Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms

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

(2021) T. Ben Francis et al.   ISME Journal

Diatom fucan polysaccharide precipitates carbon during algal blooms

(2021) Silvia Vidal-Melgosa et al.   Nature Communications

A catalog of the diversity and ubiquity of bacterial microcompartments

(2021) Markus Sutter et al.   Nature Communications

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

(2020) Greta Reintjes et al.   ENVIRONMENTAL MICROBIOLOGY

High-throughput cultivation of heterotrophic bacteria during a spring phytoplankton bloom in the North Sea

(2020) Carlota Alejandre-Colomo et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

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

Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan

(2020) Andreas Sichert et al.   Nature Microbiology

Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences

(2020) Luis M. Rodriguez‐R et al.   ENVIRONMENTAL MICROBIOLOGY

Roadmap for naming uncultivated Archaea and Bacteria

(2020) Alison E. Murray et al.   Nature Microbiology

Characterization of sponge‐associated Verrucomicrobia : microcompartment‐based sugar utilization and enhanced toxin–antitoxin modules as features of host‐associated Opitutales

(2020) Sofia Sizikov et al.   ENVIRONMENTAL MICROBIOLOGY

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

A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan

(2019) Lukas Reisky et al.   Nature Chemical Biology

Niche differentiation among annually recurrent coastal Marine Group II Euryarchaeota

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

Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered lakes

(2018) Patricia Tran et al.   ENVIRONMENTAL MICROBIOLOGY

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

The Molecular Basis of Polysaccharide Sulfatase Activity and a Nomenclature for Catalytic Subsites in this Class of Enzyme

(2018) Andrew G. Hettle et al.   STRUCTURE

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

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 Pfam protein families database in 2019

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

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Recurrent patterns of microdiversity in a temperate coastal marine environment

(2017) Meghan Chafee et al.   ISME Journal

Uncultivated microbes in need of their own taxonomy

(2017) Konstantinos T Konstantinidis et al.   ISME Journal

Polysaccharide Utilization Loci: Fueling Microbial Communities

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

Complex pectin metabolism by gut bacteria reveals novel catalytic functions

(2017) Didier Ndeh et al.   NATURE

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

(2017) Neil D Rawlings et al.   NUCLEIC ACIDS RESEARCH

Clustal Omega for making accurate alignments of many protein sequences

(2017) Fabian Sievers et al.   PROTEIN SCIENCE

Reconstruction of Diverse Verrucomicrobial Genomes from Metagenome Datasets of Freshwater Reservoirs

(2017) Pedro J. Cabello-Yeves et al.   Frontiers in Microbiology

Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes

(2017) Shaomei He et al.   mSphere

Biological roles of glycans

(2016) Ajit Varki   GLYCOBIOLOGY

Characterization of the first cultured representative of Verrucomicrobia subdivision 5 indicates the proposal of a novel phylum

(2016) Stefan Spring et al.   ISME Journal

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

Matching the Diversity of Sulfated Biomolecules: Creation of a Classification Database for Sulfatases Reflecting Their Substrate Specificity

(2016) Tristan Barbeyron et al.   PLoS One

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

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

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

The Transporter Classification Database (TCDB): recent advances

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

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

(2015) A. Murat Eren et al.   PeerJ

Verrucomicrobia Are Candidates for Polysaccharide-Degrading Bacterioplankton in an Arctic Fjord of Svalbard

(2014) Z. Cardman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of a Planctomycetal Organelle: a Novel Bacterial Microcompartment for the Aerobic Degradation of Plant Saccharides

(2014) Onur Erbilgin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Production of dissolved organic carbon enriched in deoxy sugars representing an additional sink for biological C drawdown in the Amazon River plume

(2014) Travis B. Meador et al.   GLOBAL BIOGEOCHEMICAL CYCLES

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method

(2014) Seth D. Axen et al.   PLoS Computational Biology

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Capturing Single Cell Genomes of Active Polysaccharide Degraders: An Unexpected Contribution of Verrucomicrobia

(2012) Manuel Martinez-Garcia et al.   PLoS One

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

(2012) H. Teeling et al.   SCIENCE

Important Determinants for Fucoidan Bioactivity: A Critical Review of Structure-Function Relations and Extraction Methods for Fucose-Containing Sulfated Polysaccharides from Brown Seaweeds

(2011) Marcel Tutor Ale et al.   Marine Drugs

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

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

Fucoidan: Structure and Bioactivity

(2008) Bo Li et al.   MOLECULES