Nature Search

Evolutionary loss of the rdar morphotype in Salmonella as a result of high mutation rates during laboratory passage

Carla J Davidson
Aaron P White
Michael G Surette
Research07 Feb 2008
The ISME Journal

Volume: 2, P: 293-307
Author Correction: Discovery and artificial intelligence-guided mechanistic elucidation of a narrow-spectrum antibiotic

Denise B. Catacutan
Vian Tran
Jonathan M. Stokes
Amendments and Corrections24 Oct 2025
Nature Microbiology

Volume: 10, P: 3363
An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense

Using a CRISPR interference genetic approach, Bullen, Johnson, and colleagues discover a type IV restriction (TIV-RE) enzyme encoded on a mobilizable plasmid of multidrug resistant Enterococcus faecalis. This TIV-RE is a potent inhibitor of bacteriophage infection.

Nathan P. Bullen
Cydney N. Johnson
Breck A. Duerkop
ResearchOpen Access13 Aug 2024
Nature Communications

Volume: 15, P: 1-13
Erratum: Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age

Jennifer C Stearns
Carla J Davidson
Michael G Surette
Amendments and Corrections21 Apr 2015
The ISME Journal

Volume: 9, P: 1268
Discovery and artificial intelligence-guided mechanistic elucidation of a narrow-spectrum antibiotic

Enterololin is a narrow-spectrum antibiotic that selectively kills Enterobacteriaceae in vitro and in a mouse model of adherent-invasive Escherichia coli gut infection. AI-guided mechanism-of-action studies identified LolCDE as its molecular target.

Denise B. Catacutan
Vian Tran
Jonathan M. Stokes
Research03 Oct 2025
Nature Microbiology

Volume: 10, P: 2808-2822
The interplay between the intestinal microbiota and the brain

A bidirectional neurohumoral communication system known as the gut–brain axis integrates the activities of the intestine and the brain. In this Progress article, Collins, Surette and Bercik describe recent evidence suggesting that the intestinal microbiota is intimately connected with the gut–brain axis and can influence animal behaviour, development and health.

Stephen M. Collins
Michael Surette
Premysl Bercik
Reviews24 Sept 2012
Nature Reviews Microbiology

Volume: 10, P: 735-742
A comprehensive library of fluorescent transcriptional reporters for Escherichia coli

Alon Zaslaver
Anat Bren
Uri Alon
Research21 Jul 2006
Nature Methods

Volume: 3, P: 623-628
Detecting microbial engraftment after FMT using placebo sequencing and culture enriched metagenomics to sort signals from noise

Here, the authors profile bacterial engraftment in UC patients receiving FMT from a single donor and placebo samples to estimate noise, showing a significant level of false-positive engraftment, which confounds the prediction of true engraftment, while analyzing engraftment across multiple patients from a single donor enhances the accuracy of detection.

Shahrokh Shekarriz
Jake C. Szamosi
Michael G. Surette
ResearchOpen Access11 Apr 2025
Nature Communications

Volume: 16, P: 1-12
Communication in bacteria: an ecological and evolutionary perspective

Quorum sensing is a bacterial cell-to-cell communication process that involves secreted chemical-signalling molecules. Laurent Keller and Michael Surette discuss quorum sensing and cell?cell communication from an evolutionary and ecological perspective, and reveal that the nature of the interactions goes beyond simple cooperative communication.

Laurent Keller
Michael G. Surette
Reviews27 Feb 2006
Nature Reviews Microbiology

Volume: 4, P: 249-258
Coniontins, lipopetaibiotics active against Candida auris identified from a microbial natural product fractionation library

In this work, authors utilise a prefractionation natural product extract screening platform, which uncovers coniotins, lipopeptaibiotics with broad antifungal activity and a mechanism of action that targets fungal cell wall β-glucan.

Xuefei Chen
Kalinka Koteva
Gerard D. Wright
ResearchOpen Access08 Aug 2025
Nature Communications

Volume: 16, P: 1-19
Mutation rate plasticity in rifampicin resistance depends on Escherichia coli cell–cell interactions

The factors varying mutation rate at a particular site in a single genotype remain elusive. Here, Krašovec et al. show that mutation rates at sites conferring resistance to rifampicin in Escherichia coli decrease with population density, and that mutation-rate plasticity is controlled by the luxSgene.

Rok Krašovec
Roman V. Belavkin
Christopher G. Knight
ResearchOpen Access29 Apr 2014
Nature Communications

Volume: 5, P: 1-8
Author Correction: Chronic exposure to synthetic food colorant Allura Red AC promotes susceptibility to experimental colitis via intestinal serotonin in mice

Yun Han Kwon
Suhrid Banskota
Waliul I. Khan
Amendments and CorrectionsOpen Access30 May 2023
Nature Communications

Volume: 14, P: 1
Culture-enriched metagenomic sequencing enables in-depth profiling of the cystic fibrosis lung microbiota

The PLate Coverage Algorithm (PLCA) determines the culture plates required for culture-enriched metagenomics and enables the recovery of greater taxonomic diversity, better quality metagenome-assembled genomes and improved functional annotations compared to metagenomics alone, indicating its utility for other microbiomes, especially those dominated by host DNA.

Fiona J. Whelan
Barbara Waddell
Michael G. Surette
Research20 Jan 2020
Nature Microbiology

Volume: 5, P: 379-390
Gain-of-function variants in SYK cause immune dysregulation and systemic inflammation in humans and mice

Individuals with SYK gain-of-function variants develop immunodeficiency and systemic inflammation, which are recapitulated in a knock-in mouse model. Treatment of these mice with bone marrow transplantation or with a SYK inhibitor ameliorates disease symptoms, highlighting potential therapeutic strategies for patients with SYK mutations.

Lin Wang
Dominik Aschenbrenner
Aleixo M. Muise
Research29 Mar 2021
Nature Genetics

Volume: 53, P: 500-510
Cost of cell–cell signalling in Pseudomonas aeruginosa: why it can pay to be signal-blind

Laurent Keller
Michael G. Surette
Correspondence01 Jul 2006
Nature Reviews Microbiology

Volume: 4, P: 562
Chronic exposure to synthetic food colorant Allura Red AC promotes susceptibility to experimental colitis via intestinal serotonin in mice

Allura Red AC is a dye used in food products. Here the authors report that chronic, long-term exposure to Allura Red AC increases susceptibility to experimental colitis in mice dependent on the serotonin biosynthetic enzyme TPH1, while intermittent exposure more typical for the human setting did not increase susceptibility to experimental colitis.

Yun Han Kwon
Suhrid Banskota
Waliul I. Khan
ResearchOpen Access20 Dec 2022
Nature Communications

Volume: 13, P: 1-18
Deep learning-guided discovery of an antibiotic targeting Acinetobacter baumannii

Using a neural network trained on bacterial growth inhibition data, in silico prediction of molecules with activity against Acinetobacter baumannii led to the identification of the narrow-spectrum abaucin, which perturbs lipoprotein trafficking.

Gary Liu
Denise B. Catacutan
Jonathan M. Stokes
Research25 May 2023
Nature Chemical Biology

Volume: 19, P: 1342-1350
Streptomyces uses both polar and dispersed cell wall synthesis during exploratory growth

Streptomyces venezuelae requires MreB1-dependent dispersed peptidoglycan cell wall synthesis and DivIVA-mediated polar cell wall synthesis during its rapid exploratory growth phase.

Matthew P. Zambri
Christine R. Baglio
Marie A. Elliot
ResearchOpen Access08 Aug 2025
Nature Microbiology

Volume: 10, P: 2245-2256
Genetic signature of bacterial pathogen adaptation during chronic pulmonary infections

To establish and maintain chronic infections, many pathogens adapt in response to selective pressures within the host, leaving unique genetic signatures. A new study uses whole-genome and population sequencing approaches to identify evidence of adaptive evolution in Burkholderia dolosa genomes isolated from chronic infections in patients with cystic fibrosis.

Steve P Bernier
Matthew L Workentine
Michael G Surette
News & Views27 Dec 2013
Nature Genetics

Volume: 46, P: 5-6
Fetal meconium does not have a detectable microbiota before birth

Fetal meconium does not have a detectable microbiota, as shown using 16S rRNA sequencing and culture of rectal swabs collected during elective breech caesarean sections without labour and before antibiotics, indicating that colonization occurs during and after birth.

Katherine M. Kennedy
Max J. Gerlach
Thorsten Braun
Research10 May 2021
Nature Microbiology

Volume: 6, P: 865-873
Just-in-time transcription program in metabolic pathways

Alon Zaslaver
Avi E Mayo
Uri Alon
Research25 Apr 2004
Nature Genetics

Volume: 36, P: 486-491
Duodenal bacterial proteolytic activity determines sensitivity to dietary antigen through protease-activated receptor-2

Gluten triggers celiac disease in genetically predisposed individuals, but additional unknown mechanisms are required. Here, the authors show that proteases from Pseudomonas aeruginosa can modulate inflammatory pathways that are relevant to the development of food sensitivities, independently of the trigger antigen.

Alberto Caminero
Justin L. McCarville
Elena F. Verdu
ResearchOpen Access13 Mar 2019
Nature Communications

Volume: 10, P: 1-14
Intrapartum antibiotics for GBS prophylaxis alter colonization patterns in the early infant gut microbiome of low risk infants

Jennifer C. Stearns
Julia Simioni
Eileen K. Hutton
ResearchOpen Access28 Nov 2017
Scientific Reports

Volume: 7, P: 1-9
Credible inferences in microbiome research: ensuring rigour, reproducibility and relevance in the era of AI

Artificial intelligence (AI) is a powerful tool that could be applied to microbiome research. This Perspective discusses best practices and current limitations with the application of AI in microbiome data research, giving insights into future use and practical advice and recommendations on its use.

Alberto Caminero
Carolina Tropini
Elena F. Verdu
Reviews31 Jul 2025
Nature Reviews Gastroenterology & Hepatology

Volume: 22, P: 788-803
Type 2 diabetes influences bacterial tissue compartmentalisation in human obesity

Anhê et al. demonstrate that bacterial signatures of plasma, liver and three distinct adipose tissue depots can distinguish between type 2 diabetes and normoglycaemia in people with obesity.

