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mstdn.science

Stop codon reassignment to tryptophan in members of the bacterial phylum Actinomycetota

Reassignment of stop codons is a significant evolutionary event with recoding of UGA to tryptophan being previously identified in only three bacterial phyla, the Bacillota, Pseudomonadota and Verrucom...

microbiologyresearch.org

Habitat-specific patterns of horizontal gene transfer revealed by metagenomics across aquatic and terrestrial ecosystems

Horizontal gene transfer (HGT) is a major driver of microbial adaptation and evolution, yet how habitat type and anthropogenic pressures shape communi…

sciencedirect.com

From coral reefs to human guts: stress is stress

Reefs and colons share no taxa, no host, no timescale, but they report stress the same way, which tells us where NOT to look for solutions.

merenlab.org

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig

academic.oup.com

Evolutionary trajectory of microbial sulfur oxidation pathways recapitulates Earth’s oxygenation history - Nature Communications

Microorganisms have long driven Earth’s oxidative sulfuric cycle using complex sulfur-oxidizing systems. This study shows that this molecular machinery first originated in the anoxic Archean eon and g...

nature.com

This frog bacterium wiped out cancer tumors in mice with a single dose

A naturally occurring bacterium from amphibian intestines completely eliminated colorectal tumors in mice with a single treatment by both attacking cancer cells and activating the immune system. The f...

sciencedaily.com

Museomics reveals uncultured symbionts with biosynthetic potential in nudibranchs - Microbiome

Background Museum specimens are widely used for PCR-based pathogen detection, yet their potential for metagenomic discovery of beneficial microbes remains underexplored, largely due to difficulties in...

link.springer.com

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

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

Public microbial genomes encode an immense record of biological diversity, evolution and molecular function, but much of this information remains difficult to reuse because raw sequencing data are not...

biorxiv.org

Predicting oxygen levels in microbial habitats using a metagenome-based approach | mSystems

Oxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ. We developed a tool, OxyMetaG, that leverages differences in bacterial gene content across known aerobic and anaerobic taxa to predict the oxygen level of a given sample directly from shotgun metagenomic reads. OxyMetaG works on samples with low sequencing depth and avoids computationally expensive genome assembly, which often captures only a fraction of the microbial community in a given environment. With OxyMetaG, bacteria can be used as bioindicators of oxygen availability over broader time scales than just a single measurement and provide crucial environmental context in cases where oxygen has not been or cannot be measured. OxyMetaG is publicly available and can be used to answer a wide variety of ecological questions in both environmental and host-associated systems.

doi.org

Bipolaricaulota

Bi.po.la.ri.cau.lo'ta. N.L. masc. n. Bipolaricaulis, type genus of the phylum; -ota, ending to denote a phylum; N.L. neut. pl. n. Bipolaricaulota, the Bipolaricaulis phylum. Bipolaricaulota is a bact...

onlinelibrary.wiley.com

Models trained with noisy genomes extend bacterial phenotype prediction into deep time

Predicting phenotype from genotype in extant organisms is increasingly tractable through the accumulation of genome sequences and the development of machine-learning algorithms. Here we show that mach...

biorxiv.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

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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

Purine bias in bacterial genes is driven by runaway transcription

Nature Microbiology, Published online: 15 June 2026; doi:10.1038/s41564-026-02389-1Purine bias is critical for gene expression in bacteria, preventing premature transcription in species that exhibit runaway transcription.

go.nature.com

A Novel Pilus System in Candidate Phyla Radiation Bacteria

The Candidate Phyla Radiation (CPR) represents a bacterial superphylum estimated to include between 15–50% of all bacterial species, yet CPR bacteria remain challenging to culture and have been primar...

biorxiv.org