Core gut microbial communities are maintained by beneficial interactions and strain variability in fish

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

(2019) Alan R. Pacheco et al.   Nature Communications

Structural variation in the gut microbiome associates with host health

(2019) David Zeevi et al.   NATURE

Determining Microbial Niche Breadth in the Environment for Better Ecosystem Fate Predictions

(2019) Emilie E. L. Muller   mSystems

Microbiome niche modification drives diurnal rumen community assembly, overpowering individual variability and diet effects

(2018) Yoav Shaani et al.   ISME Journal

Evaluating the core microbiota in complex communities: A systematic investigation

(2017) Carmen Astudillo-García et al.   ENVIRONMENTAL MICROBIOLOGY

Generalist species drive microbial dispersion and evolution

(2017) Sira Sriswasdi et al.   Nature Communications

Diet-induced changes of redox potential underlie compositional shifts in the rumen archaeal community

(2016) Nir Friedman et al.   ENVIRONMENTAL MICROBIOLOGY

Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants

(2016) Sheerli Kruger Ben Shabat et al.   ISME Journal

A bacterial filter protects and structures the gut microbiome of an insect

(2016) Michele Caroline Lanan et al.   ISME Journal

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The Ecology and Evolution of Microbial Competition

(2016) Melanie Ghoul et al.   TRENDS IN MICROBIOLOGY

Diversity, structure and convergent evolution of the global sponge microbiome

(2016) Torsten Thomas et al.   Nature Communications

Microbiota and Host Nutrition across Plant and Animal Kingdoms

(2015) Stéphane Hacquard et al.   Cell Host & Microbe

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

The ecology of the microbiome: Networks, competition, and stability

(2015) K. Z. Coyte et al.   SCIENCE

The effects of space and diversity of interaction types on the stability of complex ecological networks

(2015) Miguel Lurgi et al.   Theoretical Ecology

The Application of the Biolog EcoPlate Approach in Ecotoxicological Evaluation of Dairy Sewage Sludge

(2014) Agata Gryta et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations

(2014) Torey Looft et al.   ISME Journal

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota

(2013) Zhigang Zhang et al.   ISME Journal

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The bacterial communities in plant phloem-sap-feeding insects

(2013) Xiangfeng Jing et al.   MOLECULAR ECOLOGY

Involvement of dietary salt in shaping bacterial communities in European sea bass (Dicentrarchus labrax)

(2013) Haifeng Sun et al.   Scientific Reports

NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species

(2012) Anat Kreimer et al.   BIOINFORMATICS

Quantification of the relative roles of niche and neutral processes in structuring gastrointestinal microbiomes

(2012) P. Jeraldo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecological Populations of Bacteria Act as Socially Cohesive Units of Antibiotic Production and Resistance

(2012) O. X. Cordero et al.   SCIENCE

Beyond the Venn diagram: the hunt for a core microbiome

(2011) Ashley Shade et al.   ENVIRONMENTAL MICROBIOLOGY

Comparative analyses of foregut and hindgut bacterial communities in hoatzins and cows

(2011) Filipa Godoy-Vitorino et al.   ISME Journal

Evidence for a core gut microbiota in the zebrafish

(2011) Guus Roeselers et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Ribosomal RNA diversity predicts genome diversity in gut bacteria and their relatives

(2010) Jesse R. Zaneveld et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Stability of Ecological Communities and the Architecture of Mutualistic and Trophic Networks

(2010) E. Thebault et al.   SCIENCE

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

The architecture of mutualistic networks minimizes competition and increases biodiversity

(2009) Ugo Bastolla et al.   NATURE

Niche Expansion and the Niche Variation Hypothesis: Does the Degree of Individual Variation Increase in Depauperate Assemblages?

(2008) Gabriel C. Costa et al.   AMERICAN NATURALIST

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS