☆ 4.7 Article

Trait biases in microbial reference genomes

SCIENTIFIC DATA (2023)

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Article Microbiology

Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy

Lei Liu et al.

Summary: Our study developed an iterative haplotype-resolved hierarchical clustering-based hybrid assembly approach to reconstruct (near-) complete genomes from highly complex metagenomes, demonstrating the feasibility of this method in uncovering new insights into metagenomics. The high-contiguity MAGs obtained contained various biosynthetic gene clusters, showcasing the potential for discovering new natural products synthesized by microbial communities in wastewater treatment.

MICROBIOME (2021)

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Article Microbiology

Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean

Marta Royo-Llonch et al.

Summary: Using genome-resolved metagenomics, this study identified uncultured Arctic bacterial and archaeal metagenome-assembled genomes (MAGs) and analyzed their gene expression patterns, habitat preferences, and metabolic potential. The results suggest that marine microorganisms in the Arctic Ocean play a crucial role in climate regulation, and the adaptation of Arctic MAGs to a copiotrophic lifestyle in nutrient-rich waters may influence the ecosystem. The Arctic MAGs catalogue provides insights into polar microorganisms driving global biogeochemical cycles.

NATURE MICROBIOLOGY (2021)

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Article Multidisciplinary Sciences

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing

Caitlin M. Singleton et al.

Summary: By using sequencing data and other techniques, we recovered a large number of high-quality microbial genome assemblies, unveiling abundant undescribed lineages belonging to important functional groups in wastewater treatment plants.

NATURE COMMUNICATIONS (2021)

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Article Microbiology

Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes

Robert J. Huddy et al.

Summary: The study showed that specific strains capable of degrading SCN- could be reproducibly selected based on SCN- loading and the presence or absence of added organic carbon. Despite the presence of many Rhizobiales strains, a single Afipia variant dominated the reactor without added molasses at moderately high loadings.

FRONTIERS IN MICROBIOLOGY (2021)

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Article Multidisciplinary Sciences

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

Rachel Gilroy et al.

Summary: This study provides new insights into the taxonomic diversity of the chicken gut microbiome through metagenomic and culture-based analyses. It identified hundreds of novel candidate bacterial genera and species, proposed a scalable nomenclature system, and cultured and sequenced novel bacterial species from chicken feces. The findings expand the known diversity of the chicken gut microbiome and serve as a valuable resource for future studies in this field.

PEERJ (2021)

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Article Microbiology

Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics

Yuan Lin et al.

Summary: The study identified heterogeneous heavy metal-resistance mechanisms among different taxa in DPRS, highlighting the importance of understanding individual microorganisms' heterogeneity in contributing to metabolic versatility and robustness of microbiomes in dynamic environments. This insight is crucial for manipulating microbial adaptation under adverse environmental stimuli.

MICROBIOME (2021)

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Article Biotechnology & Applied Microbiology

Diesel and Crude Oil Biodegradation by Cold-Adapted Microbial Communities in the Labrador Sea

Sean M. C. Murphy et al.

Summary: The study found that biostimulation can enhance the biodegradation of diesel and crude oil in the cold marine environment off the coast of Labrador, with certain bacteria possessing previously unrecognized capabilities for degradation.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2021)

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Article Multidisciplinary Sciences

Global biogeography of chemosynthetic symbionts reveals both localized and globally distributed

Jay T. Osvatic et al.

Summary: In the ocean, the Lucinidae family of marine bivalves is the most species-rich and widely distributed, hosting autotrophic bacterial endosymbionts. Metagenomics research revealed a cosmopolitan symbiont species associated with multiple lucinid host species, challenging our understanding of symbiont dispersal and location-specific colonization. This discovery highlights the importance of host and symbiont flexibility in the ecological and evolutionary success of the lucinid symbiosis.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Multidisciplinary Sciences

Termite gas emissions select for hydrogenotrophic microbial communities in termite mounds

Eleonora Chiri et al.

