Undervalued Pseudo- nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers

Enhancement of the nitrogen-fixing activity of paddy soils owing to iron application

(2021) Yoko Masuda et al.   SOIL SCIENCE AND PLANT NUTRITION

Evolution and function of nitrogen fixation gene clusters in sugarcane associated Bradyrhizobium strains

(2021) Gustavo Feitosa Matos et al.   ENVIRONMENTAL MICROBIOLOGY

TaxonKit: A practical and efficient NCBI taxonomy toolkit

(2021) Wei Shen et al.   Journal of Genetics and Genomics

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

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

(2021) Caitlin M. Singleton et al.   Nature Communications

Seasonal and long-term effects of nutrient additions and liming on the nifH gene in cerrado soils under native vegetation

(2021) Rafaella Silveira et al.   iScience

Dispersal strategies shape persistence and evolution of human gut bacteria

(2021) Falk Hildebrand et al.   Cell Host & Microbe

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

(2021) Juan José Pierella Karlusich et al.   Nature Communications

Metagenomics of wastewater phageome identifies an extensively cored antibiotic resistome in a swine feedlot water treatment environment

(2021) Mianzhi Wang et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Southern Chinese populations harbour non-nucleatum Fusobacteria possessing homologues of the colorectal cancer-associated FadA virulence factor

(2020) Yun Kit Yeoh et al.   GUT

Biological nitrogen fixation by alternative nitrogenases in terrestrial ecosystems: a review

(2020) J. P. Bellenger et al.   BIOGEOCHEMISTRY

PICRUSt2 for prediction of metagenome functions

(2020) Gavin M. Douglas et al.   NATURE BIOTECHNOLOGY

Metagenomic views of microbial dynamics influenced by hydrocarbon seepage in sediments of the Gulf of Mexico

(2020) Rui Zhao et al.   Scientific Reports

Diazotrophic Anaeromyxobacter Isolates from Soils

(2020) Yoko Masuda et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Co-locality to co-functionality: Eukaryotic gene neighborhoods as a resource for function discovery

(2020) Fatima Foflonker et al.   MOLECULAR BIOLOGY AND EVOLUTION

RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation

(2020) Wenjun Li et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology resource: enriching a GOld mine

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Predicting clinical resistance prevalence using sewage metagenomic data

(2020) Antti Karkman et al.   Communications Biology

MMseqs2 desktop and local web server app for fast, interactive sequence searches

(2019) M Mirdita et al.   BIOINFORMATICS

Metagenomic and Resistome Analysis of a Full-Scale Municipal Wastewater Treatment Plant in Singapore Containing Membrane Bioreactors

(2019) Charmaine Ng et al.   Frontiers in Microbiology

Time Series Genome-Centric Analysis Unveils Bacterial Response to Operational Disturbance in Activated Sludge

(2019) María Victoria Pérez et al.   mSystems

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

(2019) Takuya Aramaki et al.   BIOINFORMATICS

MICAN-SQ: a sequential protein structure alignment program that is applicable to monomers and all types of oligomers

(2018) Shintaro Minami et al.   BIOINFORMATICS

The microbial nitrogen-cycling network

(2018) Marcel M. M. Kuypers et al.   NATURE REVIEWS MICROBIOLOGY

Evaluation of Primers Targeting the Diazotroph Functional Gene and Development of NifMAP – A Bioinformatics Pipeline for Analyzing nifH Amplicon Data

(2018) Roey Angel et al.   Frontiers in Microbiology

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

(2018) Tom O. Delmont et al.   Nature Microbiology

The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales

(2018) Hong-Yi Li et al.   Microbiome

Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome

(2017) Tao Zuo et al.   GUT

A genomic perspective on stoichiometric regulation of soil carbon cycling

(2017) Wyatt H Hartman et al.   ISME Journal

Predominant but Previously-overlooked Prokaryotic Drivers of Reductive Nitrogen Transformation in Paddy Soils, Revealed by Metatranscriptomics

(2017) Yoko Masuda et al.   MICROBES AND ENVIRONMENTS

Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment

(2017) Julia Fukuyama et al.   PLoS Computational Biology

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

(2017) Sonny T. M. Lee et al.   Microbiome

The biosynthetic pathway of coenzyme F430 in methanogenic and methanotrophic archaea

(2016) Kaiyuan Zheng et al.   SCIENCE

Decoupling function and taxonomy in the global ocean microbiome

(2016) S. Louca et al.   SCIENCE

Nitrogen fixation and nifH diversity in human gut microbiota

(2016) Katsura Igai et al.   Scientific Reports

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

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

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Metagenomic analysis of the microbiota in the highly compartmented hindguts of six wood- or soil-feeding higher termites

(2015) Karen Rossmassler et al.   Microbiome

Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

(2014) Emilie E. L. Muller et al.   Nature Communications

A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria

(2014) John Christian Gaby et al.   Database-The Journal of Biological Databases and Curation

Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus

(2013) Javier A Ceja-Navarro et al.   ISME Journal

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes

(2012) Patricia C Dos Santos et al.   BMC GENOMICS

A Comprehensive Evaluation of PCR Primers to Amplify the nifH Gene of Nitrogenase

(2012) John Christian Gaby et al.   PLoS One

Emerging patterns of marine nitrogen fixation

(2011) Jill A. Sohm et al.   NATURE REVIEWS MICROBIOLOGY

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Genetic Co-Occurrence Network across Sequenced Microbes

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