Adaptations of Alteromonas sp. 76-1 to Polysaccharide Degradation: A CAZyme Plasmid for Ulvan Degradation and Two Alginolytic Systems

Structural and biochemical characterization of a multidomain alginate lyase reveals a novel role of CBM32 in CAZymes

(2018) Qianqian Lyu et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Evolution of a Vegetarian Vibrio: Metabolic Specialization of Vibrio breoganii to Macroalgal Substrates

(2018) Christopher H. Corzett et al.   JOURNAL OF BACTERIOLOGY

Structure–function analyses of a PL24 family ulvan lyase reveal key features and suggest its catalytic mechanism

(2018) ThirumalaiSelvi Ulaganathan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction

(2018) Seong-In Na et al.   JOURNAL OF MICROBIOLOGY

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

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Biochemical characterization of a novel ulvan lyase from Pseudoalteromonas sp. strain PLSV

(2018) Hui-Min Qin et al.   RSC Advances

A Novel Enzyme Portfolio for Red Algal Polysaccharide Degradation in the Marine Bacterium Paraglaciecola hydrolytica S66T Encoded in a Sizeable Polysaccharide Utilization Locus

(2018) Mikkel Schultz-Johansen et al.   Frontiers in Microbiology

Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore

(2018) Angélique Gobet et al.   Microbiome

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

(2018) Hanna Koch et al.   ISME Journal

A novel ulvan lyase family with broad-spectrum activity from the ulvan utilisation loci of Formosa agariphila KMM 3901

(2018) Venkat Rao Konasani et al.   Scientific Reports

Evolutionary Evidence of Algal Polysaccharide Degradation Acquisition by Pseudoalteromonas carrageenovora 9T to Adapt to Macroalgal Niches

(2018) Angélique Gobet et al.   Frontiers in Microbiology

Genetic analyses unravel the crucial role of a horizontally acquired alginate lyase for brown algal biomass degradation by Z obellia galactanivorans

(2017) Yongtao Zhu et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

Methylamine as a nitrogen source for microorganisms from a coastal marine environment

(2017) Martin Taubert et al.   ENVIRONMENTAL MICROBIOLOGY

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

Novel Molecular Insights into the Catalytic Mechanism of Marine Bacterial Alginate Lyase AlyGC from Polysaccharide Lyase Family 6

(2017) Fei Xu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

Coastal bacterioplankton community response to diatom-derived polysaccharide microgels

(2017) Joe D Taylor et al.   Environmental Microbiology Reports

Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria

(2017) Elizabeth Ficko-Blean et al.   Nature Communications

The chromosomal organization of horizontal gene transfer in bacteria

(2017) Pedro H. Oliveira et al.   Nature Communications

Functional characterization of a novel “ulvan utilization loci” found in Alteromonas sp. LOR genome

(2017) Elizabeth Foran et al.   Algal Research-Biomass Biofuels and Bioproducts

Gene Expression Analysis of Zobellia galactanivorans during the Degradation of Algal Polysaccharides Reveals both Substrate-Specific and Shared Transcriptome-Wide Responses

(2017) François Thomas et al.   Frontiers in Microbiology

Effect of the environment on horizontal gene transfer between bacteria and archaea

(2017) Clara A. Fuchsman et al.   PeerJ

Functional and Structural Studies of a Multidomain Alginate Lyase from Persicobacter sp. CCB-QB2

(2017) Pei-Fang Sim et al.   Scientific Reports

Effects of Actinomycete Secondary Metabolites on Sediment Microbial Communities

(2016) Nastassia V. Patin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomics unveils the attributes of the alginolytic guilds of sediments from four distant cold coastal environments

(2016) Marina N. Matos et al.   ENVIRONMENTAL MICROBIOLOGY

Response of bacterial communities from California coastal waters to alginate particles and an alginolytic Alteromonas macleodii strain

(2016) Maximilian Mitulla et al.   ENVIRONMENTAL MICROBIOLOGY

New Family of Ulvan Lyases Identified in Three Isolates from the Alteromonadales Order

(2016) Moran Kopel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Siderophore-based microbial adaptations to iron scarcity across the eastern Pacific Ocean

(2016) Rene M. Boiteau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

(2016) Jan-Hendrik Hehemann et al.   Nature Communications

Complete genome sequence and transcriptomic analysis of a novel marine strain Bacillus weihaiensis reveals the mechanism of brown algae degradation

(2016) Yueming Zhu et al.   Scientific Reports

Genome-wide transcriptional responses of Alteromonas naphthalenivorans SN2 to contaminated seawater and marine tidal flat sediment