Summary: Organoheterotrophs are dominant in most soils, but termite mounds feature a unique community dominated by diverse hydrogenotrophic Actinobacteriota and Dormibacterota. These bacteria efficiently consume termite-derived H2 emissions and act as net sinks of atmospheric H2, while also releasing small amounts of methane. The availability of H2 shapes microbial communities and activities, highlighting a unique arthropod-bacteria interaction dependent on H2 transfer.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Engineering, Environmental

Selective enrichment of comammox from activated sludge using antibiotics

Yulin Wang et al.

Summary: The study found that different types and concentrations of antibiotics can affect the taxonomic composition of microbial communities in activated sludge, including comammox. Four antibiotics were selectively enriched comammox Nitrospira, and genomic analysis showed shared metabolic potentials among the enriched comammox. The findings suggest that comammox in activated sludge ecosystems have higher metabolic versatility and can be selectively enriched by certain antibiotics.

WATER RESEARCH (2021)

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Article Multidisciplinary Sciences

Purple sulfur bacteria fix N-2 via molybdenum-nitrogenase in a low molybdenum Proterozoic ocean analogue

Miriam Philippi et al.

Summary: The research found that purple sulfur bacteria fix nitrogen using molybdenum-nitrogenase in Lake Cadagno, which is an analogue system to the sulfidic Proterozoic continental margins, providing the first direct evidence for PSB in situ nitrogen fixation. It was surprising to note that no alternative nitrogenases were detectable and nitrogen fixation was exclusively catalyzed by molybdenum-nitrogenase, functioning even under low molybdenum conditions.

NATURE COMMUNICATIONS (2021)

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Letter Multidisciplinary Sciences

Re-evaluating the evidence for a universal genetic boundary among microbial species

Connor S. Murray et al.

NATURE COMMUNICATIONS (2021)

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Article Multidisciplinary Sciences

Distinct microbial community along the chronic oil pollution continuum of the Persian Gulf converge with oil spill accidents

Maryam Rezaei Somee et al.

Summary: The Persian Gulf, with 48% of the world's oil reserves, is continuously exposed to natural oil seepage. Studies have shown that chronic exposure to trace amounts of pollution in the Gulf promotes the growth of oil-degrading microbes, leading to shifts in the microbial community composition in polluted areas. Hydrocarbon type, exposure time, and sediment depth are identified as the main factors determining microbial response to pollution in oil-polluted marine samples.

SCIENTIFIC REPORTS (2021)

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Article Microbiology

Protein Family Content Uncovers Lineage Relationships and Bacterial Pathway Maintenance Mechanisms in DPANN Archaea

Cindy J. Castelle et al.

Summary: DPANN are small-celled archaea predicted to be symbionts, with proteome content revealing their relationships and potential genetic overlap with bacteria. The separation of DPANN genomes from other archaea parallels the separation of CPR bacteria from all other bacteria, indicating potential symbiosis-related functions. Pacearchaeota and Woesearchaeota, with limited metabolic capacities, show features suggesting scavenged nucleotide metabolisms and episymbiont relationships with bacteria. Additionally, some DPANN genomes contain pathways for unusual nucleotide synthesis and systems for protein refolding, indicating efficient folding of both archaeal and horizontally acquired bacterial proteins.

FRONTIERS IN MICROBIOLOGY (2021)

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Article Microbiology

Genome-Resolved Metagenomics of the Chicken Gut Microbiome

Maia Segura-Wang et al.

Summary: Increasing evidence suggests that chicken gastrointestinal microbiota plays a crucial role in metabolic functions and is associated with economic parameters. This study utilized metagenomic assembled genomes (MAGs) from chicken GIT samples to better understand the metabolic potential at different ages. Results showed age-dependent shifts in the abundance of genes involved in carbohydrate digestion and SCFA production, highlighting the importance of specific enzyme families in the microbial community.

FRONTIERS IN MICROBIOLOGY (2021)

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Article Multidisciplinary Sciences

309 metagenome assembled microbial genomes from deep sediment samples in the Gulfs of Kathiawar Peninsula

Neelam M. Nathani et al.

