Understanding microbial community dynamics to improve optimal microbiome selection

Modular Assembly of Polysaccharide-Degrading Marine Microbial Communities

(2019) Tim N. Enke et al.   CURRENT BIOLOGY

Consistent changes in the taxonomic structure and functional attributes of bacterial communities during primary succession

(2018) Rüdiger Ortiz-Álvarez et al.   ISME Journal

Structural basis for chitin acquisition by marine Vibrio species

(2018) Anuwat Aunkham et al.   Nature Communications

Microscale ecology regulates particulate organic matter turnover in model marine microbial communities

(2018) Tim N. Enke et al.   Nature Communications

Genetic Analysis of Human Norovirus Strains in Japan in 2016–2017

(2018) Koo Nagasawa et al.   Frontiers in Microbiology

Marine chitinolytic enzymes, a biotechnological treasure hidden in the ocean?

(2018) Azadeh Beygmoradi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Cooperation in microbial communities and their biotechnological applications

(2017) Matteo Cavaliere et al.   ENVIRONMENTAL MICROBIOLOGY

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing

(2017) Luisa W. Hugerth et al.   Frontiers in Microbiology

Nutrient recycling facilitates long-term stability of marine microbial phototroph–heterotroph interactions

(2017) Joseph A. Christie-Oleza et al.   Nature Microbiology

Growth on Chitin Impacts the Transcriptome and Metabolite Profiles of Antibiotic-Producing Vibrio coralliilyticus S2052 and Photobacterium galatheae S2753

(2017) Sonia Giubergia et al.   mSystems

Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities

(2016) Ian M. Bradley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Microbial interactions lead to rapid micro-scale successions on model marine particles

(2016) Manoshi S. Datta et al.   Nature Communications

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Biogeography and environmental genomics of the Roseobacter-affiliated pelagic CHAB-I-5 lineage

(2016) Sara Billerbeck et al.   Nature Microbiology

Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre

(2016) Jessica A. Bryant et al.   mSystems

Metabolic interactions in microbial communities: untangling the Gordian knot

(2015) Olga Ponomarova et al.   CURRENT OPINION IN MICROBIOLOGY

Levels and limits in artificial selection of communities

(2015) Manuel Blouin et al.   ECOLOGY LETTERS

Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples

(2015) Alma E. Parada et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial Surface Colonization and Biofilm Development in Marine Environments

(2015) Hongyue Dang et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre

(2015) Kristina M. Fontanez et al.   Frontiers in Microbiology

Grazing resistant freshwater bacteria profit from chitin and cell-wall-derived organic carbon

(2013) Ester M. Eckert 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

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Bacterial chitin degradation—mechanisms and ecophysiological strategies

(2013) Sara Beier et al.   Frontiers in Microbiology

Bacterial Chitinolytic Communities Respond to Chitin and pH Alteration in Soil

(2012) Anna M. Kielak et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Public good dynamics drive evolution of iron acquisition strategies in natural bacterioplankton populations

(2012) O. X. Cordero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

Bacterial Chitin Hydrolysis in Two Lakes with Contrasting Trophic Statuses

(2011) Krista E. Köllner et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial Communities as Experimental Units

(2011) Mitch D. Day et al.   BIOSCIENCE

Uncoupling of chitinase activity and uptake of hydrolysis products in freshwater bacterioplankton

(2011) Sara Beier et al.   LIMNOLOGY AND OCEANOGRAPHY

The Importance of Chitin in the Marine Environment

(2011) Claudiana P. Souza et al.   MARINE BIOTECHNOLOGY

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Members of Gammaproteobacteria and Bacilli represent the culturable diversity of chitinolytic bacteria in chitin-enriched soils

(2010) Subha Narayan Das et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Culturing marine bacteria - an essential prerequisite for biodiscovery

(2010) Ian Joint et al.   Microbial Biotechnology

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY