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Global Genetic Cartography of Urban Metagenomes and Anti-Microbial Resistance

https://doi.org/10.1101/724526
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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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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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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Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics
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Mechanisms of Resistance and Clinical Relevance of Resistance to β-Lactams, Glycopeptides, and Fluoroquinolones
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Wastewater for Urban Agriculture: A Significant Factor in Dissemination of Antibiotic Resistance
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Functional metagenomics reveals diverse β-lactamases in a remote Alaskan soil
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Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology
inferredcites →https://doi.org/10.1038/ismej.2017.126openalex-snapshot
dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication
inferredcites →https://doi.org/10.1038/nature08821openalex-snapshot
A human gut microbial gene catalogue established by metagenomic sequencing
inferredcites →https://doi.org/10.1038/nature11234openalex-snapshot
Structure, function and diversity of the healthy human microbiome
inferredcites →https://doi.org/10.1038/nature18927openalex-snapshot
Mobile genes in the human microbiome are structured from global to individual scales
inferredcites →https://doi.org/10.1038/nature19094openalex-snapshot
Uncovering Earth’s virome
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Strains, functions and dynamics in the expanded Human Microbiome Project
inferredcites →https://doi.org/10.1038/nature24621openalex-snapshot
A communal catalogue reveals Earth’s multiscale microbial diversity
inferredcites →https://doi.org/10.1038/nbt.3893openalex-snapshot
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
inferredcites →https://doi.org/10.1038/nbt0718-660aopenalex-snapshot
Correction: Corrigendum: Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
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Ecological and genetic basis of metapopulation persistence of the Glanville fritillary butterfly in fragmented landscapes
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.2066openalex-snapshot
Metagenomic microbial community profiling using unique clade-specific marker genes
inferredcites →https://doi.org/10.1038/nmeth.3176openalex-snapshot
Fast and sensitive protein alignment using DIAMOND
inferredcites →https://doi.org/10.1038/nprot.2017.063openalex-snapshot
Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data
inferredcites →https://doi.org/10.1038/nrg.2017.88openalex-snapshot
Towards a genomics-informed, real-time, global pathogen surveillance system
inferredcites →https://doi.org/10.1038/s41396-018-0103-3openalex-snapshot
Why do microbes exhibit weak biogeographic patterns?
inferredcites →https://doi.org/10.1038/s41396-019-0467-zopenalex-snapshot
Patterns of protist diversity associated with raw sewage in New York City
inferredcites →https://doi.org/10.1038/s41467-017-02018-wopenalex-snapshot
Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome
inferredcites →https://doi.org/10.1038/s41467-019-08853-3openalex-snapshot
Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage
inferredcites →https://doi.org/10.1038/s41564-017-0083-5openalex-snapshot
Author Correction: Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
inferredcites →https://doi.org/10.1038/s41579-018-0065-5openalex-snapshot
Microbiology of the built environment
inferredcites →https://doi.org/10.1038/s41586-018-0386-6openalex-snapshot
Structure and function of the global topsoil microbiome
inferredcites →https://doi.org/10.1038/s41586-019-1058-xopenalex-snapshot
New insights from uncultivated genomes of the global human gut microbiome
inferredcites →https://doi.org/10.1038/s41591-019-0345-2openalex-snapshot
Precision epidemiology for infectious disease control
inferredcites →https://doi.org/10.1038/s41592-018-0176-yopenalex-snapshot
Species-level functional profiling of metagenomes and metatranscriptomes
inferredcites →https://doi.org/10.1042/ebc20160053openalex-snapshot
Antimicrobial resistance in healthcare, agriculture and the environment: the biochemistry behind the headlines
inferredcites →https://doi.org/10.1056/nejmoa1803396openalex-snapshot
Clinical Metagenomic Sequencing for Diagnosis of Meningitis and Encephalitis
inferredcites →https://doi.org/10.1073/pnas.1503141112openalex-snapshot
Global trends in antimicrobial use in food animals
inferredcites →https://doi.org/10.1073/pnas.1717295115openalex-snapshot
Global increase and geographic convergence in antibiotic consumption between 2000 and 2015
inferredcites →https://doi.org/10.1073/pnas.1812826115openalex-snapshot
A long-term survey unveils strong seasonal patterns in the airborne microbiome coupled to general and regional atmospheric circulations
inferredcites →https://doi.org/10.1080/07420528.2018.1424718openalex-snapshot
Population level evidence for seasonality of the human microbiome
inferredcites →https://doi.org/10.1093/bioinformatics/btr077openalex-snapshot
Topological entropy of DNA sequences
inferredcites →https://doi.org/10.1093/bioinformatics/btv428openalex-snapshot
dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
inferredcites →https://doi.org/10.1093/bioinformatics/btz848openalex-snapshot
GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
inferredcites →https://doi.org/10.1093/nar/gkw1009openalex-snapshot
MEGARes: an antimicrobial resistance database for high throughput sequencing
inferredcites →https://doi.org/10.1093/nar/gkx1321openalex-snapshot
PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures
inferredcites →https://doi.org/10.1093/nar/gky1127openalex-snapshot
