4.6 Article

Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemistry & Molecular Biology

The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Yasset Perez-Riverol et al.

Summary: PRIDE is the largest data repository of mass spectrometry-based proteomics data in the world, with around 500 datasets submitted per month. In addition to continuous improvements in data pipelines and infrastructure, PRIDE has developed the Spectra Archive and MAGE-TAB file format to enhance sample metadata annotation and access to mass spectra.

NUCLEIC ACIDS RESEARCH (2022)

Article Ecology

Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms

Luis H. Orellana et al.

Summary: The study found that small, coccoid, free-living Verrucomicrobiota specialize in consuming fucose and rhamnose during spring algal blooms in the North Sea. These Verrucomicrobiota populations accounted for up to 8% of the bacterioplankton and actively expressed proteins critical for the consumption of fucosylated and sulfated polysaccharides during consecutive spring bloom events. Specialized metabolic pathways of Verrucomicrobiota could determine the fate of complex polysaccharides consumed during algae blooms, particularly those containing methyl pentose sugars.

ISME JOURNAL (2022)

Article Biotechnology & Applied Microbiology

Improved metagenome binning and assembly using deep variational autoencoders

Jakob Nybo Nissen et al.

Summary: Despite recent advances in metagenomic binning, reconstruction of microbial species from metagenomics data remains challenging. Here we develop variational autoencoders for metagenomic binning (VAMB), a program that outperforms existing state-of-the-art binners in reconstructing near-complete genomes on simulated and real data. VAMB is able to separate closely related strains with high accuracy and showcase different geographical distribution patterns of human gut microbiome species.

NATURE BIOTECHNOLOGY (2021)

Article Marine & Freshwater Biology

Integrating novel tools to elucidate the metabolic basis of microbial symbiosis in reef holobionts

J. Pamela Engelberts et al.

Summary: Researchers use various molecular techniques and experimental approaches to study microbial interactions and symbiotic functions in coral reefs, but face challenges in their application. They aim to uncover the role of microorganisms in coral reef ecosystems and address these challenges.

MARINE BIOLOGY (2021)

Article Microbiology

Subcellular view of host-microbiome nutrient exchange in sponges: insights into the ecological success of an early metazoan-microbe symbiosis

Meggie Hudspith et al.

Summary: Sponges are recognized as key ecosystem engineers in aquatic habitats, with the ability to process organic matter efficiently. Through experiments, it is found that microbial communities in high and low microbial abundance sponges interact with hosts in nutrient exchange and symbiotic relationships.

MICROBIOME (2021)

Article Biochemistry & Molecular Biology

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

Ivica Letunic et al.

Summary: The Interactive Tree Of Life is an online tool for displaying, manipulating, and annotating phylogenetic and other trees. The latest version 5 introduces a new tree display engine and several new features, such as a new dataset type and expanded annotation options. Users can now also manually annotate trees by hand, providing more flexibility and control.

NUCLEIC ACIDS RESEARCH (2021)

Article Microbiology

DNA-stable isotope probing DNA-stable isotope probing (DNA-SIP) identifies marine sponge-associated bacteria actively utilizing dissolved organic matter (DOM)

Sara Campana et al.

Summary: This study used DNA stable isotope probing and 16S rRNA amplicon sequencing to identify metabolically active bacterial taxa involved in dissolved organic matter (DOM) uptake in a sponge holobiont. The results revealed that specific bacterial taxa belonging to PAUC34f, Poribacteria, and Chloroflexi phyla are active consumers of DOM through heterotrophic carbon metabolism, while Nitrospirae may have mixotrophic capabilities. This research provides new insights into the interaction between diverse sponge-associated bacteria and DOM consumption in marine ecosystems.

ENVIRONMENTAL MICROBIOLOGY (2021)

Article Biochemistry & Molecular Biology

Pfam: The protein families database in 2021

Jaina Mistry et al.

