Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences

A strong link between marine microbial community composition and function challenges the idea of functional redundancy

(2018) Pierre E. Galand et al.   ISME Journal

Sediment bacterial community structures and their predicted functions implied the impacts from natural processes and anthropogenic activities in coastal area

(2018) Zhiguo Su et al.   MARINE POLLUTION BULLETIN

Human Gut Microbiome: Function Matters

(2018) Anna Heintz-Buschart et al.   TRENDS IN MICROBIOLOGY

Variations in bacterial and archaeal communities along depth profiles of Alaskan soil cores

(2018) Binu Mani Tripathi et al.   Scientific Reports

CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software

(2018) Toby J. Wilkinson et al.   Frontiers in Microbiology

Function and functional redundancy in microbial systems

(2018) Stilianos Louca et al.   Nature Ecology & Evolution

Antibiotic Effects on Microbial Communities Responsible for Denitrification and N2O Production in Grassland Soils

(2018) Miguel Semedo et al.   Frontiers in Microbiology

Using meta‐omics of contaminated sediments to monitor changes in pathways relevant to climate regulation

(2018) Simone C. Birrer et al.   ENVIRONMENTAL MICROBIOLOGY

Rumen microbiome in dairy calves fed copper and grape-pomace dietary supplementations: Composition and predicted functional profile

(2018) Filippo Biscarini et al.   PLoS One

Responses of soil biological traits and bacterial communities to nitrogen fertilization mediate maize yields across three soil types

(2018) Hailing Yu et al.   SOIL & TILLAGE RESEARCH

How Rainforest Conversion to Agricultural Systems in Sumatra (Indonesia) Affects Active Soil Bacterial Communities

(2018) Dirk Berkelmann et al.   Frontiers in Microbiology

Microbial community function in the bleaching disease of the marine macroalgae Delisea pulchra

(2017) Enrique Zozaya-Valdés et al.   ENVIRONMENTAL MICROBIOLOGY

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica

(2017) Hyunmin Koo et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Archaeal and bacterial communities of Xestospongia testudinaria and sediment differ in diversity, composition and predicted function in an Indonesian coral reef environment

(2017) Ana Rita Moura Polónia et al.   JOURNAL OF SEA RESEARCH

Metatranscriptomic data reveal the effect of different community properties on multifunctional redundancy

(2017) Sara Beier et al.   MOLECULAR ECOLOGY

The Effects of Cropping Regimes on Fungal and Bacterial Communities of Wheat and Faba Bean in a Greenhouse Pot Experiment Differ between Plant Species and Compartment

(2017) Sandra Granzow et al.   Frontiers in Microbiology

Deciphering composition and function of the root microbiome of a legume plant

(2017) Kyle Hartman et al.   Microbiome

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Bacterial endophyte communities of three agricultural important grass species differ in their response towards management regimes

(2017) Franziska Wemheuer et al.   Scientific Reports

Lack of functional redundancy in the relationship between microbial diversity and ecosystem functioning

(2016) Manuel Delgado-Baquerizo et al.   JOURNAL OF ECOLOGY

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

Functional Redundancy-Induced Stability of Gut Microbiota Subjected to Disturbance

(2016) Andrés Moya et al.   TRENDS IN MICROBIOLOGY

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes

(2016) Shoko Iwai et al.   PLoS One

Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

(2016) Kristin Kaiser et al.   Scientific Reports

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

Low multifunctional redundancy of soil fungal diversity at multiple scales

(2015) Akira S. Mori et al.   ECOLOGY LETTERS

The importance of the microbiome of the plant holobiont

(2015) Philippe Vandenkoornhuyse et al.   NEW PHYTOLOGIST

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

The extent of functional redundancy changes as species’ roles shift in different environments

(2015) Ingo Fetzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The green impact: bacterioplankton response toward a phytoplankton spring bloom in the southern North Sea assessed by comparative metagenomic and metatranscriptomic approaches

(2015) Bernd Wemheuer et al.   Frontiers in Microbiology

Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula

(2015) Jeff S. Bowman et al.   PLoS One

Effects of Fertilization and Sampling Time on Composition and Diversity of Entire and Active Bacterial Communities in German Grassland Soils

(2015) Sarah Herzog et al.   PLoS One

UProC: tools for ultra-fast protein domain classification

(2014) Peter Meinicke   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Core sediment bacteria drive community response to anthropogenic contamination over multiple environmental gradients

(2013) Melanie Y. Sun et al.   ENVIRONMENTAL MICROBIOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Biodiversity and multifunctionality in a microbial community: a novel theoretical approach to quantify functional redundancy

(2013) T. Miki et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Substrate-Controlled Succession of Marine Bacterioplankton Populations Induced by a Phytoplankton Bloom

(2012) H. Teeling et al.   SCIENCE

Multifunctionality and Diversity in Bacterial Biofilms

(2011) Hannes Peter et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

MULTIPLE FUNCTIONS INCREASE THE IMPORTANCE OF BIODIVERSITY FOR OVERALL ECOSYSTEM FUNCTIONING

(2008) Lars Gamfeldt et al.   ECOLOGY

Resistance, resilience, and redundancy in microbial communities

(2008) S. D. Allison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE