Article
|
Open Access
Featured
-
-
Article |
Bile salt hydrolase acyltransferase activity expands bile acid diversity
Acyltransferase activity of the enzyme bile salt hydrolase is identified and shown to mediate microbial bile acid conjugation, diversifying the bile acid pool and expanding their role in gut physiology.
- Douglas V. Guzior
- , Maxwell Okros
- & Robert A. Quinn
-
Article
| Open AccessRedefining the treponemal history through pre-Columbian genomes from Brazil
Reconstruction of four Treponema pallidum genomes associated with human remains from around 2,000 years ago suggests that T. pallidum existed in the Americas and diverged to its modern subspecies before the fifteenth century European contact with the Americas.
- Kerttu Majander
- , Marta Pla-Díaz
- & Verena J. Schuenemann
-
Article |
Phages overcome bacterial immunity via diverse anti-defence proteins
A study reports the discovery and characterization of four distinct families of phage-encoded anti-defence proteins that inhibit a variety of bacterial defence systems.
- Erez Yirmiya
- , Azita Leavitt
- & Rotem Sorek
-
Article
| Open AccessBacteriophages suppress CRISPR–Cas immunity using RNA-based anti-CRISPRs
In response to bacterial CRISPR–Cas immunity, phages and plasmids have evolved small non-coding RNA anti-CRISPRs, known as Racrs, that sequester Cas proteins in abberrant complexes and thereby inhibit immunity.
- Sarah Camara-Wilpert
- , David Mayo-Muñoz
- & Rafael Pinilla-Redondo
-
Article |
Transposon-encoded nucleases use guide RNAs to promote their selfish spread
TnpB and IscB nucleases use transposon-encoded guide RNAs to target genomic sequences for cleavage, thereby favouring copying and spreading of transposable elements.
- Chance Meers
- , Hoang C. Le
- & Samuel H. Sternberg
-
Article
| Open AccessEvolution of a minimal cell
An engineered minimal cell evolves to escape the negative consequences of genome streamlining.
- R. Z. Moger-Reischer
- , J. I. Glass
- & J. T. Lennon
-
Article
| Open AccessA Pseudomonas aeruginosa small RNA regulates chronic and acute infection
A study examining bacterial gene expression in human-derived samples identifies a gene encoding a small RNA and describes how it orchestrates the transition between chronic and acute infection in Pseudomonas aeruginosa.
- Pengbo Cao
- , Derek Fleming
- & Marvin Whiteley
-
Article
| Open AccessMirusviruses link herpesviruses to giant viruses
A phylogeny-guided genome-resolved metagenomic analysis of DNA viruses in the ocean reveals atypical plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota.
- Morgan Gaïa
- , Lingjie Meng
- & Tom O. Delmont
-
Article |
Adeno-associated virus 2 infection in children with non-A–E hepatitis
A case–control study investigating the causes of recent cases of acute hepatitis of unknown aetiology in 32 children identifies an association between adeno-associated virus infection and host genetics in disease susceptibility.
- Antonia Ho
- , Richard Orton
- & Emma C. Thomson
-
Article |
A swapped genetic code prevents viral infections and gene transfer
A study details the creation of an Escherichia coli genetically recoded organism that is resistant to viral infection, and describes a further modification that keeps the organism and its genetic information biocontained.
- Akos Nyerges
- , Svenja Vinke
- & George M. Church
-
Article
| Open AccessThe person-to-person transmission landscape of the gut and oral microbiomes
Data from more than 9,700 human stool and oral metagenomes has been used to decipher the strain transmission patterns of the human microbiome from mother to infant, within households and within populations.
- Mireia Valles-Colomer
- , Aitor Blanco-Míguez
- & Nicola Segata
-
Article |
Two broadly conserved families of polyprenyl-phosphate transporters
A study identifies two broadly conserved families of flippases that catalyse the transport of undecaprenyl phosphate in bacteria and could function to recycle dolichol phosphate in eukaryotes and archaea.
- Ian J. Roney
- & David Z. Rudner
-
Article
| Open AccessUndecaprenyl phosphate translocases confer conditional microbial fitness
Members of the DUF368-containing and DedA transmembrane protein families have conditional roles in undecaprenyl phosphate translocation in Gram-negative and Gram-positive bacteria and may have a widely conserved function in the biogenesis of microbial cell surface glycopolymers.
