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2026
Comprehensive genomic analysis of a novel Bacillus cereus decomposing toluene potentially applicable in bioremediation
Microbiology Spectrum
2026
Bark microbiota modulate climate-active gas fluxes in Australian forests
Science
2026
Biophysics of Life
2025
Plastic degradation by enzymes from uncultured deep sea microorganisms
The ISME Journal
2025
Deep origin of eukaryotes outside Heimdallarchaeia within Asgardarchaeota
Nature
2025
Analysis of metagenomic data
Nature Reviews Methods Primers
2025
Halophilic archaea produce wax esters and use an alternative fatty acyl-coenzyme A reductase for precursor synthesis
The ISME Journal
2025
Forest Microbiology
2025
Solar-enhanced low-temperature biological wastewater treatment
Nature Sustainability
2025
Adjustable microbial cross-feedings adapt to landforms in the Yangtze River
Water & Ecology
2025
Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms
Environmental Microbiology
2025
Interspecies hydrogen transfer between cyanobacteria and symbiotic bacteria drives nitrogen loss
Nature Communications
2025
Metagenomics
2025
Identification of key steps in the evolution of anaerobic methanotrophy in Candidatus Methanovorans (ANME-3) archaea
Science Advances
2025
Phenotypic plasticity in cell elongation among closely related bacterial species
Nature Communications
2025
Siderophore-Mediated Cooperation in Anammox Consortia
Environmental Science & Technology
2025
An archaeal genetic code with all TAG codons as pyrrolysine
Science
2025
Computational Genomics and Structural Bioinformatics in Microbial Science
2025
RNA, Reuse, Recycle: The Analysis of Multiple Known Human Microbiome Communities Using Unmapped Next‐Generation Sequencing Data
Advanced Gut & Microbiome Research
2024
Generation of accurate, expandable phylogenomic trees with uDance
Nature Biotechnology
2024
Physiological and metabolic insights into the first cultured anaerobic representative of deep-sea Planctomycetes bacteria
eLife
2024
Genomic comparison of deep-sea hydrothermal genera related to Aeropyrum, Thermodiscus and Caldisphaera, and proposed emended description of the family Acidilobaceae
Systematic and Applied Microbiology
2024
High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality
mBio
2024
Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence
Neural Regeneration Research
2024
Asgard archaea modulate potential methanogenesis substrates in wetland soil
Nature Communications
2024
Hyperexpansion of genetic diversity and metabolic capacity of extremophilic bacteria and archaea in ancient Andean lake sediments
Microbiome
2024
mbctools: A User-Friendly Metabarcoding and Cross-Platform Pipeline for Analyzing Multiple Amplicon Sequencing Data across a Large Diversity of Organisms
Peer Community Journal
2024
GCompip: a pipeline for estimating the gene abundance in microbial communities
Bioinformatics Advances
2024
Globally distributed marine Gemmatimonadota have unique genomic potentials
Microbiome
2024
Blue-light irradiation induced partial nitrification
Water Research
2024
The faecal microbiome of the Australian silver gull contains phylogenetically diverse ExPEC, aEPEC and Escherichia coli carrying the transmissible locus of stress tolerance
Science of The Total Environment
2024
Step-by-Step Metagenomics for Food Microbiome Analysis: A Detailed Review
Foods
2024
Metaproteogenomics resolution of a high-CO2 aquifer community reveals a complex cellular adaptation of groundwater Gracilibacteria to a host-dependent lifestyle
Microbiome
2024
Computational methods in the analysis of SARS-CoV-2 in mammals: A systematic review of the literature
Computers in Biology and Medicine
2024
Integrative Omics
2024
Critical steps in an environmental metaproteomics workflow
Environmental Microbiology
2024
Microbiome Drivers of Ecosystem Function
2024
Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes
PLOS Computational Biology
2024
Sheaths are diverse and abundant cell surface layers in archaea
The ISME Journal
2024
Scaling DEPP phylogenetic placement to ultra-large reference trees: a tree-aware ensemble approach
Bioinformatics
2024
Physiological and metabolic insights into the first cultured anaerobic representative of deep-sea Planctomycetes bacteria
eLife
2024
Adjusted bacterial cooperation in anammox community to adapt to high ammonium in wastewater treatment plant
Water Research X
2024
The parasitic lifestyle of an archaeal symbiont
Nature Communications
2023
A predicted CRISPR-mediated symbiosis between uncultivated archaea
Nature Microbiology
2023
Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean
mSystems
2023
Privacy Preservation of Genomic and Medical Data
2023
Polycyclic aromatic hydrocarbon (PAH) biodegradation capacity revealed by a genome-function relationship approach
Environmental Microbiome
2023
An integrated complete-genome sequencing and systems biology approach to predict antimicrobial resistance genes in the virulent bacterial strains of Moraxella catarrhalis
Briefings in Functional Genomics
2023
Gut microbiota interspecies interactions shape the response of Clostridioides difficile to clinically relevant antibiotics
PLOS Biology
2023
Relative timing information and orthology in evolutionary scenarios
Algorithms for Molecular Biology
2023
Expansion of Armatimonadota through marine sediment sequencing describes two classes with unique ecological roles
ISME Communications
2023
Whole genome analysis of Rhizopus species causing rhino-cerebral mucormycosis during the COVID-19 pandemic
Frontiers in Cellular and Infection Microbiology
2023
Complex interactions between diverse mobile genetic elements drive the evolution of metal‐resistant bacterial genomes
Environmental Microbiology
2023
Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater
MicrobiologyOpen
2023
Dominance of Escherichia coli sequence types ST73, ST95, ST127 and ST131 in Australian urine isolates: a genomic analysis of antimicrobial resistance and virulence linked to F plasmids
Microbial Genomics
2023
Control points for design of taxonomic composition in synthetic human gut communities
Cell Systems
2023
Performance, microbial growth and community interactions of iron-dependent denitrification in freshwaters
Environment International
2023
MiR-199a-3p Regulates the PTPRF/β-Catenin Axis in Hair Follicle Development: Insights into the Pathogenic Mechanism of Alopecia Areata
International Journal of Molecular Sciences
2023
Gut Bacteroides act in a microbial consortium to cause susceptibility to severe malaria
Nature Communications
2023
Diversity, distribution, and expression of opsin genes in freshwater lakes
Molecular Ecology
2023
Potential bacterial isolation by dosing metabolites in cross-feedings
Water Research
2023
Microbial Niche Differentiation during Nitrite-Dependent Anaerobic Methane Oxidation
Environmental Science & Technology
2023
Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research
FEMS Microbiology Reviews
2023
Genomic insight of sulfate reducing bacterial genus Desulfofaba reveals their metabolic versatility in biogeochemical cycling
BMC Genomics
2022
Hyphal compartmentalization and sporulation in Streptomyces require the conserved cell division protein SepX
Nature Communications
2022
Cell Cycle Regulation and Development in Alphaproteobacteria
2022
Urban Wildlife Crisis: Australian Silver Gull Is a Bystander Host to Widespread Clinical Antibiotic Resistance
mSystems
2022
Insights into agar and secondary metabolite pathways from the genome of the red alga Gracilaria domingensis (Rhodophyta, Gracilariales)
Journal of Phycology
2022
Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice
Genes
2022
Phylogenomic diversity of Vibrio species and other Gammaproteobacteria isolated from Pacific oysters (Crassostrea gigas) during a summer mortality outbreak
Microbial Genomics
2022
Genome-centric metagenomics analysis revealed the metabolic function of abundant microbial communities in thermal hydrolysis-assisted thermophilic anaerobic digesters under propionate stress
Bioresource Technology
2022
Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts
The ISME Journal
2022
Incorporating genome‐based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes
Environmental Microbiology
2022
Геномика древних патогенов: первые успехи и перспективы
Биохимия
2022
Comammox biogeography subject to anthropogenic interferences along a high-altitude river
Water Research
2022
New globally distributed bacterial phyla within the FCB superphylum
Nature Communications
2022
The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea
mLife
2022
Music of metagenomics—a review of its applications, analysis pipeline, and associated tools
Functional & Integrative Genomics
2022
Heterotrophic bacterial diazotrophs are more abundant than their cyanobacterial counterparts in metagenomes covering most of the sunlit ocean
The ISME Journal
2022
K2Mem: Discovering Discriminative K-mers From Sequencing Data for Metagenomic Reads Classification
IEEE/ACM Transactions on Computational Biology and Bioinformatics
2022
Metagenomic Analysis Using Phylogenetic Placement—A Review of the First Decade
Frontiers in Bioinformatics
2022
Metagenomic Features Characterized with Microbial Iron Oxidoreduction and Mineral Interaction in Southwest Indian Ridge
Microbiology Spectrum
2022
Genomic Analysis of Carbapenem-Resistant Comamonas in Water Matrices: Implications for Public Health and Wastewater Treatments
Applied and Environmental Microbiology
2022
Methods in Molecular Biology
2022
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties
NAR Genomics and Bioinformatics
2022
Methods in Molecular Biology
2022
The Molecular Life of Diatoms
2022
Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission
Current Research in Microbial Sciences
2022
Insight into co-hosts of nitrate reduction genes and antibiotic resistance genes in an urban river of the qinghai-tibet plateau
Water Research
2022
Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups
The ISME Journal
2022
Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing
Nature Communications
2022
Soil plastisphere: Exploration methods, influencing factors, and ecological insights
Journal of Hazardous Materials
2022
Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling
Science Advances
2022
Lecture Notes in Computer Science
2022
Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans
Microbiome
2022
SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs
BMC Genomics
2022
Characterization of the First Cultured Representative of “ Candidatus Thermofonsia” Clade 2 within Chloroflexi Reveals Its Phototrophic Lifestyle
mBio
2022
Molecular Genetics and Genomics Tools in Biodiversity Conservation
2022
Complete Genome Sequence of Pasteurella multocida Sequence Type 394, Isolated from a Case of Bovine Respiratory Disease in Australia
Microbiology Resource Announcements
2022
Complete genome sequence data of tropical thermophilic bacterium Parageobacillus caldoxylosilyticus ER4B
Data in Brief
2022
Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments
The ISME Journal
2022
Fast and accurate distance‐based phylogenetic placement using divide and conquer
Molecular Ecology Resources
2022
Biotechnology in Healthcare, Volume 1
2022
Deep-branching ANME-1c archaea grow at the upper temperature limit of anaerobic oxidation of methane
Frontiers in Microbiology
2022
Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig
PLOS ONE
2022
Identification of nosZ-expressing microorganisms consuming trace N2O in microaerobic chemostat consortia dominated by an uncultured Burkholderiales
The ISME Journal
2022
Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods
mSystems
2022
Distance-Based Phylogenetic Placement with Statistical Support
Biology
2022
Cultivation and Functional Characterization of a Deep-Sea Lentisphaerae Representative Reveals Its Unique Physiology and Ecology
Frontiers in Marine Science
2022
Genome-resolved metagenomics provides insights into the functional complexity of microbial mats in Blue Holes, Shark Bay
FEMS Microbiology Ecology
2022
Genomics of Ancient Pathogens: First Advances and Prospects
Biochemistry (Moscow)
2021
Temperature modulates stress response in mainstream anammox reactors
Communications Biology
2021
App-SpaM: phylogenetic placement of short reads without sequence alignment
Bioinformatics Advances
2021
Metagenomic Insights into the Metabolic and Ecological Functions of Abundant Deep-Sea Hydrothermal Vent DPANN Archaea
Applied and Environmental Microbiology
2021
Museum Genomics Illuminate the High Specificity of a Bioluminescent Symbiosis for a Genus of Reef Fish
Frontiers in Ecology and Evolution
2021
A diverse uncultivated microbial community is responsible for organic matter degradation in the Black Sea sulphidic zone
Environmental Microbiology
2021
Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community
The ISME Journal
2021
Comparative genomic analysis of Methanimicrococcus blatticola provides insights into host adaptation in archaea and the evolution of methanogenesis
ISME Communications
2021
Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site
Frontiers in Microbiology
2021
Metabolic flexibility allows bacterial habitat generalists to become dominant in a frequently disturbed ecosystem
The ISME Journal
2021
Leave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core
Microbiome
2021
Reconstruction of Metagenome-Assembled Genomes from Aquaria
Microbiology Resource Announcements
2021
Bioinformatics in Rice Research
2021
