

The Great Barrier Reef Microbial Genomes Database compiles prokaryotic, viral and eukaryotic genomes from seawater collected from the Great Barrier Reef, providing a rich resource for the study of mar...

nature.com

Inferring single-cell heterogeneity of bacteriophage lysis-associated life-history traits from population-scale dynamics

Theory-guided experiments reveal single-cell heterogeneity of lysis-associated bacteriophage traits from population scale data.

science.org

Long read and short read whole genome sequencing are equivalent for genomic characterisation of bacteriophage: considerations for high throughput analysis

Background Antimicrobial resistance (AMR) is a global health crisis, necessitating alternative antibacterial strategies. Bacteriophages (phages) offer a promising solution, and their use as a therapeu...

biorxiv.org

Standalone nanopore sequencing for foodborne pathogen surveillance: a large-scale evaluation and quality control framework

Whole-genome sequencing (WGS) is central to foodborne pathogen surveillance and cross-border outbreak detection. Long-read sequencing using Oxford Nanopore Technologies (ONT) promises rapid, complete,...

biorxiv.org

Global distribution of isoprenoid quinones across Bacteria | mSystems

Isoprenoid quinones are small electron-carrying molecules found in the membranes of organisms that produce energy through photosynthesis or respiration and participate in other important cellular processes. Recent advances in the characterization of their biosynthesis pathways enable their automated annotation from genome analyses. In this article, we performed the genomic analysis of over 26,000 cultured and uncultured bacteria, which was complemented by literature data compiled on over 6,000 cultured bacteria. This enabled us to provide an unprecedented overview of quinone distribution across the bacterial diversity. Creating such a comprehensive data set revealed new information about quinone distribution and evolutionary paths and will facilitate future exploration of various aspects of quinone biology, including their role in the evolution and diversification of bacterial metabolism.

journals.asm.org

A simple mathematical model for the discontinuity in average nucleotide identity distributions in prokaryotes

Microbial species exist as discrete genomic clusters, and evidence of this is the well-documented discontinuity in average nucleotide identity distributions—the ANI gap. Today, thresholds within...

doi.org

Dorado v2.0.0 part 2: assembly polishing

a blog for miscellaneous bioinformatics stuff

rrwick.github.io

Isolation of genome-predicted Caldatribacterium (Atribacterota) reveals pervasive microbial cultivation problem due to folate precipitation - Nature Communications

Most bacterial phyla have few or no representatives in pure culture. Here, Hedlund et al. isolate two new species within the phylum Atribacterota with unique cell biological features. In addition, the...

doi.org

Frontiers | A multilayered cell envelope of a member of the Chloroflexota offers an anchoring platform for the archaellum

In a previous study, we discovered that Litorilinea aerophila, a member of the bacterial phylum Chloroflexota, had acquired a bona fide archaellum gene clust...

frontiersin.org