- Brandon Sit
- , Veerasak Srisuknimit
- & Matthew K. Waldor
-
Article |
Distinct gene clusters drive formation of ferrosome organelles in bacteria
A fez gene cluster drives formation of ferrosomes, a distinct lipid-bounded organelle for iron storage, in diverse bacterial species.
- Carly R. Grant
- , Matthieu Amor
- & Arash Komeili
-
Article
| Open AccessIntron-mediated induction of phenotypic heterogeneity
Experiments in yeast show that introns have a role in inducing phenotypic heterogeneity and that intron-mediated regulation of ribosomal proteins confers a fitness advantage by enabling yeast populations to diversify under nutrient-scarce conditions.
- Martin Lukačišin
- , Adriana Espinosa-Cantú
- & Tobias Bollenbach
-
Article |
Two defence systems eliminate plasmids from seventh pandemic Vibrio cholerae
Two defence systems are identified in pandemic Vibrio cholerae that act both cooperatively and independently to eliminate invasive plasmids and bacteriophages.
- Milena Jaskólska
- , David W. Adams
- & Melanie Blokesch
-
Article |
A gut-derived metabolite alters brain activity and anxiety behaviour in mice
The gut-derived molecule 4-ethylphenol influences complex behaviours in mice through effects on oligodendrocyte function and myelin patterning in the brain.
- Brittany D. Needham
- , Masanori Funabashi
- & Sarkis K. Mazmanian
-
Article |
Antiviral activity of bacterial TIR domains via immune signalling molecules
The mechanism of Thoeris—a bacterial anti-phage defence system—is described in detail, revealing that bacterial TIR-domain proteins recognize infection and produce signalling molecules to execute cell death, akin to the roles of these proteins in plants.
- Gal Ofir
- , Ehud Herbst
- & Rotem Sorek
-
Article |
A single sulfatase is required to access colonic mucin by a gut bacterium
A single sulfatase produced by a bacterium found in the human colon is essential for degradation of sulfated O-glycans in secreted mucus.
- Ana S. Luis
- , Chunsheng Jin
- & Eric C. Martens
-
Review Article |
Unconventional viral gene expression mechanisms as therapeutic targets
This Review outlines the gene and protein expression strategies used by viruses to expand the efficiency of their coding and regulatory sequences, and the implications of these mechanisms for developing antiviral agents.
- Jessica Sook Yuin Ho
- , Zeyu Zhu
- & Ivan Marazzi
-
Article |
C. difficile exploits a host metabolite produced during toxin-mediated disease
RNA-sequencing experiments determine that sorbitol, a metabolite produced by the host enzyme aldose reductase, is exploited by Clostridium difficile in its adaptation to inflammatory conditions in the gut.
- Kali M. Pruss
- & Justin L. Sonnenburg
-
Article
| Open AccessAnaerobic endosymbiont generates energy for ciliate host by denitrification
‘Candidatus Azoamicus ciliaticola’ transfers energy to its ciliate host in the form of ATP and enables this host to breathe nitrate, demonstrating that eukaryotes with remnant mitochondria can secondarily acquire energy-providing endosymbionts.
- Jon S. Graf
- , Sina Schorn
- & Jana Milucka
-
Article |
The functional proteome landscape of Escherichia coli
Thermal proteome profiling combined with a reverse genetics approach provides insights into the abundance and thermal stability of the global proteome of Escherichia coli.
- André Mateus
- , Johannes Hevler
- & Mikhail M. Savitski
-
Article |
Cyclic GMP–AMP signalling protects bacteria against viral infection
cGAMP signalling in bacteria mediates anti-phage defence, as part of a genetic system suggested to be the ancient ancestor of the animal cGAS–STING innate immune pathway.
- Daniel Cohen
- , Sarah Melamed
- & Rotem Sorek
-
Article |
Mapping human microbiome drug metabolism by gut bacteria and their genes
High-throughput genetic analyses combined with mass spectrometry reveal that the gene products of diverse human gut bacteria affect a wide range of oral drugs, as well as drug metabolism in mice.
- Michael Zimmermann
- , Maria Zimmermann-Kogadeeva
- & Andrew L. Goodman
-
Article |
Structural variation in the gut microbiome associates with host health
The authors systematically characterize structural variation in the genomes of gut microbiota and show that they are associated with bacterial fitness and with host risk factors, and that examining genes coded in these regions facilitates investigation of mechanisms that may underlie these associations.