A primer and discussion on DNA-based microbiome data and related bioinformatics analyses
Peer Community Journal
2021
Two Archaeal Metagenome-Assembled Genomes from El Tatio Provide New Insights into the Crenarchaeota Phylum
Genes
2021
Aerobic and anaerobic iron oxidizers together drive denitrification and carbon cycling at marine iron-rich hydrothermal vents
The ISME Journal
2021
Heminiphilus faecis gen. nov., sp. nov., a member of the family Muribaculaceae, isolated from mouse faeces and emended description of the genus Muribaculum
Antonie van Leeuwenhoek
2021
Endozoicomonadaceae symbiont in gills of Acesta clam encodes genes for essential nutrients and polysaccharide degradation
FEMS Microbiology Ecology
2021
Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities
Applied and Environmental Microbiology
2021
Genome Reduction Is Associated with Bacterial Pathogenicity across Different Scales of Temporal and Ecological Divergence
Molecular Biology and Evolution
2021
Diverse Viruses in Deep-Sea Hydrothermal Vent Fluids Have Restricted Dispersal across Ocean Basins
mSystems
2021
Evolution of a σ–(c-di-GMP)–anti-σ switch
Proceedings of the National Academy of Sciences
2021
Functional Diversity within Gut Microbiomes: Implications for Conserving Biodiversity
Conservation
2021
New Microbial Biodiversity in Marine Sediments
Annual Review of Marine Science
2021
Radiation of nitrogen‐metabolizing enzymes across the tree of life tracks environmental transitions in Earth history
Geobiology
2021
Taxonomic classification of metagenomic sequences from Relative Abundance Index profiles using deep learning
Biomedical Signal Processing and Control
2021
Metagenomic insights into the effect of thermal hydrolysis pre-treatment on microbial community of an anaerobic digestion system
Science of The Total Environment
2021
Genome-resolved metagenomics using environmental and clinical samples
Briefings in Bioinformatics
2021
Discovery of nondiazotrophic Trichodesmium species abundant and widespread in the open ocean
Proceedings of the National Academy of Sciences
2021
Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome
mSystems
2021
Life and Death of Selfish Genes: Comparative Genomics Reveals the Dynamic Evolution of Cytoplasmic Incompatibility
Molecular Biology and Evolution
2021
Current challenges and best-practice protocols for microbiome analysis
Briefings in Bioinformatics
2021
Evaluation of a commercial microbial enrichment kit used prior DNA extraction to improve the molecular detection of vector-borne pathogens from naturally infected dogs
Journal of Microbiological Methods
2021
Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems
Frontiers in Microbiology
2021
Temporal Microbial Community Dynamics Within a Unique Acid Saline Lake
Frontiers in Microbiology
2021
Wastewater Treatment
2021
Brockarchaeota, a novel archaeal phylum with unique and versatile carbon cycling pathways
Nature Communications
2021
UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis
Journal of Microbiology
2021
Microbial consortia capable of reducing selenate in the presence of nitrate enriched from coalmining-impacted environments
Applied Microbiology and Biotechnology
2021
Rhizosphere Biology
2021
Cell division in the archaeon Haloferax volcanii relies on two FtsZ proteins with distinct functions in division ring assembly and constriction
Nature Microbiology
2021
Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae
The ISME Journal
2020
Literature on Applied Machine Learning in Metagenomic Classification: A Scoping Review
Biology
2020
SpringerBriefs in Environmental Science
2020
Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum
PeerJ
2020
Escherichia coli ST302: Genomic Analysis of Virulence Potential and Antimicrobial Resistance Mediated by Mobile Genetic Elements
Frontiers in Microbiology
2020
Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts
Cell Reports
2020
Whole-genome analysis of extraintestinal Escherichia coli sequence type 73 from a single hospital over a 2 year period identified different circulating clonal groups
Microbial Genomics
2020
Metabolic relationships of uncultured bacteria associated with the microalgae Gambierdiscus
Environmental Microbiology
2020
Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists
Journal of Microbiology
2020
Comammox Nitrospira within the Yangtze River continuum: community, biogeography, and ecological drivers
The ISME Journal
2020
Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients
Microbial Genomics
2020
CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data
Genome Biology
2020
Single-Nucleotide RNA Maps for the Two Major Nosocomial Pathogens Enterococcus faecalis and Enterococcus faecium
Frontiers in Cellular and Infection Microbiology
2020
Energetic and Environmental Constraints on the Community Structure of Benthic Microbial Mats in Lake Fryxell, Antarctica
FEMS Microbiology Ecology
2020
Impact of Electron Acceptor Availability on Methane-Influenced Microorganisms in an Enrichment Culture Obtained From a Stratified Lake
Frontiers in Microbiology
2020
Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents
mSystems
2020
Teredinibacter waterburyi sp. nov., a marine, cellulolytic endosymbiotic bacterium isolated from the gills of the wood-boring mollusc Bankia setacea (Bivalvia: Teredinidae) and emended description of the genus Teredinibacter
International Journal of Systematic and Evolutionary Microbiology
2020
Microbial dark matter filling the niche in hypersaline microbial mats
Microbiome
2020
A phylogenetically novel cyanobacterium most closely related to Gloeobacter
The ISME Journal
2020
Temperature and Nutrient Levels Correspond with Lineage-Specific Microdiversification in the Ubiquitous and Abundant Freshwater Genus Limnohabitans
Applied and Environmental Microbiology
2020
Reconstructing Genomes of Carbon Monoxide Oxidisers in Volcanic Deposits Including Members of the Class Ktedonobacteria
Microorganisms
2020
Metabolic acclimation of anammox consortia to decreased temperature
Environment International
2020
Metagenomic and metatranscriptomic insights into the complex nitrogen metabolic pathways in a single-stage bioreactor coupling partial denitrification with anammox
Chemical Engineering Journal
2020
Whole genome sequence analysis reveals the broad distribution of the RtxA type 1 secretion system and four novel putative type 1 secretion systems throughout the Legionella genus
PLOS ONE
2020
An Integrated Multi-Disciplinary Perspective for Addressing Challenges of the Human Gut Microbiome
Metabolites
2020
Comparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance
Frontiers in Microbiology
2020
Undinarchaeota illuminate DPANN phylogeny and the impact of gene transfer on archaeal evolution
Nature Communications
2020
To Dereplicate or Not To Dereplicate?