Summary: The Pfam database has recently added a large number of protein families and domains, made revisions for COVID-19 research, and introduced Pfam-B as a supplement. These updates and improvements can help researchers classify protein sequences more effectively and conduct related studies.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemical Research Methods

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Pierre-Alain Chaumeil et al.

BIOINFORMATICS (2020)

Review Microbiology

How bacteria recognise and respond to surface contact

Tom E. P. Kimkes et al.

FEMS MICROBIOLOGY REVIEWS (2020)

Article Multidisciplinary Sciences

A multiproducer microbiome generates chemical diversity in the marine sponge Mycale hentscheli

Michael Rust et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Microbiology

Verrucomicrobia use hundreds of enzymes to digest the algal polysaccharide fucoidan

Andreas Sichert et al.

NATURE MICROBIOLOGY (2020)

Article Microbiology

GapMind: Automated Annotation of Amino Acid Biosynthesis

Morgan N. Price et al.

MSYSTEMS (2020)

Article Microbiology

Viral ecogenomics across the Porifera

Cecilia Pascelli et al.

MICROBIOME (2020)

Article Biotechnology & Applied Microbiology

SignalP 5.0 improves signal peptide predictions using deep neural networks

Jose Juan Almagro Armenteros et al.

NATURE BIOTECHNOLOGY (2019)

Article Biochemistry & Molecular Biology

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Kai Blin et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Microbiology

Localized production of defence chemicals by intracellular symbionts of Haliclona sponges

Ma Diarey Tianero et al.

NATURE MICROBIOLOGY (2019)

Article Microbiology

A genomic view of the reef-building coral Porites lutea and its microbial symbionts

Steven J. Robbins et al.

NATURE MICROBIOLOGY (2019)

Article Microbiology

A Phage Protein Aids Bacterial Symbionts in Eukaryote Immune Evasion

Martin T. Jahn et al.

CELL HOST & MICROBE (2019)

Article Multidisciplinary Sciences

Changes in the metabolic potential of the sponge microbiome under ocean acidification

Emmanuelle S. Botte et al.

NATURE COMMUNICATIONS (2019)

Article Microbiology

Reef invertebrate viromics: diversity, host specificity and functional capacity

Patrick W. Laffy et al.

ENVIRONMENTAL MICROBIOLOGY (2018)

Article Microbiology

Abundance determines the functional role of bacterial phylotypes in complex communities

Damian W. Rivett et al.

NATURE MICROBIOLOGY (2018)

Article Microbiology

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

Christian M. K. Sieber et al.

NATURE MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

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

Chirag Jain et al.

NATURE COMMUNICATIONS (2018)

Article Biochemistry & Molecular Biology

metaSPAdes: a new versatile metagenomic assembler

Sergey Nurk et al.

GENOME RESEARCH (2017)

Article Ecology

Uncultivated microbes in need of their own taxonomy

Konstantinos T. Konstantinidis et al.

ISME JOURNAL (2017)

Article Biochemistry & Molecular Biology

KEGG as a reference resource for gene and protein annotation

Minoru Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Evolution and function of eukaryotic-like proteins from sponge symbionts

David Reynolds et al.

MOLECULAR ECOLOGY (2016)

Review Microbiology

Stuck in the Middle: Fibronectin-Binding Proteins in Gram-Positive Bacteria

Jeffrey P. Hymes et al.

FRONTIERS IN MICROBIOLOGY (2016)

Article Biochemistry & Molecular Biology

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

Donovan H. Parks et al.

GENOME RESEARCH (2015)

Article Biochemistry & Molecular Biology

Selection Maintains Low Genomic GC Content in Marine SAR11 Lineages

Haiwei Luo et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Review Microbiology

Secretion systems in Gram-negative bacteria: structural and mechanistic insights

Tiago R. D. Costa et al.

NATURE REVIEWS MICROBIOLOGY (2015)

Article Multidisciplinary Sciences

Phosphorus sequestration in the form of polyphosphate by microbial symbionts in marine sponges

Fan Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

VirSorter: mining viral signal from microbial genomic data

Simon Roux et al.