- David Zeevi
- , Tal Korem
- & Eran Segal
-
Letter |
Genomic insights into the 2016–2017 cholera epidemic in Yemen
Isolates of the Vibrio cholerae O1 serotype Ogawa from Yemen are from a single sublineage of the seventh pandemic El Tor (7PET) lineage and are susceptible to several commonly used antibiotics as well as to polymyxins.
- François-Xavier Weill
- , Daryl Domman
- & Marie-Laure Quilici
-
Letter |
An exclusive metabolic niche enables strain engraftment in the gut microbiota
Finely tuned control of strain engraftment and abundance in the mouse gut microbiota was achieved using the marine polysaccharide porphyran, which could exclusively be used by an introduced subset of wild-type or genetically modified Bacteroides strains.
- Elizabeth Stanley Shepherd
- , William C. DeLoache
- & Justin L. Sonnenburg
-
Article |
Environment dominates over host genetics in shaping human gut microbiota
Statistical analyses of a metagenomics-sequenced human cohort identify a relatively minor role for genetics in determining microbiome composition and show that several human phenotypes are as strongly associated with the gut microbiome as with host genetics.
- Daphna Rothschild
- , Omer Weissbrod
- & Eran Segal
-
Article |
Dietary trehalose enhances virulence of epidemic Clostridium difficile
Two hypervirulent ribotypes of the enteric pathogen Clostridium difficile, RT027 and RT078, have independently acquired unique mechanisms to metabolize low concentrations of the disaccharide trehalose, suggesting a correlation between the emergence of these ribotypes and the widespread adoption of trehalose in the human diet.
- J. Collins
- , C. Robinson
- & R. A. Britton
-
Letter |
Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist
Both F17-like and type 1 pili promote intestinal colonization in mouse colonic crypts, and the high-affinity mannoside M4284 reduces intestinal colonization of uropathogenic Escherichia coli while simultaneously treating urinary tract infections without disrupting the composition of the gut microbiota.
- Caitlin N. Spaulding
- , Roger D. Klein
- & Scott J. Hultgren
-
Letter |
Deletion of a mycobacterial divisome factor collapses single-cell phenotypic heterogeneity
The mycobacterial protein LamA functions as an inhibitor of cell wall synthesis at the nascent cell pole, contributing to asymmetry in polar growth, and could represent a much-needed target for the development of anti-tuberculosis therapies.
- E. Hesper Rego
- , Rebecca E. Audette
- & Eric J. Rubin
-
Letter |
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Genome sequencing of Zika virus samples from infected patients and Aedes aegypti mosquitoes in Florida shows that the virus was probably introduced into the United States on multiple occasions, and that the Caribbean is the most likely source.
- Nathan D. Grubaugh
- , Jason T. Ladner
- & Kristian G. Andersen
-
Letter |
Prophage WO genes recapitulate and enhance Wolbachia-induced cytoplasmic incompatibility
The discovery of two genes encoded by prophage WO from Wolbachia that functionally recapitulate and enhance cytoplasmic incompatibility in arthropods is the first inroad in solving the genetic basis of reproductive parasitism.
- Daniel P. LePage
- , Jason A. Metcalf
- & Seth R. Bordenstein
-
Article |
Tempo and mode of genome evolution in a 50,000-generation experiment
Whole-genome sequencing of 264 clones sampled from 12 Escherichia coli populations evolved over 50,000 generations under identical culture conditions is used to characterize the patterns and dynamics of genome evolution over time.
- Olivier Tenaillon
- , Jeffrey E. Barrick
- & Richard E. Lenski
-
Letter |
Mobile genes in the human microbiome are structured from global to individual scales
Mobile genes, which can be transferred between bacterial species in the microbiome to impart properties such as antibiotic resistance, are reflective of human activity and local diets.
- I. L. Brito
- , S. Yilmaz
- & E. J. Alm
-
Article |
Human gut microbes impact host serum metabolome and insulin sensitivity
Increased potential for branched-chain amino acid and lipopolysaccharide biosynthesis in the gut microbiome of insulin-resistant individuals suggests that changes in the serum metabolome induced by dysbiosis, and driven by only a handful of species, contribute to the development of diabetes.