mSphere
2020
TreeSwift: A massively scalable Python tree package
SoftwareX
2020
Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities
Proceedings of the National Academy of Sciences
2020
Polyphasic Characterisation of Cedecea colo sp. nov., a New Enteric Bacterium Isolated from the Koala Hindgut
Microorganisms
2020
Discovery of an Abundance of Biosynthetic Gene Clusters in Shark Bay Microbial Mats
Frontiers in Microbiology
2020
The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge
Microbiome
2020
Validating the Cyc2 Neutrophilic Iron Oxidation Pathway Using Meta-omics of Zetaproteobacteria Iron Mats at Marine Hydrothermal Vents
mSystems
2020
Methane oxidation in anoxic lake water stimulated by nitrate and sulfate addition
Environmental Microbiology
2020
Novel clostridial lineages recovered from metagenomes of a hot oil reservoir
Scientific Reports
2020
Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital
Microbial Genomics
2020
Snapshot Study of Whole Genome Sequences of Escherichia coli from Healthy Companion Animals, Livestock, Wildlife, Humans and Food in Italy
Antibiotics
2020
Metagenomics - Basics, Methods and Applications
2020
Metabolic potentials of archaeal lineages resolved from metagenomes of deep Costa Rica sediments
The ISME Journal
2020
Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0
Nature Communications
2020
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus
Microorganisms
2020
Genome-wide analysis of differentially expressed mRNAs, lncRNAs, and circRNAs in chicken bursae of Fabricius during infection with very virulent infectious bursal disease virus
BMC Genomics
2020
TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler
Bioinformatics
2020
Methanogens Within a High Salinity Oil Reservoir From the Gulf of Mexico
Frontiers in Microbiology
2020
Genome sequencing as a new window into the microbial community of membrane bioreactors – A critical review
Science of The Total Environment
2020
Genomic adaptations in information processing underpin trophic strategy in a whole-ecosystem nutrient enrichment experiment
eLife
2019
Origin of a Core Bacterial Gene via Co-option and Detoxification of a Phage Lysin
Current Biology
2019
Gut microbiome differences between wild and captive black rhinoceros – implications for rhino health
Scientific Reports
2019
Ancient Microbial DNA in Dental Calculus: A New method for Studying Rapid Human Migration Events
The Journal of Island and Coastal Archaeology
2019
Sequencing and Phylogenetic Analysis of Chloroplast Genes in Freshwater Raphidophytes
Genes
2019
Gut anatomical properties and microbial functional assembly promote lignocellulose deconstruction and colony subsistence of a wood-feeding beetle
Nature Microbiology
2019
Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene
Microbial Genomics
2019
An Ionic Limit to Life in the Deep Subsurface
Frontiers in Microbiology
2019
BASTA – Taxonomic classification of sequences and sequence bins using last common ancestor estimations
Methods in Ecology and Evolution
2019
Asgard archaea capable of anaerobic hydrocarbon cycling
Nature Communications
2019
Carbon fixation and energy metabolisms of a subseafloor olivine biofilm
The ISME Journal
2019
Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol
Frontiers in Microbiology
2019
Metagenomic insights into production of zero valent sulfur from dissimilatory sulfate reduction in a methanogenic bioreactor
Bioresource Technology Reports
2019
Encyclopedia of Bioinformatics and Computational Biology
2019
Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus
eLife
2019
Genomes from bacteria associated with the canine oral cavity: A test case for automated genome-based taxonomic assignment
PLOS ONE
2019
High-throughput DNA sequencing technologies for water and wastewater analysis
Science Progress
2019
Genetic Features of mcr-1 Mediated Colistin Resistance in CMY-2-Producing Escherichia coli From Romanian Poultry
Frontiers in Microbiology
2019
Genome-resolved metagenomics links microbial dynamics to failure and recovery of a bioreactor removing nitrate and selenate from mine-influenced water
Biochemical Engineering Journal
2019
Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea
Nature Microbiology
2019
Genome Features and Secondary Metabolites Biosynthetic Potential of the Class Ktedonobacteria
Frontiers in Microbiology
2019
“Candidatus Thermonerobacter thiotrophicus,” A Non-phototrophic Member of the Bacteroidetes/Chlorobi With Dissimilatory Sulfur Metabolism in Hot Spring Mat Communities
Frontiers in Microbiology
2019
A new symbiotic nanoarchaeote (Candidatus Nanoclepta minutus) and its host (Zestosphaera tikiterensis gen. nov., sp. nov.) from a New Zealand hot spring
Systematic and Applied Microbiology
2019
Molecular characterization of Corynebacterium diphtheriae isolates in Malaysia between 1981 and 2016
Journal of Medical Microbiology
2019
Resources and tools for the high-throughput, multi-omic study of intestinal microbiota
Briefings in Bioinformatics
2019
Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia
Scientific Reports
2019
Aggregatilinea lenta gen. nov., sp. nov., a slow-growing, facultatively anaerobic bacterium isolated from subseafloor sediment, and proposal of the new order Aggregatilineales ord. nov. within the class Anaerolineae of the phylum Chloroflexi
International Journal of Systematic and Evolutionary Microbiology
2019
Visualization and prediction of CRISPR incidence in microbial trait-space to identify drivers of antiviral immune strategy
The ISME Journal
2019
Genome-centric metagenomics resolves microbial diversity and prevalent truncated denitrification pathways in a denitrifying PAO-enriched bioprocess
Water Research
2019
Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa
The ISME Journal
2019
A review of methods and databases for metagenomic classification and assembly
Briefings in Bioinformatics
2019
Complete genome sequence of Pelolinea submarina MO-CFX1T within the phylum Chloroflexi, isolated from subseafloor sediment
Marine Genomics
2019
Predominance of Anaerobic, Spore-Forming Bacteria in Metabolically Active Microbial Communities from Ancient Siberian Permafrost
Applied and Environmental Microbiology
2019
Analytical Geomicrobiology
2019
Multidrug Resistant Uropathogenic Escherichia coli ST405 With a Novel, Composite IS26 Transposon in a Unique Chromosomal Location
Frontiers in Microbiology
2019
SpringerBriefs in Computer Science
2019
Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea
Nature Communications
2019
Integrated Omic Analyses Provide Evidence that a “ Candidatus Accumulibacter phosphatis” Strain Performs Denitrification under Microaerobic Conditions
mSystems
2019
Gene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions
mSphere
2019
Not Just a Pathogen? Description of a Plant-Beneficial Pseudomonas syringae Strain
Frontiers in Microbiology
2019
Tracking of the activity of individual bacteria in temperate forest soils shows guild-specific responses to seasonality
Soil Biology and Biochemistry
2019
Genome-centered omics insight into the competition and niche differentiation of Ca. Jettenia and Ca. Brocadia affiliated to anammox bacteria
Applied Microbiology and Biotechnology
2019
Discrepant gene functional potential and cross-feedings of anammox bacteria Ca. Jettenia caeni and Ca. Brocadia sinica in response to acetate
Water Research
2019
Genome‐resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep‐sea hydrothermal vents
Environmental Microbiology
2018
Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome
The ISME Journal
2018
Metatranscriptomic and Thermodynamic Insights into Medium-Chain Fatty Acid Production Using an Anaerobic Microbiome
mSystems
2018
Disentangling the drivers of functional complexity at the metagenomic level in Shark Bay microbial mat microbiomes
The ISME Journal
2018
Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research
mSystems
2018
A Novel Glaesserella sp. Isolated from Pigs with Severe Respiratory Infections Has a Mosaic Genome with Virulence Factors Putatively Acquired by Horizontal Transfer
Applied and Environmental Microbiology
2018
Nitrogen fixation in a landrace of maize is supported by a mucilage-associated diazotrophic microbiota
PLOS Biology
2018
Genomic insights into metabolic potentials of two simultaneous aerobic denitrification and phosphorus removal bacteria, Achromobacter sp. GAD3 and Agrobacterium sp. LAD9
FEMS Microbiology Ecology
2018
Review: The application of omics to rumen microbiota function
Animal
2018
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts
Genome Biology
2018
Dual Role of Humic Substances As Electron Donor and Shuttle for Dissimilatory Iron Reduction
Environmental Science & Technology
2018
Metagenomic Insights into the Phylogenetic and Metabolic Diversity of the Prokaryotic Community Dwelling in Hypersaline Soils from the Odiel Saltmarshes (SW Spain)
Genes
2018
Metagenomics
2018
Genomic Approaches in Earth and Environmental Sciences
2018
Co-Option and Detoxification of a Phage Lysin for Housekeeping Function
SSRN Electronic Journal
2018
The multi-omics promise in context: from sequence to microbial isolate
Critical Reviews in Microbiology
2018
Spatially distinct, temporally stable microbial populations mediate biogeochemical cycling at and below the seafloor in hydrothermal vent fluids
Environmental Microbiology
2018
Genomics of the Uncultivated, Periodontitis-Associated Bacterium Tannerella sp. BU045 (Oral Taxon 808)
mSystems
2018
Computational Biology
2018
SNP hot-spots in the clam parasite QPX
BMC Genomics
2018
Genome Sequences of Two Cyanobacterial Strains, Toxic Green Microcystis aeruginosa KW (KCTC 18162P) and Nontoxic Brown Microcystis sp. Strain MC19, under Xenic Culture Conditions
Genome Announcements
2018
Cultivation of Peptidiphaga gingivicola from subgingival plaque: The first representative of a novel genus of Actinomycetaceae
Molecular Oral Microbiology
2018
Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors
Biotechnology for Biofuels
2018
GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas
Frontiers in Microbiology
2018
Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes
Nature Microbiology
2018
Expressed protein profile of a Tectomicrobium and other microbial symbionts in the marine sponge Aplysina aerophoba as evidenced by metaproteomics
Scientific Reports
2018
Use of genomics to design a diagnostic assay to discriminate between Streptococcus pneumoniae and Streptococcus pseudopneumoniae
Microbial Genomics
2018
Oral microbiomes from hunter‐gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet
Molecular Ecology
2018
Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments
Nature Communications
2018
Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity
Microbiome
2018
Insights from the Genomes of Microbes Thriving in Uranium-Enriched Sediments
Microbial Ecology
2018
Discovering novel enzymes from marine ecosystems: a metagenomic approach
Botanica Marina
2018
Linking pangenomes and metagenomes: the Prochlorococcus metapangenome
PeerJ
2018
Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia
Translational Psychiatry
2018
Chronic Rhinosinusitis: Potential Role of Microbial Dysbiosis and Recommendations for Sampling Sites
Frontiers in Cellular and Infection Microbiology
2018
Single cell genomes of Prochlorococcus, Synechococcus, and sympatric microbes from diverse marine environments
Scientific Data
2018
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Microbiome
2018
Deciphering microbial interactions in synthetic human gut microbiome communities
Molecular Systems Biology
2018
Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection
Nature Biotechnology
2018
Exploitation of microbial forensics and nanotechnology for the monitoring of emerging pathogens
Critical Reviews in Microbiology
2018
2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2018
Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
PeerJ
2018
GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes
Nucleic Acids Research
2018
A closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales
Harmful Algae
2018
Genome-Centered Metagenomics Analysis Reveals the Symbiotic Organisms Possessing Ability to Cross-Feed with Anammox Bacteria in Anammox Consortia
Environmental Science & Technology
2018
Restricted Localization of Photosynthetic Intracytoplasmic Membranes (ICMs) in Multiple Genera of Purple Nonsulfur Bacteria
mBio
2018
Functional Analysis of Methylomonas sp. DH-1 Genome as a Promising Biocatalyst for Bioconversion of Methane to Valuable Chemicals
Catalysts
2018
Genomic Approaches in Earth and Environmental Sciences
2018
Microbial community and metagenome dynamics during biodegradation of dispersed oil reveals potential key-players in cold Norwegian seawater
Marine Pollution Bulletin
2018
Removal of selenate from brine using anaerobic bacteria and zero valent iron
Journal of Environmental Management
2018
Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses
Microbiome
2018
A phylogenetic and evolutionary analysis of antimycin biosynthesis
Microbiology
2018