Summary: Genomes of prokaryoplankton from deep marine sediments are less explored, with the Gulfs of Kathiawar peninsula experiencing varied currents and inputs from on-shore activities. Perturbations may directly influence the microbiome stability. 309 bacterial and archaeal genomes from deep sediments will aid in understanding the physiology, adaptation, and impact of on-shore anthropogenic activities on marine microbes.

SCIENTIFIC DATA (2021)

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Article Microbiology

Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil

Evan P. Starr et al.

Summary: This study used stable-isotope tracing to track carbon flow in plant root-associated soil, revealing the significant role of bacteriophages in the turnover of plant-derived carbon in soil. It also identified various bacteria, viruses, and eukaryotes involved in plant growth and plant-microbe interactions.

MSPHERE (2021)

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Article Microbiology

Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes

Antti J. Rissanen et al.

Summary: Vertical structuring of methanotrophic communities in oxygen-stratified lakes was found to be influenced by oxygen gradients, with Alphaproteobacterial methanotrophs preferring oxic water layers and Methylococcales methanotrophs thriving at and below the oxic-anoxic interface, showing distinct depth variation patterns not completely predictable by taxonomic classification. Genomic differences among Methylococcales methanotrophs explained their variable vertical depth patterns, with genetic adaptations for stress tolerance and motility at different depths.

FEMS MICROBIOLOGY ECOLOGY (2021)

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Article Microbiology

Enrichment of novel Verrucomicrobia, Bacteroidetes, and Krumholzibacteria in an oxygen-limited methane- and iron-fed bioreactor inoculated with Bothnian Sea sediments

Paula Dalcin Martins et al.

Summary: Microbial methane oxidation plays a crucial role in preventing methane emissions into the atmosphere from coastal areas. This study investigated microbial methane and iron cycling in low oxygen conditions, revealing potential for methane oxidation, organic matter degradation, and iron cycling. Metagenomic analysis unveiled new insights into the diverse metabolic capabilities of microorganisms in coastal marine sediments.

MICROBIOLOGYOPEN (2021)

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Article Ecology

Crystalline iron oxides stimulate methanogenic benzoate degradation in marine sediment-derived enrichment cultures

David A. Aromokeye et al.

Summary: The study reveals that iron oxide phases with different crystallinity have varying effects on the degradation of aromatic compounds in methanic sediments, with magnetite and hematite stimulating methane generation while lepidocrocite inhibits the degradation and methane production. These findings provide insights into the mechanisms of organic matter degradation in rapidly accumulating marine sediments with implications for the cycling of iron and methane in coastal and continental margin environments.

ISME JOURNAL (2021)

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Article Biotechnology & Applied Microbiology

A genomic catalog of Earth's microbiomes

Stephen Nayfach et al.

Summary: Reconstructing bacterial and archaeal genomes from shotgun metagenomes has led to the creation of a comprehensive catalog representing a significant expansion of the known phylogenetic diversity of bacteria and archaea. This resource is available for streamlined comparative analyses, interactive exploration, metabolic modeling, and bulk download, demonstrating the utility of genome-centric approaches for understanding genomic properties of uncultivated microorganisms.

NATURE BIOTECHNOLOGY (2021)

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Article Evolutionary Biology

A General and Efficient Algorithm for the Likelihood of Diversification and Discrete-Trait Evolutionary Models

Stilianos Louca et al.

SYSTEMATIC BIOLOGY (2020)

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Article Biochemical Research Methods

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

Takuya Aramaki et al.

BIOINFORMATICS (2020)

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Article Limnology

Stratification of microbiomes during the holomictic period of Lake Fuxian, an alpine monomictic lake

Peng Xing et al.

LIMNOLOGY AND OCEANOGRAPHY (2020)

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Article Limnology

Microbial community composition and functional potential in Bothnian Sea sediments is linked to Fe and S dynamics and the quality of organic matter

Olivia Rasigraf et al.

LIMNOLOGY AND OCEANOGRAPHY (2020)

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Article Limnology

Microbial genomes retrieved from High Arctic lake sediments encode for adaptation to cold and oligotrophic environments

Matti O. Ruuskanen et al.

LIMNOLOGY AND OCEANOGRAPHY (2020)

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Article Environmental Sciences

Phylogenetic and structural diversity of aromatically dense pili from environmental metagenomes

Marcus S. Bray et al.

ENVIRONMENTAL MICROBIOLOGY REPORTS (2020)

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Article Biotechnology & Applied Microbiology

New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

Stefano Campanaro et al.

BIOTECHNOLOGY FOR BIOFUELS (2020)

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Article Ecology

Characterization of a sponge microbiome using an integrative genome-centric approach

J. Pamela Engelberts et al.

ISME JOURNAL (2020)

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Article Ecology

Niche differentiation is spatially and temporally regulated in the rhizosphere

Erin E. Nuccio et al.

ISME JOURNAL (2020)

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Article Ecology

Comparative genome-centric analysis reveals seasonal variation in the function of coral reef microbiomes

Bettina Glasl et al.

ISME JOURNAL (2020)

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Article Limnology

Microbiome of the deep Lake Baikal, a unique oxic bathypelagic habitat

Pedro J. Cabello-Yeves et al.

LIMNOLOGY AND OCEANOGRAPHY (2020)

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Article Multidisciplinary Sciences

Ecological drivers of bacterial community assembly in synthetic phycospheres

He Fu et al.

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

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Article Microbiology

Genome- and Community-Level Interaction Insights in Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment

Zhichao Zhou et al.

MSYSTEMS (2020)

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Article Microbiology

Consistent Metagenome-Derived Metrics Verify and Delineate Bacterial Species Boundaries

Matthew R. Olm et al.

MSYSTEMS (2020)

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Review Biochemistry & Molecular Biology

Accurate and complete genomes from metagenomes

Lin-Xing Chen et al.

GENOME RESEARCH (2020)

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Article Multidisciplinary Sciences

Phylogenomic analysis of 589 metagenome-assembled genomes encompassing all major prokaryotic lineages from the gut of higher termites

Vincent Herve et al.

PEERJ (2020)

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Article Biotechnology & Applied Microbiology

Contrasting bacterial and archaeal distributions reflecting different geochemical processes in a sediment core from the Pearl River Estuary

Wenxiu Wang et al.

AMB EXPRESS (2020)

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Article Ecology

High functional diversity among Nitrospira populations that dominate rotating biological contactor microbial communities in a municipal wastewater treatment plant

Emilie Spasov et al.

ISME JOURNAL (2020)

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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)

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Article Multidisciplinary Sciences

Genome-scale metabolic models of Microbacterium species isolated from a high altitude desert environment

Dinka Mandakovic et al.

SCIENTIFIC REPORTS (2020)

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Article Microbiology

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

L. Alteio et al.

MSYSTEMS (2020)

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Letter Biotechnology & Applied Microbiology

PICRUSt2 for prediction of metagenome functions

Gavin M. Douglas et al.

NATURE BIOTECHNOLOGY (2020)

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Article Microbiology

Genomic Comparison and Spatial Distribution of DifferentSynechococcusPhylotypes in the Black Sea

Andrea Di Cesare et al.

FRONTIERS IN MICROBIOLOGY (2020)

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Article Microbiology

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys

Jialin Hou et al.

MICROBIOME (2020)

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Article Microbiology

Catabolism and interactions of uncultured organisms shaped by eco-thermodynamics in methanogenic bioprocesses

Masaru K. Nobu et al.

MICROBIOME (2020)

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Article Microbiology

Roadmap for naming uncultivated Archaea and Bacteria

Alison E. Murray et al.

NATURE MICROBIOLOGY (2020)

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Article Genetics & Heredity

Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences

Franziska Wemheuer et al.

ENVIRONMENTAL MICROBIOME (2020)

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Article Microbiology

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community

Ga Gong et al.

BMC MICROBIOLOGY (2020)

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Article Engineering, Environmental

Metagenomic profiling of ammonia- and methane-oxidizing microorganisms in two sequential rapid sand filters

Lianna Poghosyan et al.

WATER RESEARCH (2020)

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Article Ecology

Gammaproteobacteria mediating utilization of methyl-, sulfur- and petroleum organic compounds in deep ocean hydrothermal plumes

Zhichao Zhou et al.

ISME JOURNAL (2020)

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Article Multidisciplinary Sciences

Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance

Malte Herold et al.

NATURE COMMUNICATIONS (2020)

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Article Microbiology

Estimate of the sequenced proportion of the global prokaryotic genome

Zheng Zhang et al.

MICROBIOME (2020)

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Article Multidisciplinary Sciences

Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota

Anton Lavrinienko et al.

SCIENTIFIC DATA (2020)

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Article Genetics & Heredity

Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands

Finlay Maguire et al.

MICROBIAL GENOMICS (2020)

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Article Microbiology

Distinct gut microbiotas between southern elephant seals and Weddell seals of Antarctica

Mincheol Kim et al.

JOURNAL OF MICROBIOLOGY (2020)

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Article Multidisciplinary Sciences

Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities

Anna-Louise Reysenbach et al.

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

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Article Multidisciplinary Sciences

Thermogenic hydrocarbon biodegradation by diverse depth-stratified microbial populations at a Scotian Basin cold seep

Xiyang Dong et al.

NATURE COMMUNICATIONS (2020)

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Article Multidisciplinary Sciences

Disease-associated gut microbiome and metabolome changes in patients with chronic obstructive pulmonary disease

Kate L. Bowerman et al.

NATURE COMMUNICATIONS (2020)

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Article Microbiology

Characterization of Metagenome-Assembled Genomes and Carbohydrate-Degrading Genes in the Gut Microbiota of Tibetan Pig

Saisai Zhou et al.

FRONTIERS IN MICROBIOLOGY (2020)

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Article Microbiology

DNA-Stable Isotope Probing Shotgun Metagenomics Reveals the Resilience of Active Microbial Communities to Biochar Amendment in Oxisol Soil

Julian Yu et al.

FRONTIERS IN MICROBIOLOGY (2020)

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Article Microbiology

New viral biogeochemical roles revealed through metagenomic analysis of Lake Baikal

F. H. Coutinho et al.

MICROBIOME (2020)

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Review Biotechnology & Applied Microbiology

Applications of Microbial β-Mannanases

Aneesa Dawood et al.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2020)

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Article Microbiology

Dysbiosis in marine aquaculture revealed through microbiome analysis: reverse ecology for environmental sustainability

Jose M. Haro-Moreno et al.

FEMS MICROBIOLOGY ECOLOGY (2020)

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Article Engineering, Environmental

Flocs are the main source of nitrous oxide in a high-rate anammox granular sludge reactor: insights from metagenomics and fed-batch experiments

Jin-long Zhuang et al.

WATER RESEARCH (2020)

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Article Materials Science, Multidisciplinary

Soil microbiomes mediate degradation of vinyl ester-based polymer composites

Adam M. Breister et al.

COMMUNICATIONS MATERIALS (2020)

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Article Biotechnology & Applied Microbiology

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

Alon Shaiber et al.

GENOME BIOLOGY (2020)

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Article Microbiology

High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method

Lei Liu et al.

MICROBIOME (2020)

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Article Biology

Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes

Johannes Alneberg et al.

COMMUNICATIONS BIOLOGY (2020)

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Article Multidisciplinary Sciences

New insights from uncultivated genomes of the global human gut microbiome

Stephen Nayfach et al.

NATURE (2019)

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Article Biotechnology & Applied Microbiology

A human gut bacterial genome and culture collection for improved metagenomic analyses

Samuel C. Forster et al.

NATURE BIOTECHNOLOGY (2019)

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Article Multidisciplinary Sciences

Biological composition and microbial dynamics of sinking particulate organic matter at abyssal depths in the oligotrophic open ocean

Dominique Boeuf et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

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Article Microbiology

The Water Microbiome Through a Pilot Scale Advanced Treatment Facility for Direct Potable Reuse

Rose S. Kantor et al.

FRONTIERS IN MICROBIOLOGY (2019)

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Article Microbiology

Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms

Spencer Diamond et al.

NATURE MICROBIOLOGY (2019)

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Article Microbiology

Casting light on Asgardarchaeota metabolism in a sunlit microoxic niche

Paul-Adrian Bulzu et al.

NATURE MICROBIOLOGY (2019)

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Article Multidisciplinary Sciences

Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria

Alex Greenlon et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

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Article Multidisciplinary Sciences

Metabolic potential of uncultured bacteria and archaea associated with petroleum seepage in deep-sea sediments

Xiyang Dong et al.

NATURE COMMUNICATIONS (2019)

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Article Biology

Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake

Charlotte D. Vavourakis et al.

BMC BIOLOGY (2019)

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Article Environmental Sciences

Metagenomic analysis exhibited the co-metabolism of polycyclic aromatic hydrocarbons by bacterial community from estuarine sediment

Shuangfei Zhang et al.

ENVIRONMENT INTERNATIONAL (2019)

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Article Microbiology

Geomicrobiology of the carbon, nitrogen and sulphur cycles in Powell Lake: a permanently stratified water column containing ancient seawater

Sebastian Haas et al.

ENVIRONMENTAL MICROBIOLOGY (2019)

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Article Biotechnology & Applied Microbiology

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

Robert D. Stewart et al.

NATURE BIOTECHNOLOGY (2019)

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Article Microbiology

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

Steven J. Robbins et al.

NATURE MICROBIOLOGY (2019)

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Correction Microbiology

Quantitatively Partitioning Microbial Genomic Traits among Taxonomic Ranks across the Microbial Tree of Life (vol 4, e00446-19, 2019)

Taylor M. Royalty et al.

MSPHERE (2019)

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Article Microbiology

Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents

David Galambos et al.

ENVIRONMENTAL MICROBIOLOGY (2019)

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Article Microbiology

Enrichment of Marinobacter sp. and Halophilic Homoacetogens at the Biocathode of Microbial Electrosynthesis System Inoculated With Red Sea Brine Pool

Manal F. Alqahtani et al.

FRONTIERS IN MICROBIOLOGY (2019)

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Article Biochemistry & Molecular Biology

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Edoardo Pasolli et al.

CELL (2019)

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Article Biochemistry & Molecular Biology

Charting the Complexity of the Marine Microbiome through Single-Cell Genomics

Maria G. Pachiadaki et al.

CELL (2019)

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Article Biochemistry & Molecular Biology

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Jaime Huerta-Cepas et al.

NUCLEIC ACIDS RESEARCH (2019)

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Article Multidisciplinary Sciences

Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea

Qiyun Zhu et al.

NATURE COMMUNICATIONS (2019)

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Article Ecology

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

Benjamin J. Tully et al.

ISME JOURNAL (2018)

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Review Biochemistry & Molecular Biology

Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life

Cindy J. Castelle et al.

CELL (2018)

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Article Biology

Dating phototrophic microbial lineages with reticulate gene histories

C. Magnabosco et al.

GEOBIOLOGY (2018)

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Article Ecology

Genome-resolved metagenomics identifies genetic mobility, metabolic interactions, and unexpected diversity in perchloratereducing communities

Tyler P. Barnum et al.

ISME JOURNAL (2018)

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Article Environmental Sciences

PhyMet2: a database and toolkit for phylogenetic and metabolic analyses of methanogens

Burdukiewicz Michal et al.

ENVIRONMENTAL MICROBIOLOGY REPORTS (2018)

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Article Multidisciplinary Sciences

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

Robert D. Stewart et al.

NATURE COMMUNICATIONS (2018)

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Article Microbiology

Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment

Jose M. Haro-Moreno et al.

MICROBIOME (2018)

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Article Multidisciplinary Sciences

The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

Benjamin J. Tully et al.

SCIENTIFIC DATA (2018)

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Review Ecology

Function and functional redundancy in microbial systems

Stilianos Louca et al.

NATURE ECOLOGY & EVOLUTION (2018)

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Article Multidisciplinary Sciences

Deep mitochondrial origin outside the sampled alphaproteobacteria

Joran Martijn et al.

NATURE (2018)

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Article Multidisciplinary Sciences

Genome-centric view of carbon processing in thawing permafrost

Ben J. Woodcroft et al.

NATURE (2018)

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