- Helle Krogh Pedersen
- , Valborg Gudmundsdottir
- & Oluf Pedersen
-
Letter |
The nature of mutations induced by replication–transcription collisions
When transcription and replication machineries collide on DNA, they can cause mutations to occur in the area near the collision; these mutations are now shown to include two types—duplications/deletions within the transcription unit and base substitutions in the cis-regulatory element of gene expression.
- T. Sabari Sankar
- , Brigitta D. Wastuwidyaningtyas
- & Jue D. Wang
-
Letter |
Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing
Maximum-depth sequencing (MDS), a new method of detecting extremely rare variants within a bacterial population, is used to show that mutation rates in Escherichia coli vary across the genome by at least an order of magnitude, and also to uncover mechanisms of antibiotic-induced mutagenesis.
- Justin Jee
- , Aviram Rasouly
- & Evgeny Nudler
-
Letter |
The bacterial DnaA-trio replication origin element specifies single-stranded DNA initiator binding
The bacterial chromosome replication origin contains an indispensable element composed of a repeating trinucleotide motif, termed the DnaA-trio, that stabilizes DnaA binding on single-stranded DNA.
- Tomas T. Richardson
- , Omar Harran
- & Heath Murray
-
Letter
| Open AccessCulturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation
A novel approach is used to cultivate a substantial proportion of the human gut microbiota, representing an important step forward in characterizing the role of these bacteria in health and disease.
- Hilary P. Browne
- , Samuel C. Forster
- & Trevor D. Lawley
-
Letter |
Real-time, portable genome sequencing for Ebola surveillance
A nanopore DNA sequencer is used for real-time genomic surveillance of the Ebola virus epidemic in the field in Guinea; the authors demonstrate that it is possible to pack a genomic surveillance laboratory in a suitcase and transport it to the field for on-site virus sequencing, generating results within 24 hours of sample collection.
- Joshua Quick
- , Nicholas J. Loman
- & Miles W. Carroll
-
Article |
Endosymbiotic origin and differential loss of eukaryotic genes
Eukaryotes acquired their prokaryotic genes in two episodes of evolutionary influx corresponding to the origin of mitochondria and plastids, respectively, followed by extensive differential gene loss, uncovering a massive imprint of endosymbiosis in the nuclear genomes of complex cells.
- Chuan Ku
- , Shijulal Nelson-Sathi
- & William F. Martin
-
Letter |
Eye-like ocelloids are built from different endosymbiotically acquired components
Dinoflagellate eye-like ocelloids are built from pre-existing organelles of disparate origin, including a cornea-like layer made of mitochondria and a retinal body made of anastomosing plastids.
- Gregory S. Gavelis
- , Shiho Hayakawa
- & Brian S. Leander
-
Article |
CRISPR adaptation biases explain preference for acquisition of foreign DNA
In the bacterial immunity system CRISPR, spacer acquisition is facilitated near replication-termination regions.
- Asaf Levy
- , Moran G. Goren
- & Rotem Sorek
-
Letter |
Transferred interbacterial antagonism genes augment eukaryotic innate immune function
Documented cases of horizontal gene transfer from bacteria to eukaryotes are rare, but now, not only is a new class of transferred genes identified, the function of one representative is also demonstrated in its new setting, where it controls bacterial growth.
- Seemay Chou
- , Matthew D. Daugherty
- & Joseph D. Mougous
-
Article |
Biogeography and individuality shape function in the human skin metagenome
Previous work has shown that human skin is home to a rich and varied microbiota; here a metagenomic approach for samples from physiologically diverse body sites illuminates that the skin microbiota, including bacterial, fungal and viral members, is shaped by the local biogeography and yet marked by strong individuality.
- Julia Oh
- , Allyson L. Byrd
- & Julia A. Segre
-
Letter |
Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis
Three 1,000-year-old mycobacterial genomes from Peruvian human skeletons reveal that a member of the Mycobacterium tuberculosis complex derived from seals caused human disease before contact in the Americas.
- Kirsten I. Bos
- , Kelly M. Harkins
- & Johannes Krause
-
Article
| Open AccessInsights into the phylogeny and coding potential of microbial dark matter
Uncultivated archaeal and bacterial cells of major uncharted branches of the tree of life are targeted and sequenced using single-cell genomics; this enables resolution of many intra- and inter-phylum-level relationships, uncovers unexpected metabolic features that challenge established boundaries between the three domains of life, and leads to the proposal of two new superphyla.
- Christian Rinke
- , Patrick Schwientek
- & Tanja Woyke