(2016) Hyun Mi Jin et al.   Scientific Reports

Comparing polysaccharide decomposition between the type strains Gramella echinicola KMM 6050T (DSM 19838T) and Gramella portivictoriae UST040801-001T (DSM 23547T), and emended description of Gramella echinicola Nedashkovskaya et al. 2005 emend. Shahina et al. 2014 and Gramella portivictoriae Lau et al. 2005

(2016) Irina Panschin et al.   Standards in Genomic Sciences

Recurring patterns in bacterioplankton dynamics during coastal spring algae blooms

(2016) Hanno Teeling et al.   eLife

BPGA- an ultra-fast pan-genome analysis pipeline

(2016) Narendrakumar M. Chaudhari et al.   Scientific Reports

Microbial Evolution: Towards Resolving the Plasmid Paradox

(2015) R. Craig MacLean et al.   CURRENT BIOLOGY

Bacterial community dynamics during polysaccharide degradation at contrasting sites in the Southern and Atlantic Oceans

(2015) Matthias Wietz et al.   ENVIRONMENTAL 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

Identification of a 4-Deoxy-l-erythro-5-hexoseulose Uronic Acid Reductase, FlRed, in an Alginolytic Bacterium Flavobacterium sp. Strain UMI-01

(2015) Akira Inoue et al.   Marine Drugs

Cloning, expression, and biochemical characterization of a novel GH16 β-agarase AgaG1 from Alteromonas sp. GNUM-1

(2014) Won-Jae Chi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

A sweet new wave: structures and mechanisms of enzymes that digest polysaccharides from marine algae

(2014) Jan-Hendrik Hehemann et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Functional characterization of polysaccharide utilization loci in the marine Bacteroidetes ‘Gramella forsetii’ KT0803

(2014) Antje Kabisch et al.   ISME Journal

Molecular Insight into the Role of the N-terminal Extension in the Maturation, Substrate Recognition, and Catalysis of a Bacterial Alginate Lyase from Polysaccharide Lyase Family 18

(2014) Sheng Dong et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structure of a PL17 Family Alginate Lyase Demonstrates Functional Similarities among Exotype Depolymerases

(2014) David Park et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Anthropogenic loads and biogeochemical role of urea in the Gulf of Trieste

(2014) Stefano Cozzi et al.   SCIENCE OF THE TOTAL ENVIRONMENT

The Genome of the Alga-Associated Marine Flavobacterium Formosa agariphila KMM 3901TReveals a Broad Potential for Degradation of Algal Polysaccharides

(2013) Alexander J. Mann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

Ecology of marine Bacteroidetes: a comparative genomics approach

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

The β-GlucanaseZgLamA fromZobellia galactanivoransEvolved a Bent Active Site Adapted for Efficient Degradation of Algal Laminarin

(2013) Aurore Labourel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Comparative Characterization of Two Marine Alginate Lyases fromZobellia galactanivoransReveals Distinct Modes of Action and Exquisite Adaptation to Their Natural Substrate

(2013) François Thomas et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Detecting Sequence Homology at the Gene Cluster Level with MultiGeneBlast

(2013) Marnix H. Medema et al.   MOLECULAR BIOLOGY AND EVOLUTION

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Phylogenetic diversity of Flavobacteria isolated from the North Sea on solid media

(2013) Richard L. Hahnke et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Characterization of the first alginolytic operons in a marine bacterium: from their emergence in marine Flavobacteriia to their independent transfers to marine Proteobacteria and human gut Bacteroides

(2012) François Thomas et al.   ENVIRONMENTAL MICROBIOLOGY

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Biochemical and Structural Characterization of the Complex Agarolytic Enzyme System from the Marine BacteriumZobellia galactanivorans

(2012) Jan-Hendrik Hehemann et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Comparative Genomics Reveals Adaptation by Alteromonas sp. SN2 to Marine Tidal-Flat Conditions: Cold Tolerance and Aromatic Hydrocarbon Metabolism

(2012) Renukaradhya K. Math et al.   PLoS One

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

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Latitudinal Gradients in Degradation of Marine Dissolved Organic Carbon

(2011) Carol Arnosti et al.   PLoS One

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Growth phase-dependent global protein and metabolite profiles ofPhaeobacter gallaeciensisstrain DSM 17395, a member of the marineRoseobacter-clade

(2009) Hajo Zech et al.   PROTEOMICS

Environmental factors controlling the phytoplankton blooms at the Patagonia shelf-break in spring

(2008) Virginia M.T. Garcia et al.   DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS