Nature Search

Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

Simon Roux
Mart Krupovic
Emiley A. Eloe-Fadrosh
Amendments and CorrectionsOpen Access11 Feb 2020
Nature Microbiology

Volume: 5, P: 527
Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2’-fucosyllactose utilization can be facilitated by coexisting species

Here, Lou et al. apply metagenomics and microbiome cultivation to infant fecal samples and uncover co-existing members encoding extracellular fucosidases that initiate 2’-fucosyllactose (2’FL) breakdown and can promote extensive growth of Bifidobacterium breve.

Yue Clare Lou
Benjamin E. Rubin
Jillian F. Banfield
ResearchOpen Access16 Nov 2023
Nature Communications

Volume: 14, P: 1-14
Experimental validation that human microbiome phages use alternative genetic coding

Previous bioinformatic analyses have indicated that bacteriophages can use genetic codes different from those of their host bacteria. Here, Peters et al. use metaproteomics to provide experimental evidence of reassignment of stop codon TAG to glutamine in phages found in the human gut microbiome.

Samantha L. Peters
Adair L. Borges
Robert L. Hettich
ResearchOpen Access29 Sept 2022
Nature Communications

Volume: 13, P: 1-7
Machine-learning approach expands the repertoire of anti-CRISPR protein families

CRISPR-Cas is a host adaptive immunity system and viruses harbor diverse anti-CRISPR proteins (Acrs). Here, the authors develop a random forest machine-learning approach to predict Acrs, identifying 2500 candidate Acr families, which expand the current repertoire of predicted Acrs by two orders of magnitude.

Ayal B. Gussow
Allyson E. Park
Eugene V. Koonin
ResearchOpen Access29 Jul 2020
Nature Communications

Volume: 11, P: 1-12
Species- and site-specific genome editing in complex bacterial communities

A suite of methods enables programmable species- and locus-specific editing of bacteria in communities.

Benjamin E. Rubin
Spencer Diamond
Jennifer A. Doudna
Research06 Dec 2021
Nature Microbiology

Volume: 7, P: 34-47
Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

A machine learning approach was used to recover over 10,000 inovirus-like sequences from existing microbial genomes and metagenomes, consequently proposing the reclassification of the Inoviridae family to a viral order, and uncover the previously unrecognized diversity of these viruses across hosts and environments.

Simon Roux
Mart Krupovic
Emiley A. Eloe-Fadrosh
ResearchOpen Access22 Jul 2019
Nature Microbiology

Volume: 4, P: 1895-1906
Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes

Computational analyses reveal widespread recoding in gut phages, which is hypothesized to control timing of lysis.

Adair L. Borges
Yue Clare Lou
Jillian F. Banfield
Research26 May 2022
Nature Microbiology

Volume: 7, P: 918-927
Bacterial alginate regulators and phage homologs repress CRISPR–Cas immunity

The identification of the KinB–AlgB two-component system, known to modulate alginate biosynthesis, together with downstream proteins that repress the Type I-F CRISPR–Cas system in Pseudomonas aeruginosa, elucidates how bacteria control the expression of nucleolytic host defence systems to minimize the potential risks of self-targeting.

Adair L. Borges
Bardo Castro
Joseph Bondy-Denomy
Research23 Mar 2020
Nature Microbiology

Volume: 5, P: 679-687
Phage-encoded ribosomal protein S21 expression is linked to late-stage phage replication

Lin-Xing Chen
Alexander L. Jaffe
Jillian F. Banfield
ResearchOpen Access30 Mar 2022
ISME Communications

Volume: 2, P: 1-10

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Author Correction: Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2’-fucosyllactose utilization can be facilitated by coexisting species

Experimental validation that human microbiome phages use alternative genetic coding

Machine-learning approach expands the repertoire of anti-CRISPR protein families

Species- and site-specific genome editing in complex bacterial communities

Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

Widespread stop-codon recoding in bacteriophages may regulate translation of lytic genes

Bacterial alginate regulators and phage homologs repress CRISPR–Cas immunity

Phage-encoded ribosomal protein S21 expression is linked to late-stage phage replication

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