Changing expression patterns of TonB-dependent transporters suggest shifts in polysaccharide consumption over the course of a spring phytoplankton bloom

Short‐term changes in polysaccharide utilization mechanisms of marine bacterioplankton during a spring phytoplankton bloom

(2020) Greta Reintjes et al.   ENVIRONMENTAL MICROBIOLOGY

Polysaccharide niche partitioning of distinct Polaribacter clades during North Sea spring algal blooms

(2020) Burak Avcı et al.   ISME Journal

Laminarin is a major molecule in the marine carbon cycle

(2020) Stefan Becker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A TonB-dependent transporter is required for secretion of protease PopC across the bacterial outer membrane

(2019) Nuria Gómez-Santos et al.   Nature Communications

In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes

(2019) Karen Krüger et al.   ISME Journal

Bacteroidetes use thousands of enzyme combinations to break down glycans

(2019) Pascal Lapébie et al.   Nature Communications

Niche differentiation among annually recurrent coastal Marine Group II Euryarchaeota

(2019) Luis H. Orellana et al.   ISME Journal

Dynamics and interactions of highly resolved marine plankton via automated high-frequency sampling

(2018) David M. Needham et al.   ISME Journal

Genetic Variation of the SusC/SusD Homologs from a Polysaccharide Utilization Locus Underlies Divergent Fructan Specificities and Functional Adaptation in Bacteroides thetaiotaomicron Strains

(2018) Payal Joglekar et al.   mSphere

Polysaccharide utilization loci of North Sea Flavobacteriia as basis for using SusC/D-protein expression for predicting major phytoplankton glycans

(2018) Lennart Kappelmann et al.   ISME Journal

Biphasic cellular adaptations and ecological implications of Alteromonas macleodii degrading a mixture of algal polysaccharides

(2018) Hanna Koch et al.   ISME Journal

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Candidatus Prosiliicoccus vernus, a spring phytoplankton bloom associated member of the Flavobacteriaceae

(2018) T. Ben Francis et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Aquatic adaptation of a laterally acquired pectin degradation pathway in marine gammaproteobacteria

(2017) Jan-Hendrik Hehemann et al.   ENVIRONMENTAL MICROBIOLOGY

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Recurrent patterns of microdiversity in a temperate coastal marine environment

(2017) Meghan Chafee et al.   ISME Journal

An alternative polysaccharide uptake mechanism of marine bacteria

(2017) Greta Reintjes et al.   ISME Journal

Polysaccharide Utilization Loci: Fueling Microbial Communities

(2017) Julie M. Grondin et al.   JOURNAL OF BACTERIOLOGY

Structural basis for nutrient acquisition by dominant members of the human gut microbiota

(2017) Amy J. Glenwright et al.   NATURE

PULDB: the expanded database of Polysaccharide Utilization Loci

(2017) Nicolas Terrapon et al.   NUCLEIC ACIDS RESEARCH

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics

(2017) Kristin Bergauer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Combined Carbohydrates Support Rich Communities of Particle-Associated Marine Bacterioplankton

(2017) Martin Sperling et al.   Frontiers in Microbiology

The Sus operon: a model system for starch uptake by the human gut Bacteroidetes

(2016) Matthew H. Foley et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

(2016) Hanno Teeling et al.   eLife

Pronounced daily succession of phytoplankton, archaea and bacteria following a spring bloom

(2016) David M. Needham et al.   Nature Microbiology

Different utilization of alginate and other algal polysaccharides by marineAlteromonas macleodiiecotypes

(2015) Anna M. Neumann et al.   ENVIRONMENTAL MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

(2015) Fiona Cuskin et al.   NATURE

The Transporter Classification Database (TCDB): recent advances

(2015) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

Catching the tip of the iceberg - Evaluation of sample preparation protocols for metaproteomic studies of the rumen microbiota

(2015) Simon Deusch et al.   PROTEOMICS

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Automatic prediction of polysaccharide utilization loci in Bacteroidetes species

(2014) Nicolas Terrapon et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Master recyclers: features and functions of bacteria associated with phytoplankton blooms

(2014) Alison Buchan et al.   NATURE REVIEWS MICROBIOLOGY

Metaproteomics reveals the major microbial players and their biogeochemical functions in a productive coastal system in the northern South China Sea

(2014) Hong-Po Dong et al.   Environmental Microbiology Reports

Ecology of marine Bacteroidetes: a comparative genomics approach

(2013) Beatriz Fernández-Gómez et al.   ISME Journal

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

The role of planktonicFlavobacteriain processing algal organic matter in coastal East Antarctica revealed using metagenomics and metaproteomics

(2012) Timothy J. Williams et al.   ENVIRONMENTAL MICROBIOLOGY

A metaproteomic assessment of winter and summer bacterioplankton from Antarctic Peninsula coastal surface waters

(2012) Timothy J Williams et al.   ISME Journal

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Distribution and Functions of TonB-Dependent Transporters in Marine Bacteria and Environments: Implications for Dissolved Organic Matter Utilization

(2012) Kai Tang et al.   PLoS One

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

(2012) H. Teeling et al.   SCIENCE

A novel protocol for determining the concentration and composition of sugars in particulate and in high molecular weight dissolved organic matter (HMW-DOM) in seawater

(2011) Anja Engel et al.   MARINE CHEMISTRY

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Environmental and Gut Bacteroidetes: The Food Connection

(2011) François Thomas et al.   Frontiers in Microbiology

TonB-Dependent Transporters: Regulation, Structure, and Function

(2010) Nicholas Noinaj et al.   Annual Review of Microbiology

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Comparative metaproteomics reveals ocean-scale shifts in microbial nutrient utilization and energy transduction

(2010) Robert M Morris et al.   ISME Journal

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Microbial community transcriptomes reveal microbes and metabolic pathways associated with dissolved organic matter turnover in the sea

(2010) J. McCarren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TonB-dependent transporters and their occurrence in cyanobacteria

(2009) Oliver Mirus et al.   BMC BIOLOGY

Carbon catabolite repression in bacteria: many ways to make the most out of nutrients

(2008) Boris Görke et al.   NATURE REVIEWS MICROBIOLOGY

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

New substrates for TonB-dependent transport: do we only see the ‘tip of the iceberg’?

(2008) Kristine Schauer et al.   TRENDS IN BIOCHEMICAL SCIENCES