Nature Search

The emergence of microbiome centres

As microbiome science expands, academic centres scramble to fill many needs, from service provider to industry liaison. A newly created network aims to share strategies and accelerate knowledge transfer, and invites others to join the efforts.

Jennifer B. H. Martiny
Katrine L. Whiteson
Joel L. Sachs
Comments & Opinion19 Dec 2019
Nature Microbiology

Volume: 5, P: 2-3
Auto-deconvolution and molecular networking of gas chromatography–mass spectrometry data

A machine learning workflow enables auto-deconvolution of gas chromatography–mass spectrometry data.

Alexander A. Aksenov
Ivan Laponogov
Kirill Veselkov
Research09 Nov 2020
Nature Biotechnology

Volume: 39, P: 169-173
Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents

Martin J Blaser
Maria G Dominguez-Bello
Rob Knight
Research16 Aug 2012
The ISME Journal

Volume: 7, P: 85-95
The Western English Channel contains a persistent microbial seed bank

J Gregory Caporaso
Konrad Paszkiewicz
Jack A Gilbert
ResearchOpen Access10 Nov 2011
The ISME Journal

Volume: 6, P: 1089-1093
Biphasic assembly of the murine intestinal microbiota during early development

Ida Gisela Pantoja-Feliciano
Jose C Clemente
Maria Gloria Dominguez-Bello
ResearchOpen Access28 Mar 2013
The ISME Journal

Volume: 7, P: 1112-1115
Regional variation limits applications of healthy gut microbiome reference ranges and disease models

The definition of a 'healthy' microbiome is impacted by geographic regional variations.

Yan He
Wei Wu
Hong-Wei Zhou
Research27 Aug 2018
Nature Medicine

Volume: 24, P: 1532-1535
Farm-like indoor microbiota in non-farm homes protects children from asthma development

Exposure to a farm-like house dust microbiome is associated with protection against asthma development in children living in urban environments.

Pirkka V. Kirjavainen
Anne M. Karvonen
Juha Pekkanen
Research17 Jun 2019
Nature Medicine

Volume: 25, P: 1089-1095
ReDU: a framework to find and reanalyze public mass spectrometry data

Repository-scale reanalysis of public mass spectrometry-based metabolomics data is facilitated by the Reanalysis of Data User (ReDU) interface, a system that uses consistent formatting and controlled vocabularies for metadata capture.

Alan K. Jarmusch
Mingxun Wang
Pieter C. Dorrestein
Research17 Aug 2020
Nature Methods

Volume: 17, P: 901-904
Antibiotic-perturbed microbiota and the role of probiotics

In this Review, Szajewska, Scott and colleagues discuss the evidence for antibiotic-mediated perturbation of the gut microbiota and whether probiotics can help restore an antibiotic-disrupted microbiota.

Hania Szajewska
Karen P. Scott
Mary Ellen Sanders
Reviews11 Dec 2024
Nature Reviews Gastroenterology & Hepatology

Volume: 22, P: 155-172
Unlocking the potential of metagenomics through replicated experimental design

Rob Knight
Janet Jansson
Jack A Gilbert
Reviews07 Jun 2012
Nature Biotechnology

Volume: 30, P: 513-520
Microbiota restoration: natural and supplemented recovery of human microbial communities

The composition of the human microbiota at various body sites can become altered following injury, infection and antibiotic treatment. In this Review, Gregor Reid and colleagues describe how a healthy microbiota can be restored, either naturally or aided by probiotic treatment, following such challenge.

Gregor Reid
Jessica A. Younes
Henk J. Busscher
Reviews29 Nov 2010
Nature Reviews Microbiology

Volume: 9, P: 27-38
Genome-wide association analysis of more than 120,000 individuals identifies 15 new susceptibility loci for breast cancer

Doug Easton and colleagues report the results of a large-scale genome-wide association study of breast cancer. They discover 15 new susceptibility loci and highlight likely target genes in several of the newly associated regions.

Kyriaki Michailidou
Jonathan Beesley
Douglas F Easton
Research09 Mar 2015
Nature Genetics

Volume: 47, P: 373-380
Leveling up citizen science

Jérôme Waldispühl
Attila Szantner
Randy Pitchford
Correspondence24 Sept 2020
Nature Biotechnology

Volume: 38, P: 1124-1126
Enhancing untargeted metabolomics using metadata-based source annotation

Metabolomics is improved by using a reference library of both known and unknown molecules.

Julia M. Gauglitz
Kiana A. West
Pieter C. Dorrestein
Research07 Jul 2022
Nature Biotechnology

Volume: 40, P: 1774-1779
Mass spectrometry searches using MASST

Mingxun Wang
Alan K. Jarmusch
Pieter C. Dorrestein
Correspondence01 Jan 2020
Nature Biotechnology

Volume: 38, P: 23-26
UniFrac: an effective distance metric for microbial community comparison

Catherine Lozupone
Manuel E Lladser
Rob Knight
Comments & Opinion09 Sept 2010
The ISME Journal

Volume: 5, P: 169-172
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

The functional composition of microbial community samples from several environments is predicted based on 16S ribosomal RNA gene sequencing data.

Morgan G I Langille
Jesse Zaneveld
Curtis Huttenhower
Research25 Aug 2013
Nature Biotechnology

Volume: 31, P: 814-821
GABA-modulating bacteria of the human gut microbiota

A bacterial strain that requires the neurotransmitter GABA for growth was identified and used to isolate GABA-producing bacteria, including Bacteroides spp., from human stool samples; the relative abundance of Bacteroides was negatively correlated with an altered GABA-mediated response in a depression patient cohort.

Philip Strandwitz
Ki Hyun Kim
Kim Lewis
Research10 Dec 2018
Nature Microbiology

Volume: 4, P: 396-403
Home chemical and microbial transitions across urbanization

Here, the authors use metabolomics and sequencing to assess changes in chemicals and microbial communities, including fungi and microeukaryotes, across an urbanization gradient in South America.

Laura-Isobel McCall
Chris Callewaert
Maria G. Dominguez-Bello
Research04 Nov 2019
Nature Microbiology

Volume: 5, P: 108-115
Reporting guidelines for human microbiome research: the STORMS checklist

The STORMS tool provides guidance for concise and complete reporting of microbiome studies to facilitate manuscript preparation, peer review, reader comprehension of publications, and comparative analysis of published results.

Chloe Mirzayi
Audrey Renson
Levi Waldron
Reviews17 Nov 2021
Nature Medicine

Volume: 27, P: 1885-1892
Postprandial remodeling of the gut microbiota in Burmese pythons

Elizabeth K Costello
Jeffrey I Gordon
Rob Knight
Research03 Jun 2010
The ISME Journal

Volume: 4, P: 1375-1385
Patterns of Oral Microbiota Diversity in Adults and Children: A Crowdsourced Population Study

Zachary M. Burcham
Nicole L. Garneau
Willy Reusser
ResearchOpen Access07 Feb 2020
Scientific Reports

Volume: 10, P: 1-15
Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat

J Kirk Harris
J Gregory Caporaso
Norman R Pace
ResearchOpen Access26 Jul 2012
The ISME Journal

Volume: 7, P: 50-60
Bacterial communities of disease vectors sampled across time, space, and species

Ryan T Jones
Rob Knight
Andrew P Martin
Research29 Oct 2009
The ISME Journal

Volume: 4, P: 223-231
Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

Jeffrey J Werner
Omry Koren
Ruth E Ley
Research30 Jun 2011
The ISME Journal

Volume: 6, P: 94-103
A comprehensive survey of soil acidobacterial diversity using pyrosequencing and clone library analyses

Ryan T Jones
Michael S Robeson
Noah Fierer
Research08 Jan 2009
The ISME Journal

Volume: 3, P: 442-453
A core gut microbiome in obese and lean twins

The human microbiota has been implicated in many health-related issues. In this study, the microbiota composition of monozygotic and dizygotic twins and their mothers is examined. Although a core microbiome could not be defined on a phylogenetic level, the data suggests that core functions are conserved.

Peter J. Turnbaugh
Micah Hamady
Jeffrey I. Gordon
Research30 Nov 2008
Nature

Volume: 457, P: 480-484
New loci associated with birth weight identify genetic links between intrauterine growth and adult height and metabolism

Rachel Freathy and colleagues report results of a large-scale genome-wide association study of birth weight. They identify four loci newly associated with this trait and find overlap between birth weight–associated loci and those influencing adult height and metabolism.

Momoko Horikoshi
Hanieh Yaghootkar
Rachel M Freathy
Research02 Dec 2012
Nature Genetics

Volume: 45, P: 76-82
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
Research21 May 2014
Nature

Volume: 509, P: 612-616
Consuming a modified Mediterranean ketogenic diet reverses the peripheral lipid signature of Alzheimer’s disease in humans

Neth, Huynh et al. evaluate whether consuming a modified Mediterranean ketogenic diet alters parts of the plasma lipidome associated with development of Alzheimer’s disease (AD). Consuming the ketogenic diet alters the plasma lipidome, with changes inversely linked to Alzheimer’s disease (AD) biomarkers and lipidomic signatures.

