Nature Search

Shipped and shifted: modeling collection-induced bias in microbiome multi-omics using a tractable fermentation system

Annina R. Meyer
Jan Patrick Tan
Nicholas A. Bokulich
ResearchOpen Access09 Jan 2026
npj Biofilms and Microbiomes

P: 1-18
Rising together: exploring sourdough fermentation diversity through co-design in the HealthFerm citizen science initiative

Annina R. Meyer
Thomas Gettemans
Nicholas A. Bokulich
ResearchOpen Access27 Jan 2026
npj Science of Food

P: 1-14
Grape expectations: disentangling environmental drivers of microbiome establishment in winegrowing ecosystems

Lena Flörl
Patrik Schönenberger
Nicholas A. Bokulich
ResearchOpen Access16 Jan 2026
npj Biofilms and Microbiomes

P: 1-18
Species abundance information improves sequence taxonomy classification accuracy

Taxonomy classification of amplicon sequences is an important step in investigating microbial communities in microbiome analysis. Here, the authors show incorporating environment-specific taxonomic abundance information can lead to improved species-level classification accuracy across common sample types.

Benjamin D. Kaehler
Nicholas A. Bokulich
Gavin A. Huttley
ResearchOpen Access11 Oct 2019
Nature Communications

Volume: 10, P: 1-10
Reply to: Examining microbe–metabolite correlations by linear methods

James T. Morton
Daniel McDonald
Rob Knight
Research04 Jan 2021
Nature Methods

Volume: 18, P: 40-41
The microbiota vault initiative: safeguarding Earth’s microbial heritage for future generations

Maria G. Dominguez-Bello
Dominik Steiger
Martin J. Blaser
ReviewsOpen Access27 Jun 2025
Nature Communications

Volume: 16, P: 1-6
Learning representations of microbe–metabolite interactions

mmvec, a neural-network-based algorithm, uses paired multiomics data (microbial sequence counts and metabolite abundances) to compute the conditional probability of observing a metabolite in the presence of a specific microorganism.

James T. Morton
Alexander A. Aksenov
Rob Knight
Research04 Nov 2019
Nature Methods

Volume: 16, P: 1306-1314
Author Correction: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Evan Bolyen
Jai Ram Rideout
J. Gregory Caporaso
Amendments and Corrections09 Aug 2019
Nature Biotechnology

Volume: 37, P: 1091
Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer

The microbiota of cesarean-born infants can be partially restored to that of vaginally born infants immediately after birth.

Maria G Dominguez-Bello
Kassandra M De Jesus-Laboy
Jose C Clemente
Research01 Feb 2016
Nature Medicine

Volume: 22, P: 250-253
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

A systematic evaluation of parameters that affect short amplicons sequenced on Illumina platforms provides guidelines for how to eliminate erroneous reads and improve data interpretation.

Nicholas A Bokulich
Sathish Subramanian
J Gregory Caporaso
Research01 Jan 2013
Nature Methods

Volume: 10, P: 57-59
Partial convergence of the human vaginal and rectal maternal microbiota in late gestation and early post-partum

Hakdong Shin
Keith A. Martinez II
Maria Gloria Dominguez-Bello
ResearchOpen Access13 Jun 2023
npj Biofilms and Microbiomes

Volume: 9, P: 1-6
A communal catalogue reveals Earth’s multiscale microbial diversity

As phase 1 of the Earth Microbiome Project, analysis of 16S ribosomal RNA sequences from more than 27,000 environmental samples delivers a global picture of the basic structure and drivers of microbial distribution.

Luke R. Thompson
Jon G. Sanders
Hongxia Zhao
ResearchOpen Access01 Nov 2017
Nature

Volume: 551, P: 457-463
Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment

The potential recovery of the human gut microbiota after an antibiotic treatment, and its effects on our health, are poorly understood. Here, the authors use a mouse model mimicking paediatric antibiotic use to shed new light into these processes.

Yael R. Nobel
Laura M. Cox
Martin J. Blaser
ResearchOpen Access30 Jun 2015
Nature Communications

Volume: 6, P: 1-15
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
Microbial melatonin metabolism in the human intestine as a therapeutic target for dysbiosis and rhythm disorders

Petra Zimmermann
Salome Kurth
Nicholas A. Bokulich
ReviewsOpen Access27 Nov 2024
npj Biofilms and Microbiomes

Volume: 10, P: 1-17

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