A global metagenomic map of urban microbiomes and antimicrobial resistance

SciPy 1.0: fundamental algorithms for scientific computing in Python

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A complete domain-to-species taxonomy for Bacteria and Archaea

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Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

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

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Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters

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Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

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Precision epidemiology for infectious disease control

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Novel insights from uncultivated genomes of the global human gut microbiome

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Interactive Tree Of Life (iTOL) v4: recent updates and new developments

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Green Infrastructure Design Influences Communities of Urban Soil Bacteria

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Patterns of protist diversity associated with raw sewage in New York City

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Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis

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MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

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Soil Microbial Assemblages Are Linked to Plant Community Composition and Contribute to Ecosystem Services on Urban Green Roofs

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Longitudinal Comparison of Bacterial Diversity and Antibiotic Resistance Genes in New York City Sewage

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

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Population level evidence for seasonality of the human microbiome

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Why do microbes exhibit weak biogeographic patterns?

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Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2018) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

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Global increase and geographic convergence in antibiotic consumption between 2000 and 2015

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A global atlas of the dominant bacteria found in soil

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Structure and function of the global topsoil microbiome

(2018) Mohammad Bahram et al.   NATURE

Microbiology of the built environment

(2018) Jack A. Gilbert et al.   NATURE REVIEWS MICROBIOLOGY

The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome

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Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes

(2018) David Paez-Espino et al.   NUCLEIC ACIDS RESEARCH

A long-term survey unveils strong seasonal patterns in the airborne microbiome coupled to general and regional atmospheric circulations

(2018) Joan Cáliz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wastewater for Urban Agriculture: A Significant Factor in Dissemination of Antibiotic Resistance

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Antimicrobial resistance in healthcare, agriculture and the environment: the biochemistry behind the headlines

(2017) Henrietta Venter et al.   Essays in Biochemistry

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Strains, functions and dynamics in the expanded Human Microbiome Project

(2017) Jason Lloyd-Price et al.   NATURE

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data

(2017) David Paez-Espino et al.   Nature Protocols

Towards a genomics-informed, real-time, global pathogen surveillance system

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Microbial mass movements

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Bacterial colonization and succession in a newly opened hospital

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Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome

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Metagenomic characterization of ambulances across the USA

(2017) Niamh B. O’Hara et al.   Microbiome

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Mobile genes in the human microbiome are structured from global to individual scales

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Uncovering Earth’s virome

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MEGARes: an antimicrobial resistance database for high throughput sequencing

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Antimicrobial Resistance in Agriculture

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Review of Antimicrobial Resistance in the Environment and Its Relevance to Environmental Regulators

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The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report

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Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment

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dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

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

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Urban stress is associated with variation in microbial species composition—but not richness—in Manhattan

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Global trends in antimicrobial use in food animals

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Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

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Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics

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UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

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XSEDE: Accelerating Scientific Discovery

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Fast and sensitive protein alignment using DIAMOND

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A Metagenomic Framework for the Study of Airborne Microbial Communities

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Mechanisms of Resistance and Clinical Relevance of Resistance to β-Lactams, Glycopeptides, and Fluoroquinolones

(2012) Louis B. Rice   MAYO CLINIC PROCEEDINGS

Structure, function and diversity of the healthy human microbiome

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Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Topological entropy of DNA sequences

(2011) David Koslicki   BIOINFORMATICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil

(2008) Heather K Allen et al.   ISME Journal

Antibiotics and Antibiotic Resistance Genes in Natural Environments

(2008) J. L. Martinez   SCIENCE