Bacterial genomics

Article
20 March 2024 | Open Access

A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche

A study reveals that Fusobacterium nucleatum subspecies animalis is bifurcated into two distinct clades, and shows that only one of these dominates the colorectal cancer niche, probably through increased colonization of the human gastrointestinal tract.

Martha Zepeda-Rivera
, Samuel S. Minot
& Christopher D. Johnston

Article
28 February 2024 | Open Access

Incomplete transcripts dominate the Mycobacterium tuberculosis transcriptome

A study reveals that most transcripts in Mycobacterium tuberculosis are incomplete, likely because of the tendency of the transcription machinery in this species to pause on genomic DNA.

Xiangwu Ju
, Shuqi Li
& Shixin Liu

Article
14 June 2023 | Open Access

Genome expansion by a CRISPR trimmer-integrase

CRISPR systems lacking Cas4 can use fused or recruited exonucleases for faithful acquisition of new CRISPR immune sequences.

Joy Y. Wang
, Owen T. Tuck
& Jennifer A. Doudna

Article
11 February 2019 | Open Access

A new genomic blueprint of the human gut microbiota

The known species repertoire of the collective human gut microbiota is substantially expanded with the discovery of 1,952 uncultured bacterial species that greatly improve classification of understudied African and South American samples.

Alexandre Almeida
, Alex L. Mitchell
& Robert D. Finn

Article | 16 May 2018

Mutant phenotypes for thousands of bacterial genes of unknown function

A large-scale mutagenesis screen identifies mutant phenotypes for over 11,000 protein-coding genes in bacteria that had previously not been assigned a specific function.

Morgan N. Price
, Kelly M. Wetmore
& Adam M. Deutschbauer

Letter | 15 June 2015

Unusual biology across a group comprising more than 15% of domain Bacteria

More than 15% of the bacterial domain consists of a radiation of phyla about which very little is known; here, metagenomics is used to reconstruct 8 complete and 789 draft genomes from more than 35 of these phyla, revealing a shared evolutionary history, metabolic limitations, and unusual ribosome compositions.

Christopher T. Brown
, Laura A. Hug
& Jillian F. Banfield

Letter | 21 May 2014

Bacterial phylogeny structures soil resistomes across habitats

Functional metagenomic selections for resistance to 18 antibiotics in 18 different soils reveal that bacterial community composition is the primary determinant of soil antibiotic resistance gene content.

Kevin J. Forsberg
, Sanket Patel
& Gautam Dantas

Article | 03 July 2013

The Mycobacterium tuberculosis regulatory network and hypoxia

Mycobacterium tuberculosis has the ability to survive within the host for months to decades in an asymptomatic state, and adaptations to hypoxia are thought to have an important role in pathogenesis; here a systems-wide reconstruction of the regulatory network provides a framework for understanding mycobacterial persistence in the host.