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2026
Two worlds beneath: Distinct microbial strategies of the rock-attached and planktonic subsurface biosphere
Microbiome
2026
Diversity and ecological roles of hidden viral players in groundwater microbiomes
Nature Communications
2026
2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction
mSystems
2025
Chemoautotrophy in subzero environments and the potential for cold-adapted Rubisco
Applied and Environmental Microbiology
2025
Seasonal transcriptomic shifts reveal metabolic flexibility of chemosynthetic symbionts in an upwelling region
mSystems
2025
Genome-resolved metagenomics from short-read sequencing data in the era of artificial intelligence
Functional & Integrative Genomics
2025
Disentangling the microbial genomic traits associated with aromatic hydrocarbon degradation in a jet fuel-contaminated aquifer
Biodegradation
2025
Microbial community differentiation in vent chimneys of the Lost City Hydrothermal Field reflects habitat heterogeneity
Frontiers in Microbiomes
2025
From Low‐Loaded Mesophilic to High‐Loaded Thermophilic Anaerobic Digestion: Changes in Reactor Performance and Microbiome
Microbial Biotechnology
2025
A ubiquitous and diverse methanogenic community drives microbial methane cycling in eutrophic coastal sediments
FEMS Microbiology Ecology
2025
Biological methane removal by groundwater trickling biofiltration for emissions reduction
Water Research
2025
Diversification, niche adaptation, and evolution of a candidate phylum thriving in the deep Critical Zone
Proceedings of the National Academy of Sciences
2024
Metagenomics reveal the potential for geosmin and 2‐methylisoborneol production across multiple bacterial phyla in recirculating aquaculture systems
Environmental Microbiology
2024
Genome streamlining in Parcubacteria transitioning from soil to groundwater
Environmental Microbiome
2024
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree
Nature Biotechnology
2024
Discovery of novel treponemes associated with pododermatitis in elk ( Cervus canadensis )
Applied and Environmental Microbiology
2024
Living in mangroves: a syntrophic scenario unveiling a resourceful microbiome
BMC Microbiology
2024
Characterization of Ligilactobacillus salivarius CRISPR-Cas systems
mSphere
2024
MAGqual: a stand-alone pipeline to assess the quality of metagenome-assembled genomes
Microbiome
2024
Microbiota of pest insect Nezara viridula mediate detoxification and plant defense repression
The ISME Journal
2024
Microbial acidification by N, S, Fe and Mn oxidation as a key mechanism for deterioration of subsea tunnel sprayed concrete
Scientific Reports
2024
Solving genomic puzzles: computational methods for metagenomic binning
Briefings in Bioinformatics
2024
Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea
Nature Communications
2024
Metagenome‐assembled genome of the glacier alga Ancylonema yields insights into the evolution of streptophyte life on ice and land
New Phytologist
2023
Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel
FEMS Microbiology Letters
2023
Mosaic environment-driven evolution of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont
Microbiome
2023
An untargeted exometabolomics approach to characterize dissolved organic matter in groundwater of the Samail Ophiolite
Frontiers in Microbiology
2023
Metagenomic and Genomic Sequences from a Methanogenic Benzene-Degrading Consortium
Microbiology Resource Announcements
2023
Actin cytoskeleton and complex cell architecture in an Asgard archaeon
Nature
2023
Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton
mBio
2023
Metagenome-Assembled Genome of a Novel Cyclobacteriaceae Epibiont of a Heterotrophic Diazotroph
Microbiology Resource Announcements
2023
Genome Sequence of a Heterocystous Diazotroph Isolated from a Trichodesmium Consortium from the North Pacific Subtropical Gyre
Microbiology Resource Announcements
2023
Bioinformatic approaches for studying the microbiome of fermented food
Critical Reviews in Microbiology
2023
Exploring microbial functional biodiversity at the protein family level—From metagenomic sequence reads to annotated protein clusters
Frontiers in Bioinformatics
2023
Identification of microbial metabolic functional guilds from large genomic datasets
Frontiers in Microbiology
2023
Metagenome-Assembled Genome HetDA_MAG_MH13 of the Family Devosiaceae , from a Marine N2-fixing Cyanobacterial Enrichment Culture
Microbiology Resource Announcements
2023
Metagenome-Assembled Genome of an Alphaproteobacterium Isolated from an HetDA Enrichment from the North Pacific Subtropical Gyre
Microbiology Resource Announcements
2023
Metagenome-Assembled Genome of a Cyclobacteriaceae Bacterium, HetDA_MAG_MS6, Isolated from a Trichodesmium Consortium from Station ALOHA
Microbiology Resource Announcements
2023
MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities
Genome Biology
2023
Genome Sequence of the Euphotic Hawaiian Gammaproteobacterium HetDA_MAG_MS8, in the Order Nevskiales , Family Oceanococcaceae , Genus Oceanococcus
Microbiology Resource Announcements
2023
Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies
Microbiome
2023
The hologenome ofDaphnia magnareveals possible DNA methylation and microbiome-mediated evolution of the host genome
Nucleic Acids Research
2022
Oceanic Crustal Fluid Single Cell Genomics Complements Metagenomic and Metatranscriptomic Surveys With Orders of Magnitude Less Sample Volume
Frontiers in Microbiology
2022
Amsterdam urban canals contain novel niches for methane‐cycling microorganisms
Environmental Microbiology
2022
Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers
mBio
2022
Evolutionary Ecology of Natural Comammox Nitrospira Populations
mSystems
2022
Reduced representation sequencing accurately quantifies relative abundance and reveals population-level variation in Pseudo-nitzschia spp.