Metagenomes from deep Baltic Sea sediments reveal how past and present environmental conditions determine microbial community composition
Marine Genomics
2018
Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations
The ISME Journal
2018
UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction
Journal of Microbiology
2018
Stable Isotope Probing for Microbial Iron Reduction in Chocolate Pots Hot Spring, Yellowstone National Park
Applied and Environmental Microbiology
2018
Metagenomic analyses highlight the symbiotic association between the glacier stonefly Andiperla willinki and its bacterial gut community
Environmental Microbiology
2018
ComM is a hexameric helicase that promotes branch migration during natural transformation in diverse Gram-negative species
Nucleic Acids Research
2017
Draft Genome Sequence of Pseudomonas sp. Strain DrBHI1 (Phylum Proteobacteria )
Genome Announcements
2017
Genome sequencing and comparative analysis of an NDM-1-producingKlebsiella pneumoniaeST15 isolated from a refugee patient
Pathogens and Global Health
2017
DNA Sequencing as a Tool to Monitor Marine Ecological Status
Frontiers in Marine Science
2017
Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches
The ISME Journal
2017
Metabolic network analysis reveals microbial community interactions in anammox granules
Nature Communications
2017
Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments
The ISME Journal
2017
Draft Genome Sequence of Arthrobacter sp. Strain UCD-GKA (Phylum Actinobacteria )
Genome Announcements
2017
Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes
mSphere
2017
Effect of anaerobic soil disinfestation on the bacterial community and key soilborne phytopathogenic agents under walnut tree-crop nursery conditions
Plant and Soil
2017
Genomic Attributes of Extended-Spectrum β-Lactamase-Producing Escherichia Coli Isolated from Patients in Lebanon
Future Microbiology
2017
Genomic variation in microbial populations inhabiting the marine subseafloor at deep-sea hydrothermal vents
Nature Communications
2017
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico “Dead Zone”
mBio
2017
Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing
Scientific Reports
2017
Porcine commensal Escherichia coli: a reservoir for class 1 integrons associated with IS26
Microbial Genomics
2017
Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter
Environmental Microbiology
2017
Selective Isolation of a Eucalyptus spp. Woodchip Bacterial Community and Its Taxonomic and Metabolic Profiling
BioEnergy Research
2017
Izhakiella australiensis sp. nov. isolated from an Australian desert soil
International Journal of Systematic and Evolutionary Microbiology
2017
Functional Metagenomics: Tools and Applications
2017
Typing and comparative genome analysis of Brucella melitensis isolated from Lebanon
FEMS Microbiology Letters
2017
Draft Genome Sequence of “ Candidatus Synechococcus spongiarum” m9, Binned from a Metagenome of South China Sea Sponge Theonella swinhoei
Genome Announcements
2017
1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life
Nature Biotechnology
2017
Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters
Microbiome
2017
Microbial Functional Capacity Is Preserved Within Engineered Soil Formulations Used In Mine Site Restoration
Scientific Reports
2017
Chemolithotrophic processes in the bacterial communities on the surface of mineral-enriched biochars
The ISME Journal
2017
Methods in Molecular Biology
2017
A longitudinal study of the diabetic skin and wound microbiome
PeerJ
2017
Optimizing and evaluating the reconstruction of Metagenome-assembled microbial genomes
BMC Genomics
2017
Draft Genome Sequences of Pseudomonas moraviensis UCD-KL30, Vibrio ostreicida UCD-KL16, Colwellia sp. Strain UCD-KL20, Shewanella sp. Strain UCD-KL12, and Shewanella sp. Strain UCD-KL21, Isolated from Seagrass
Genome Announcements
2017
Draft genome sequences of eight bacteria isolated from the indoor environment: Staphylococcus capitis strain H36, S. capitis strain H65, S. cohnii strain H62, S. hominis strain H69, Microbacterium sp. strain H83, Mycobacterium iranicum strain H39, Plantibacter sp. strain H53, and Pseudomonas oryzihabitans strain H72
Standards in Genomic Sciences
2017
phyloSkeleton: taxon selection, data retrieval and marker identification for phylogenomics
Bioinformatics
2017
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Nature Biotechnology
2017
Microdiversity of an Abundant Terrestrial Bacterium Encompasses Extensive Variation in Ecologically Relevant Traits
mBio
2017
Complete genome sequence of the heavy metal resistant bacterium Agromyces aureus AR33T and comparison with related Actinobacteria
Standards in Genomic Sciences
2017
Genetic adaptation of microbial populations present in high-intensity catfish production systems with therapeutic oxytetracycline treatment
Scientific Reports
2017
Draft Genome Sequences of Dermacoccus nishinomiyaensis Strains UCD-KPL2534 and UCD-KPL2528 Isolated from an Indoor Track Facility
Genome Announcements
2017
Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture
Standards in Genomic Sciences
2017
Draft Genome Sequence of Propionibacterium avidum Strain UCD-PD2 Isolated from a Feline Anal Sac
Genome Announcements
2017
Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI
mSystems
2017
Genome-Enabled Insights into the Ecophysiology of the Comammox Bacterium “ Candidatus Nitrospira nitrosa”
mSystems
2017
Clostridium chauvoei, an Evolutionary Dead-End Pathogen
Frontiers in Microbiology
2017
Transcriptomic differentiation underlying marine‐to‐freshwater transitions in the South American silversides Odontesthes argentinensis and O. bonariensis (Atheriniformes)
Ecology and Evolution
2017
Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy
PeerJ
2017
Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems
PeerJ
2017
Draft Genome Sequences of Two Unclassified Bacteria, Sphingomonas sp. Strains IBVSS1 and IBVSS2, Isolated from Environmental Samples
Genome Announcements
2017
Functional Metagenomics: Tools and Applications
2017
Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics
Microbiome
2017
The growing tree of Archaea: new perspectives on their diversity, evolution and ecology
The ISME Journal
2017
Whole-Community Metagenomics in Two Different Anammox Configurations: Process Performance and Community Structure
Environmental Science & Technology
2017
Energy and carbon metabolisms in a deep terrestrial subsurface fluid microbial community
The ISME Journal
2017