Fernando F. Anhê
Benjamin Anderschou Holbech Jensen
André Marette
Research09 Mar 2020
Nature Metabolism

Volume: 2, P: 233-242
Author Correction: Gain-of-function variants in SYK cause immune dysregulation and systemic inflammation in humans and mice

Lin Wang
Dominik Aschenbrenner
Aleixo M. Muise
Amendments and Corrections05 Jan 2022
Nature Genetics

Volume: 54, P: 213
Synthesis of metal-doped nanoplastics and their utility to investigate fate and behaviour in complex environmental systems

Analytical challenges in detecting nanoplastics have hindered the understanding of their behaviour in environmental systems, but these difficulties can be circumvented by synthesizing metal-doped nanoplastics (where the metal can be measured as a proxy for the plastic) to undertake mechanistic investigations of particle fate, transport and biological interactions in lab and pilot-scale studies.

Denise M. Mitrano
Anna Beltzung
Felix Schmidt
Research04 Feb 2019
Nature Nanotechnology

Volume: 14, P: 362-368
Impact of CFTR modulation with Ivacaftor on Gut Microbiota and Intestinal Inflammation

Chee Y. Ooi
Saad A. Syed
Tanja Gonska
ResearchOpen Access13 Dec 2018
Scientific Reports

Volume: 8, P: 1-8
An excitable gene regulatory circuit induces transient cellular differentiation

Time-lapse imaging is used to follow the activity of several promoters that regulate competence genes in Bacillus subtilis, and the data used to develop a mathematical model of the gene circuitry — revealing that excitable dynamics underlies the positive and negative feedback loops that regulate entry into, and exit from, competence in an individual cell.

Gürol M. Süel
Jordi Garcia-Ojalvo
Michael B. Elowitz
Research23 Mar 2006
Nature

Volume: 440, P: 545-550
Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

This Perspective reviews the evidence for and against the existence of a fetal microbiome and concludes that detected microbial signals are most likely the result of contamination, suggesting that the ‘sterile womb’ hypothesis is correct.

Katherine M. Kennedy
Marcus C. de Goffau
Jens Walter
Reviews25 Jan 2023
Nature

Volume: 613, P: 639-649
The natural history and genetic diversity of Haemophilus influenzae infecting the airways of adults with cystic fibrosis

Conrad Izydorczyk
Barbara J. Waddell
Michael D. Parkins
ResearchOpen Access21 Sept 2022
Scientific Reports

Volume: 12, P: 1-13
A genetic screen identifies a role for oprF in Pseudomonas aeruginosa biofilm stimulation by subinhibitory antibiotics

Luke N. Yaeger
Michael R. M. Ranieri
Lori L. Burrows
ResearchOpen Access23 Mar 2024
npj Biofilms and Microbiomes

Volume: 10, P: 1-12
Modulation of Salmonella gene expression by subinhibitory concentrations of quinolones

Grace Yim
JoAnn McClure
Julian E Davies
Research24 Nov 2010
The Journal of Antibiotics

Volume: 64, P: 73-78
Milk Fat Globule Membrane Supplementation in Formula Modulates the Neonatal Gut Microbiome and Normalizes Intestinal Development

Ganive Bhinder
Joannie M. Allaire
Bruce A. Vallance
ResearchOpen Access28 Mar 2017
Scientific Reports

Volume: 7, P: 1-15
Obesity during pregnancy results in maternal intestinal inflammation, placental hypoxia, and alters fetal glucose metabolism at mid-gestation

Jessica G. Wallace
Christian J. Bellissimo
Deborah M. Sloboda
ResearchOpen Access26 Nov 2019
Scientific Reports

Volume: 9, P: 1-16
Oral selective serotonin reuptake inhibitors activate vagus nerve dependent gut-brain signalling

Karen-Anne McVey Neufeld
John Bienenstock
Paul Forsythe
ResearchOpen Access03 Oct 2019
Scientific Reports

Volume: 9, P: 1-11
Commensal microbiota induces colonic barrier structure and functions that contribute to homeostasis

Christina L. Hayes
Jasmine Dong
Elena F. Verdu
ResearchOpen Access21 Sept 2018
Scientific Reports

Volume: 8, P: 1-14
Association of host genome with intestinal microbial composition in a large healthy cohort

Kenneth Croitoru, Andrew Paterson and colleagues perform genome-wide association analysis for gut microbiome composition. They identify 58 SNPs significantly associated with relative abundance of 33 taxa and replicate 4 of the associations in an independent cohort, providing further evidence that host genetics can influence the gut microbiota.

Williams Turpin
Osvaldo Espin-Garcia
Kenneth Croitoru
Research03 Oct 2016
Nature Genetics

Volume: 48, P: 1413-1417
Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age

Jennifer C Stearns
Carla J Davidson
Michael G Surette
Research09 Jan 2015
The ISME Journal

Volume: 9, P: 1246-1259

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