Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean

FeGenie: A Comprehensive Tool for the Identification of Iron Genes and Iron Gene Neighborhoods in Genome and Metagenome Assemblies

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Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan

(2020) Andreas Sichert et al.   Nature Microbiology

Seasonal microbial food web dynamics in contrasting Southern Ocean productivity regimes

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Higher contribution of globally rare bacterial taxa reflects environmental transitions across the surface ocean

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Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes

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MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

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KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

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Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

(2019) Guillem Salazar et al.   CELL

Global Trends in Marine Plankton Diversity across Kingdoms of Life

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Proteorhodopsin variability and distribution in the North Pacific Subtropical Gyre

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Identification ofEuglena gracilisβ-1,3-glucan phosphorylase and establishment of a new glycoside hydrolase (GH) family GH149

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

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Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity

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

Alpha- and beta-mannan utilization by marine Bacteroidetes

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MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

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The Pfam protein families database in 2019

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

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Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

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

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New structural insights into the cell-wall polysaccharide of the diatom Phaeodactylum tricornutum

(2017) Tinaïg Le Costaouëc et al.   Algal Research-Biomass Biofuels and Bioproducts

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

(2016) Matthew L Bendall et al.   ISME Journal

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices

(2016) Dinghua Li et al.   METHODS

The past, present and future of microbiome analyses

(2016) Richard Allen White et al.   Nature Protocols

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

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

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MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

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Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling

(2015) Markus V. Lindh 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

Shifts in bacterial community composition associated with increased carbon cycling in a mosaic of phytoplankton blooms

(2015) Marine Landa et al.   ISME Journal

Marine microbial community dynamics and their ecological interpretation

(2015) Jed A. Fuhrman et al.   NATURE REVIEWS MICROBIOLOGY

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

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The Transporter Classification Database (TCDB): recent advances

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Marine sequestration of carbon in bacterial metabolites

(2015) Oliver J. Lechtenfeld et al.   Nature Communications

Effects of iron limitation on growth and carbon metabolism in oceanic and coastal heterotrophic bacteria

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Differential control ofBradyrhizobium japonicumiron stimulon genes through variable affinity of the iron response regulator (Irr) for target gene promoters and selective loss of activator function

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Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

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

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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

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

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A method for the use of the radiotracer55Fe for microautoradiography and CARD-FISH of natural bacterial communities

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Expression patterns reveal niche diversification in a marine microbial assemblage

(2012) Scott M Gifford et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

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The type II secretion system: biogenesis, molecular architecture and mechanism

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Beyond biogeographic patterns: processes shaping the microbial landscape

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Pole-to-pole biogeography of surface and deep marine bacterial communities

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

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Streamlining and Core Genome Conservation among Highly Divergent Members of the SAR11 Clade

(2012) J. Grote et al.   mBio

Defining seasonal marine microbial community dynamics

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Analysis of a New Family of Widely Distributed Metal-independent α-Mannosidases Provides Unique Insight into the Processing ofN-Linked Glycans

(2011) Katie J. Gregg et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Distinct bacterial groups contribute to carbon cycling during a naturally iron fertilized phytoplankton bloom in the Southern Ocean

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Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

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Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations

(2010) Erica D. Sonnenburg et al.   CELL

Building Fe–S proteins: bacterial strategies

(2010) Béatrice Py et al.   NATURE REVIEWS MICROBIOLOGY

The Light-Driven Proton Pump Proteorhodopsin Enhances Bacterial Survival during Tough Times

(2010) Edward F. DeLong et al.   PLOS BIOLOGY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

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Screening and characterization of proteorhodopsin color-tuning mutations in Escherichia coli with endogenous retinal synthesis

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Global Responses of Methanococcus maripaludis to Specific Nutrient Limitations and Growth Rate

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Biogenesis of Fe/S proteins and pathogenicity: IscR plays a key role in allowing Erwinia chrysanthemi to adapt to hostile conditions

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

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Microbial community gene expression in ocean surface waters

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