Draft Genome Sequences of Two Unclassified Chitinophagaceae Bacteria, IBVUCB1 and IBVUCB2, Isolated from Environmental Samples
Genome Announcements
2017
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
Genome Biology
2017
Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms
PLOS ONE
2017
Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars
Frontiers in Microbiology
2017
Novel Large Sulfur Bacteria in the Metagenomes of Groundwater-Fed Chemosynthetic Microbial Mats in the Lake Huron Basin
Frontiers in Microbiology
2017
Simultaneous selenate reduction and denitrification by a consortium of enriched mine site bacteria
Chemosphere
2017
Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments
Microbiome
2017
Draft Genome Sequences of Two Unclassified Bacteria, Hydrogenophaga sp. Strains IBVHS1 and IBVHS2, Isolated from Environmental Samples
Genome Announcements
2017
High-throughput automated microfluidic sample preparation for accurate microbial genomics
Nature Communications
2017
Global Distribution Patterns and Pangenomic Diversity of the Candidate Phylum “Latescibacteria” (WS3)
Applied and Environmental Microbiology
2017
Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids
Scientific Data
2016
The ecologist's field guide to sequence‐based identification of biodiversity
Methods in Ecology and Evolution
2016
Draft Genome Sequence of Cobetia sp. UCD-24C, Isolated from Roots and Leaves of the Seagrass Zostera marina
Genome Announcements
2016
The single-species metagenome: subtypingStaphylococcus aureuscore genome sequences from shotgun metagenomic data
PeerJ
2016
Draft Genome Sequences of Two Vibrio splendidus Strains, Isolated from Seagrass Sediment
Genome Announcements
2016
Genome‐centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion
Environmental Microbiology
2016
Challenges in the analysis of viral metagenomes
Virus Evolution
2016
Draft Genome Sequence of Enterococcus faecalis Strain UCD-PD3
Genome Announcements
2016
A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq
PeerJ
2016
Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains
Microbiome
2016
Next-Generation Sequencing Data Analysis
2016
Genomic islands 1 and 2 play key roles in the evolution of extensively drug-resistant ST235 isolates of Pseudomonas aeruginosa
Open Biology
2016
Large-scale diversification without genetic isolation in nematode symbionts of figs
Science Advances
2016
Bacterial Communities Vary between Sinuses in Chronic Rhinosinusitis Patients
Frontiers in Microbiology
2016
Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage
Molecular Biology and Evolution
2016
Unraveling the Physiological Roles of the Cyanobacterium Geitlerinema sp. BBD and Other Black Band Disease Community Members through Genomic Analysis of a Mixed Culture
PLOS ONE
2016
Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond
Microbes and environments
2016
The Draft Genome Sequence of Paenibacillus polymyxa Strain CCI-25 Encompasses High Potential for Secondary Metabolite Production
Genome Announcements
2016
Isolation and characterization of Flexilinea flocculi gen. nov., sp. nov., a filamentous, anaerobic bacterium belonging to the class Anaerolineae in the phylum Chloroflexi
International Journal of Systematic and Evolutionary Microbiology
2016
Functional interactions of archaea, bacteria and viruses in a hypersaline endolithic community
Environmental Microbiology
2016
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics
Frontiers in Microbiology
2016
DNA Barcoding in Marine Perspectives
2016
Diversity Takes Shape: Understanding the Mechanistic and Adaptive Basis of Bacterial Morphology
PLOS Biology
2016
Microbial Fe(III) oxide reduction potential in Chocolate Pots hot spring, Yellowstone National Park
Geobiology
2016
Draft Genome Sequences of Shewanella sp. Strain UCD-FRSP16_17 and Nine Vibrio Strains Isolated from Abalone Feces
Genome Announcements
2016
HoloVir: A Workflow for Investigating the Diversity and Function of Viruses in Invertebrate Holobionts
Frontiers in Microbiology
2016
Terracidiphilus gabretensis gen. nov., sp. nov., an Abundant and Active Forest Soil Acidobacterium Important in Organic Matter Transformation
Applied and Environmental Microbiology
2016
Draft Genome Sequences of Two Pseudoalteromonas porphyrae Strains Isolated from Seagrass Sediment
Genome Announcements
2016
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
The ISME Journal
2016
Increasing Metagenomic Resolution of Microbiome Interactions Through Functional Phylogenomics and Bacterial Sub-Communities
Frontiers in Genetics
2016
Draft Genome Sequence of Gordonia sp. Strain UCD-TK1 (Phylum Actinobacteria )
Genome Announcements
2016
Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei with either Increased Virulence or Fluoroquinolone Resistance
mSphere
2016
Dissecting host-associated communities with DNA barcodes
Philosophical Transactions of the Royal Society B: Biological Sciences
2016
Draft Genome Sequence of Caloramator mitchellensis, a Thermoanaerobe Isolated from the Waters of the Great Artesian Basin
Genome Announcements
2016
Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights
PLOS Computational Biology
2016
Lentimicrobium saccharophilum gen. nov., sp. nov., a strictly anaerobic bacterium representing a new family in the phylum Bacteroidetes, and proposal of Lentimicrobiaceae fam. nov.
International Journal of Systematic and Evolutionary Microbiology
2016
Bioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation
Frontiers in Microbiology
2016
Expansion of Microbial Forensics
Journal of Clinical Microbiology
2016
Draft Genome Sequences of Two Pseudoalteromonas Strains Isolated from Roots and Leaf Blades of the Seagrass Zostera marina
Genome Announcements
2016
LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes
Bioinformatics
2016
Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics
2016
High-Quality Draft Genome Sequence of an Endophytic Pseudomonas viridiflava Strain with Herbicidal Properties against Its Host, the Weed Lepidium draba L
Genome Announcements
2016
Isolation and Genomic Characterization of ‘Desulfuromonas soudanensis WTL’, a Metal- and Electrode-Respiring Bacterium from Anoxic Deep Subsurface Brine
Frontiers in Microbiology
2016
Genome Analysis of Streptococcus pyogenes Associated with Pharyngitis and Skin Infections
PLOS ONE
2016
Phylogenetic and Functional Substrate Specificity for Endolithic Microbial Communities in Hyper-Arid Environments
Frontiers in Microbiology
2016
Metagenomic analysis of rapid gravity sand filter microbial communities suggests novel physiology ofNitrospiraspp.