Harmful Algae
2022
Universal activity-based labeling method for ammonia- and alkane-oxidizing bacteria
The ISME Journal
2022
Computational analyses of bacterial strains from shotgun reads
Briefings in Bioinformatics
2022
Microbial Populations Are Shaped by Dispersal and Recombination in a Low Biomass Subseafloor Habitat
mBio
2022
Methane-Dependent Extracellular Electron Transfer at the Bioanode by the Anaerobic Archaeal Methanotroph “Candidatus Methanoperedens”
Frontiers in Microbiology
2022
Metagenomic sequencing-driven multidisciplinary approaches to shed light on the untapped microbial natural products
Drug Discovery Today
2022
Petrobactin, a siderophore produced by Alteromonas, mediates community iron acquisition in the global ocean
The ISME Journal
2022
Metabolic Potential of Microbial Communities in the Hypersaline Sediments of the Bonneville Salt Flats
mSystems
2022
Insect Gut Isolate Pseudomonas sp. Strain Nvir Degrades the Toxic Plant Metabolite Nitropropionic Acid
Applied and Environmental Microbiology
2022
The Polar Fox Lagoon in Siberia harbours a community of Bathyarchaeota possessing the potential for peptide fermentation and acetogenesis
Antonie van Leeuwenhoek
2022
vRhyme enables binning of viral genomes from metagenomes
Nucleic Acids Research
2022
Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development
Environmental Microbiology
2022
Methods in Molecular Biology
2022
Metabolic Strategies Shared by Basement Residents of the Lost City Hydrothermal Field
Applied and Environmental Microbiology
2022
Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates
Water Research X
2022
Constructing metagenome-assembled genomes for almost all components in a real bacterial consortium for binning benchmarking
BMC Genomics
2022
MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics
mSystems
2022
SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs
BMC Genomics
2022
Microbiome structure in biofilms from a volcanic island in Maritime Antarctica investigated by genome-centric metagenomics and metatranscriptomics
Microbiological Research
2022
Music of metagenomics—a review of its applications, analysis pipeline, and associated tools
Functional & Integrative Genomics
2022
Metagenomic evidence of a novel family of anammox bacteria in a subsea environment
Environmental Microbiology
2021
An Improved Integrated Clustering Learning Strategy Based on Three‐Stage Affinity Propagation Algorithm with Density Peak Optimization Theory
Complexity
2021
Marine Dadabacteria exhibit genome streamlining and phototrophy-driven niche partitioning
The ISME Journal
2021
Benchmarking microbial growth rate predictions from metagenomes
The ISME Journal
2021
Metagenome Assembled Genome of a Novel Verrucomicrobial Methanotroph From Pantelleria Island
Frontiers in Microbiology
2021
Understanding the metabolome and metagenome as extended phenotypes: The next frontier in macroalgae domestication and improvement
Journal of the World Aquaculture Society
2021
Current production by non-methanotrophic bacteria enriched from an anaerobic methane-oxidizing microbial community
Biofilm
2021
Artificial intelligence reveals roles of gut microbiota in driving human colorectal cancer evolution
WArtificial Intelligence in Cancer
2021
The Bioinformatics Virtual Coordination Network: An Open-Source and Interactive Learning Environment
Frontiers in Education
2021
Biogeochemical Gradients in a Serpentinization‐Influenced Aquifer: Implications for Gas Exchange Between the Subsurface and Atmosphere
Journal of Geophysical Research: Biogeosciences
2021
Early response of methanogenic archaea to H2 as evaluated by metagenomics and metatranscriptomics
Microbial Cell Factories
2021
Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents
The ISME Journal
2021
Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen‐limited methane‐ and iron‐fed bioreactor inoculated with Bothnian Sea sediments
MicrobiologyOpen
2021
Draft genome of a novel methanotrophic Methylobacter sp. from the volcanic soils of Pantelleria Island
Antonie van Leeuwenhoek
2021
Enrichment and physiological characterization of a novel comammox Nitrospira indicates ammonium inhibition of complete nitrification
The ISME Journal
2021
Genome-resolved metagenomics using environmental and clinical samples
Briefings in Bioinformatics
2021
Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community
The ISME Journal
2021
Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide
Microorganisms
2020
High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies
Frontiers in Microbiology
2020
Computational Framework for High-Quality Production and Large-Scale Evolutionary Analysis of Metagenome Assembled Genomes
Molecular Biology and Evolution
2020
The spinal cord-gut-immune axis as a master regulator of health and neurological function after spinal cord injury
Experimental Neurology
2020
Digitalization in microbiology – Paving the path to sustainable circular bioeconomy
New Biotechnology
2020
Geothermal Gases Shape the Microbial Community of the Volcanic Soil of Pantelleria, Italy
mSystems
2020
Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer
mSystems
2020
Evaluating metagenomics tools for genome binning with real metagenomic datasets and CAMI datasets
BMC Bioinformatics
2020
DATMA: Distributed AuTomatic Metagenomic Assembly and annotation framework
PeerJ
2020
Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs
The ISME Journal
2020
Biases in genome reconstruction from metagenomic data
PeerJ
2020
Endosymbionts of Metazoans Dwelling in the PACManus Hydrothermal Vent: Diversity and Potential Adaptive Features Revealed by Genome Analysis
Applied and Environmental Microbiology
2020
Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota
Scientific Data
2020
Inclusion of Oxford Nanopore long reads improves all microbial and viral metagenome‐assembled genomes from a complex aquifer system
Environmental Microbiology
2020
Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents
mSystems
2020
Characterization of a sponge microbiome using an integrative genome-centric approach
The ISME Journal
2020
Metagenomic Insights Into the Cycling of Dimethylsulfoniopropionate and Related Molecules in the Eastern China Marginal Seas
Frontiers in Microbiology
2020
METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies—Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses
Journal of Proteome Research
2019
Metabolic diversity within the globally abundant Marine Group II Euryarchaea offers insight into ecological patterns
Nature Communications
2019
MetaTOR: A Computational Pipeline to Recover High-Quality Metagenomic Bins From Mammalian Gut Proximity-Ligation (meta3C) Libraries
Frontiers in Genetics
2019
Uncultured Nitrospina-like species are major nitrite oxidizing bacteria in oxygen minimum zones
The ISME Journal
2019
A siphonous macroalgal genome suggests convergent functions of homeobox genes in algae and land plants
DNA Research
2019
A Novel Self-Adaptive Affinity Propagation Clustering Algorithm Based on Density Peak Theory and Weighted Similarity
IEEE Access
2019
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
PeerJ
2019
High-Level Abundances ofMethanobacterialesandSyntrophobacteralesMay Help To Prevent Corrosion of Metal Sheet Piles
Applied and Environmental Microbiology
2019
Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes
mSystems
2018
AMBER: Assessment of Metagenome BinnERs
GigaScience
2018
Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities
mSystems
2018
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy
Nature Microbiology
2018
A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer
The ISME Journal
2018
Co-cultivation of the strictly anaerobic methanogen Methanosarcina barkeri with aerobic methanotrophs in an oxygen-limited membrane bioreactor
Applied Microbiology and Biotechnology
2018
Galacturonate Metabolism in Anaerobic Chemostat Enrichment Cultures: Combined Fermentation and Acetogenesis by the Dominant sp. nov. “Candidatus Galacturonibacter soehngenii”
Applied and Environmental Microbiology
2018
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
Scientific Data
2018
Draft Genome Sequence of Mycobacterium virginiense Strain GF75, Isolated from the Mud of a Swine Farm in Japan
Genome Announcements
2017
Mimicking microbial interactions under nitrate‐reducing conditions in an anoxic bioreactor: enrichment of novel Nitrospirae bacteria distantly related to Thermodesulfovibrio
Environmental Microbiology
2017
Marine Animal Microbiomes: Toward Understanding Host–Microbiome Interactions in a Changing Ocean
Frontiers in Marine Science
2017
290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology
PeerJ
2017
A Metagenomic Approach to Cyanobacterial Genomics
Frontiers in Microbiology
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