Review Cell Biology

Diversity of bacterial manipulation of the host ubiquitin pathways

Yan Zhou et al.

CELLULAR MICROBIOLOGY (2015)

Article Microbiology

Loss of FliL Alters Proteus mirabilis Surface Sensing and Temperature-Dependent Swarming

Yi-Ying Lee et al.

JOURNAL OF BACTERIOLOGY (2015)

Article Biochemistry & Molecular Biology

Ankyrin-repeat proteins from sponge symbionts modulate amoebal phagocytosis

Mary T. H. D. Nguyen et al.

MOLECULAR ECOLOGY (2014)

Article Multidisciplinary Sciences

An environmental bacterial taxon with a large and distinct metabolic repertoire

Micheal C. Wilson et al.

NATURE (2014)

Article Biochemical Research Methods

Binning metagenomic contigs by coverage and composition

Johannes Alneberg et al.

NATURE METHODS (2014)

Review Microbiology

Archaea in Biogeochemical Cycles

Pierre Offre et al.

ANNUAL REVIEW OF MICROBIOLOGY, VOL 67 (2013)

Article Biotechnology & Applied Microbiology

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

Mads Albertsen et al.

NATURE BIOTECHNOLOGY (2013)

Article Multidisciplinary Sciences

Surviving in a Marine Desert: The Sponge Loop Retains Resources Within Coral Reefs

Jasper M. de Goeij et al.

SCIENCE (2013)

Review Biotechnology & Applied Microbiology

Algal fucoidan: structural and size-dependent bioactivities and their perspectives

V. K. Morya et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2012)

Article Marine & Freshwater Biology

Qualitative variation in colour morphotypes of Ianthella basta (Porifera: Verongida)

Marnie L. Freckelton et al.

HYDROBIOLOGIA (2012)

Article Biochemistry & Molecular Biology

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

Yanbin Yin et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biotechnology & Applied Microbiology

Antifouling Bastadin Congeners Target Mussel Phenoloxidase and Complex Copper(II) Ions

Mirko Bayer et al.

MARINE BIOTECHNOLOGY (2011)

Article Biotechnology & Applied Microbiology

Exploring the Role of Microorganisms in the Disease-Like Syndrome Affecting the Sponge Ianthella basta

Heidi M. Luter et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2010)

Article Biochemical Research Methods

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

Frederick A. Matsen et al.

BMC BIOINFORMATICS (2010)

Article Biochemical Research Methods

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

BMC BIOINFORMATICS (2010)

Article Microbiology

Discovery and Characterization of Cadherin Domains in Saccharophagus degradans 2-40

Milana Fraiberg et al.

JOURNAL OF BACTERIOLOGY (2010)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Review Marine & Freshwater Biology

The functional roles of marine sponges

James J. Bell

ESTUARINE COASTAL AND SHELF SCIENCE (2008)

Article Plant Sciences

Cytotoxic bastadin 24 from the Australian sponge Ianthella quadrangulata

Hendrik Greve et al.

JOURNAL OF NATURAL PRODUCTS (2008)

Article Multidisciplinary Sciences

Genome streamlining in a cosmopolitan oceanic bacterium

SJ Giovannoni et al.

SCIENCE (2005)

Article Multidisciplinary Sciences

Pathogenic bacteria attach to human fibronectin through a tandem β-zipper

U Schwarz-Linek et al.

NATURE (2003)

Review Biochemistry & Molecular Biology

Circular proteoglycans from sponges: first members of the spongican family

X Fernandez-Busquets et al.

CELLULAR AND MOLECULAR LIFE SCIENCES (2003)

Review Biotechnology & Applied Microbiology

Metabolism of alkylbenzenes, alkanes, and other hydrocarbons in anaerobic bacteria

AM Spormann et al.

BIODEGRADATION (2000)