The ISME Journal
2016
Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes
Applied and Environmental Microbiology
2016
Comparative genomic analysis of toxin-negative strains of Clostridium difficile from humans and animals with symptoms of gastrointestinal disease
BMC Microbiology
2016
Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction
The ISME Journal
2016
Composting-Like Conditions Are More Efficient for Enrichment and Diversity of Organisms Containing Cellulase-Encoding Genes than Submerged Cultures
PLOS ONE
2016
Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis
Applied and Environmental Microbiology
2016
Draft Genome Sequence of Tenacibaculum soleae UCD-KL19
Genome Announcements
2016
Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs
Nature Communications
2016
High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved
Current Opinion in Biotechnology
2016
Draft Genome Sequence of Curtobacterium sp. Strain UCD-KPL2560 (Phylum Actinobacteria )
Genome Announcements
2016
Genomic Analysis of the Emergence, Evolution, and Spread of Human Respiratory RNA Viruses
Annual Review of Genomics and Human Genetics
2016
Reconstructing metabolic pathways of hydrocarbon-degrading bacteria from the Deepwater Horizon oil spill
Nature Microbiology
2015
Subsistence strategies in traditional societies distinguish gut microbiomes
Nature Communications
2015
MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome
Genome Biology
2015
Metagenome-assembled genomes uncover a global brackish microbiome
Genome Biology
2015
Lifestyle Evolution in Cyanobacterial Symbionts of Sponges
mBio
2015
Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community
Molecular Ecology
2015
Comparative genomic analysis of a multiple antimicrobial resistant enterotoxigenic E. coli O157 lineage from Australian pigs
BMC Genomics
2015
Draft Genome Sequences of 10 Microbacterium spp., with Emphasis on Heavy Metal-Contaminated Environments
Genome Announcements
2015
Metagenomic Analysis of Chicken Gut Microbiota for Improving Metabolism and Health of Chickens — A Review
Asian-Australasian Journal of Animal Sciences
2015
Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities
BMC Bioinformatics
2015
First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking
PeerJ
2015
Taxator-tk: precise taxonomic assignment of metagenomes by fast approximation of evolutionary neighborhoods
Bioinformatics
2015
Draft Genome Sequence of Bacillus safensis JPL-MERTA-8-2, Isolated from a Mars-Bound Spacecraft
Genome Announcements
2015
Draft Genome Sequence of Paenibacillus Strain P1XP2, a Polysaccharide-Degrading, Thermophilic, Facultative Anaerobic Bacterium Isolated from a Commercial Bioreactor Degrading Food Waste
Genome Announcements
2015
Draft Genome Sequence of Bacillus vietnamensis Strain UCD-SED5 (Phylum Firmicutes )
Genome Announcements
2015
Draft Genome Sequence of Burkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum Proteobacteria )
Genome Announcements
2015
Genome Sequence of the Sulfate-Reducing Thermophilic Bacterium Thermodesulfovibrio yellowstonii Strain DSM 11347 T (Phylum Nitrospirae )
Genome Announcements
2015
Draft Genome Sequence of Enterobacter sp. Strain UCD-UG_FMILLET (Phylum Proteobacteria )
Genome Announcements
2015
Whole genome sequencing of extended-spectrum β-lactamase producing Klebsiella pneumoniae isolated from a patient in Lebanon
Frontiers in Cellular and Infection Microbiology
2015
Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order – Phaeomoniellales
Molecular Phylogenetics and Evolution
2015
ConStrains identifies microbial strains in metagenomic datasets
Nature Biotechnology
2015
Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities
Frontiers in Microbiology
2015
Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities
Applied and Environmental Microbiology
2015
Swabs to genomes: a comprehensive workflow
PeerJ
2015
Update on RefSeq microbial genomes resources
Nucleic Acids Research
2015
Genomic resolution of linkages in carbon, nitrogen, and sulfur cycling among widespread estuary sediment bacteria
Microbiome
2015
Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain UCD-SED8 (Phylum Gammaproteobacteria )
Genome Announcements
2015
Draft Genome Sequence of Planomicrobium glaciei UCD-HAM (Phylum Firmicutes )
Genome Announcements
2015
Reference Module in Biomedical Sciences
2015
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
Genome Research
2015
Phylogenetics and the Human Microbiome
Systematic Biology
2015
Genome Sequence of a Sulfate-Reducing Thermophilic Bacterium, Thermodesulfobacterium commune DSM 2178 T (Phylum Thermodesulfobacteria )
Genome Announcements
2015
Draft Genome Sequence of Porphyrobacter mercurialis (sp. nov.) Strain Coronado
Genome Announcements
2015
MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes
BMC Biology
2015
gbtools: Interactive Visualization of Metagenome Bins in R
Frontiers in Microbiology
2015
Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog
Frontiers in Microbiology
2014
Archaeal “Dark Matter” and the Origin of Eukaryotes
Genome Biology and Evolution
2014
Complete Genome Sequence of Coprothermobacter proteolyticus DSM 5265
Genome Announcements
2014
Draft Genome Sequence of Tatumella sp. Strain UCD-D_suzukii (Phylum Proteobacteria ) Isolated from Drosophila suzukii Larvae
Genome Announcements
2014
A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method
PLoS Computational Biology
2014
Draft Genome Sequence of the Pyridinediol-Fermenting Bacterium Synergistes jonesii 78-1
Genome Announcements
2014
An Expanded Genomic Representation of the Phylum Cyanobacteria
Genome Biology and Evolution
2014
Integrative workflows for metagenomic analysis
Frontiers in Cell and Developmental Biology
2014
Frameshift alignment: statistics and post-genomic applications
Bioinformatics
2014
Draft Genome Sequence of Rhizobium rhizogenes Strain ATCC 15834
Genome Announcements
2014
Draft Genome Sequence of Fervidicella metallireducens Strain AeB T , an Iron-Reducing Thermoanaerobe from the Great Artesian Basin
Genome Announcements
2014
Draft Genome Sequence of the Endosymbiont “ Candidatus Ruthia magnifica” UCD-CM (Phylum Proteobacteria )
Genome Announcements
2014
Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh
Environmental Microbiology
2014
Séance: reference-based phylogenetic analysis for 18S rRNA studies
BMC Evolutionary Biology
2014
Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response
PLoS Genetics
2014
Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling
PLoS Computational Biology
2014
Automated ensemble assembly and validation of microbial genomes
BMC Bioinformatics
2014
Microbial shifts in the aging mouse gut
Microbiome
2014
An introduction to the analysis of shotgun metagenomic data
Frontiers in Plant Science
2014
Deciphering Diversity and Ecological Function From Marine Metagenomes
The Biological Bulletin
2014
Draft Genome Sequence of Bacillus subtilis Strain D7XPN1, Isolated from Commercial Bioreactor-Degrading Food Waste
Genome Announcements
2014
Complete Genome Sequence of the Extreme Thermophile Dictyoglomus thermophilum H-6-12
Genome Announcements
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