Bryan J. Neth
Kevin Huynh
Rima Kaddurah-Daouk
ResearchOpen Access09 Jan 2025
Communications Medicine

Volume: 5, P: 1-15
At-admission prediction of mortality and pulmonary embolism in an international cohort of hospitalised patients with COVID-19 using statistical and machine learning methods

Munib Mesinovic
Xin Ci Wong
David Zucman
ResearchOpen Access16 Jul 2024
Scientific Reports

Volume: 14, P: 1-43
Predicting bee community responses to land-use changes: Effects of geographic and taxonomic biases

Adriana De Palma
Stefan Abrahamczyk
Andy Purvis
ResearchOpen Access11 Aug 2016
Scientific Reports

Volume: 6, P: 1-14
The changing metabolic landscape of bile acids – keys to metabolism and immune regulation

Bile acids have important roles in human metabolism and immune regulation. In this Perspective, Dorrestein and colleagues discuss the technologies and data science-related approaches that are improving our understanding of the diversity of bile acids and their multifaceted roles.

Ipsita Mohanty
Celeste Allaband
Pieter C. Dorrestein
Reviews04 Apr 2024
Nature Reviews Gastroenterology & Hepatology

Volume: 21, P: 493-516
The Human Microbiome Project

Peter J. Turnbaugh
Ruth E. Ley
Jeffrey I. Gordon
Special Features17 Oct 2007
Nature

Volume: 449, P: 804-810
Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

GNPS is an open-access community-curated analysis platform for sharing natural product mass spectrometry data that enables continuous, automatic reanalysis of deposited 'living' data sets.

Mingxun Wang
Jeremy J Carver
Nuno Bandeira
Reviews09 Aug 2016
Nature Biotechnology

Volume: 34, P: 828-837
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

Pelin Yilmaz
Renzo Kottmann
Frank Oliver Glöckner
Reviews06 May 2011
Nature Biotechnology

Volume: 29, P: 415-420
Whole-body metabolic modelling reveals microbiome and genomic interactions on reduced urine formate levels in Alzheimer’s disease

Filippo Martinelli
Almut Heinken
Ines Thiele
ResearchOpen Access13 Mar 2024
Scientific Reports

Volume: 14, P: 1-14
ConStrains identifies microbial strains in metagenomic datasets

Different bacterial strains in a metagenome are distinguished using a method that detects SNPs in conserved genes.

Chengwei Luo
Rob Knight
Dirk Gevers
Research07 Sept 2015
Nature Biotechnology

Volume: 33, P: 1045-1052
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

The Microbiome Quality Control project consortium reports outcomes of a baseline study (MBQC) that will guide future improvements in reproducibility of microbiome analyses.

Rashmi Sinha
Galeb Abu-Ali
Curtis Huttenhower
Research02 Oct 2017
Nature Biotechnology

Volume: 35, P: 1077-1086
Creating a 3D microbial and chemical snapshot of a human habitat

Clifford A. Kapono
James T. Morton
Pieter C. Dorrestein
ResearchOpen Access27 Feb 2018
Scientific Reports

Volume: 8, P: 1-12
Soil bacterial and fungal communities across a pH gradient in an arable soil

Johannes Rousk
Erland Bååth
Noah Fierer
Research06 May 2010
The ISME Journal

Volume: 4, P: 1340-1351
Defining seasonal marine microbial community dynamics

Jack A Gilbert
Joshua A Steele
Dawn Field
ResearchOpen Access18 Aug 2011
The ISME Journal

Volume: 6, P: 298-308
Dietary input of microbes and host genetic variation shape among-population differences in stickleback gut microbiota

Chris CR Smith
Lisa K Snowberg
Daniel I Bolnick
Research24 Apr 2015
The ISME Journal

Volume: 9, P: 2515-2526
A meta-analysis of changes in bacterial and archaeal communities with time

Ashley Shade
J Gregory Caporaso
Noah Fierer
ResearchOpen Access11 Apr 2013
The ISME Journal

Volume: 7, P: 1493-1506
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

J Gregory Caporaso
Christian L Lauber
Rob Knight
ResearchOpen Access08 Mar 2012
The ISME Journal

Volume: 6, P: 1621-1624
Associations between gut microbiota and incident fractures in the FINRISK cohort

Louise Grahnemo
Oleg Kambur
Claes Ohlsson
ResearchOpen Access14 Aug 2024
npj Biofilms and Microbiomes

Volume: 10, P: 1-10
Serum and CSF metabolomics analysis shows Mediterranean Ketogenic Diet mitigates risk factors of Alzheimer’s disease

Annalise Schweickart
Richa Batra
Jan Krumsiek
ResearchOpen Access01 Jul 2024
npj Metabolic Health and Disease

Volume: 2, P: 1-11
Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols

Samuel P. Forry
Stephanie L. Servetas
Scott A. Jackson
ResearchOpen Access29 Apr 2024
Scientific Reports

Volume: 14, P: 1-14
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen
Jai Ram Rideout
J. Gregory Caporaso
Correspondence24 Jul 2019
Nature Biotechnology

Volume: 37, P: 852-857
Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota

Anton Lavrinienko
Eugene Tukalenko
Phillip C. Watts
ResearchOpen Access23 Sept 2020
Scientific Data

Volume: 7, P: 1-7

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