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes
inferredcites →https://doi.org/10.1093/nar/gkz239openalex-snapshot
Interactive Tree Of Life (iTOL) v4: recent updates and new developments
inferredcites →https://doi.org/10.1101/314112openalex-snapshot
Nonparametric analysis of contributions to variance in genomics and epigenomics data
inferredcites →https://doi.org/10.1101/gr.186072.114openalex-snapshot
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
inferredcites →https://doi.org/10.1101/gr.213959.116openalex-snapshot
metaSPAdes: a new versatile metagenomic assembler
inferredcites →https://doi.org/10.1111/j.1398-9995.2005.00961.xopenalex-snapshot
Allergic disease in urban and rural populations: increasing prevalence with increasing urbanization
inferredcites →https://doi.org/10.1126/science.1110591openalex-snapshot
Diversity of the Human Intestinal Microbial Flora
inferredcites →https://doi.org/10.1126/science.1159483openalex-snapshot
Antibiotics and Antibiotic Resistance Genes in Natural Environments
inferredcites →https://doi.org/10.1126/science.aao3007openalex-snapshot
Microbial mass movements
inferredcites →https://doi.org/10.1126/science.aap9516openalex-snapshot
A global atlas of the dominant bacteria found in soil
inferredcites →https://doi.org/10.1126/scitranslmed.aah6500openalex-snapshot
Bacterial colonization and succession in a newly opened hospital
inferredcites →https://doi.org/10.1128/aac.00419-13openalex-snapshot
The Comprehensive Antibiotic Resistance Database
inferredcites →https://doi.org/10.1128/aem.02244-14openalex-snapshot
Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics
inferredcites →https://doi.org/10.1128/mbio.02227-15openalex-snapshot
Antimicrobial Resistance in Agriculture
inferredcites →https://doi.org/10.1128/msystems.00018-16openalex-snapshot
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment
inferredcites →https://doi.org/10.1128/msystems.00123-17openalex-snapshot
Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome
inferredcites →https://doi.org/10.1128/msystems.00327-19openalex-snapshot
Longitudinal Comparison of Bacterial Diversity and Antibiotic Resistance Genes in New York City Sewage
inferredcites →https://doi.org/10.1136/oem.55.9.579openalex-snapshot
Correlation between the prevalence of certain fungi and sick building syndrome.
inferredcites →https://doi.org/10.1186/1471-2105-11-119openalex-snapshot
Prodigal: prokaryotic gene recognition and translation initiation site identification
inferredcites →https://doi.org/10.1186/gb-2004-5-2-r12openalex-snapshot
Versatile and open software for comparing large genomes
inferredcites →https://doi.org/10.1186/s13059-016-0997-xopenalex-snapshot
Mash: fast genome and metagenome distance estimation using MinHash
inferredcites →https://doi.org/10.1186/s13059-017-1299-7openalex-snapshot
Comprehensive benchmarking and ensemble approaches for metagenomic classifiers
inferredcites →https://doi.org/10.1186/s13059-018-1568-0openalex-snapshot
KrakenUniq: confident and fast metagenomics classification using unique k-mer counts
inferredcites →https://doi.org/10.1186/s13062-019-0242-0openalex-snapshot
Massive metagenomic data analysis using abundance-based machine learning
inferredcites →https://doi.org/10.1186/s13062-019-0243-zopenalex-snapshot
Identification of city specific important bacterial signature for the MetaSUB CAMDA challenge microbiome data
inferredcites →https://doi.org/10.1186/s13104-016-1900-2openalex-snapshot
AdapterRemoval v2: rapid adapter trimming, identification, and read merging
inferredcites →https://doi.org/10.1186/s40168-016-0168-zopenalex-snapshot
The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report
inferredcites →https://doi.org/10.1186/s40168-017-0237-yopenalex-snapshot
Normalization and microbial differential abundance strategies depend upon data characteristics
inferredcites →https://doi.org/10.1186/s40168-017-0267-5openalex-snapshot
Optimizing methods and dodging pitfalls in microbiome research
inferredcites →https://doi.org/10.1186/s40168-017-0339-6openalex-snapshot
Metagenomic characterization of ambulances across the USA
inferredcites →https://doi.org/10.1186/s40168-019-0648-zopenalex-snapshot
Urban metagenomics uncover antibiotic resistance reservoirs in coastal beach and sewage waters
inferredcites →https://doi.org/10.12688/gatesopenres.12772.1openalex-snapshot
The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics
inferredcites →https://doi.org/10.1371/journal.pcbi.1002195openalex-snapshot
Accelerated Profile HMM Searches
inferredcites →https://doi.org/10.1371/journal.pone.0009490openalex-snapshot
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
inferredcites →https://doi.org/10.1371/journal.pone.0081862openalex-snapshot
A Metagenomic Framework for the Study of Airborne Microbial Communities
inferredcites →https://doi.org/10.21105/joss.00861openalex-snapshot
UMAP: Uniform Manifold Approximation and Projection
inferredcites →https://doi.org/10.2307/2808041openalex-snapshot
World Urbanization Prospects: The 1996 Revision
inferredcites →https://doi.org/10.3389/fevo.2019.00198openalex-snapshot
Soil Microbial Assemblages Are Linked to Plant Community Composition and Contribute to Ecosystem Services on Urban Green Roofs
inferredcites →https://doi.org/10.3389/fmicb.2016.01728openalex-snapshot
Review of Antimicrobial Resistance in the Environment and Its Relevance to Environmental Regulators
inferredcites →https://doi.org/10.3389/fmicb.2019.00982openalex-snapshot
Green Infrastructure Design Influences Communities of Urban Soil Bacteria
inferredcites →https://doi.org/10.3402/iee.v5.27060openalex-snapshot
How urbanization affects the epidemiology of emerging infectious diseases
inferredcites →https://doi.org/10.48550/arxiv.2009.12338openalex-snapshot
The MetaSUB Microbiome Core Analysis Pipeline Enables Large Scale Metagenomic Analysis
inferredcites →https://doi.org/10.7171/jbt.17-2801-007openalex-snapshot
Precision Metagenomics: Rapid Metagenomic Analyses for Infectious Disease Diagnostics and Public Health Surveillance
inferredcites →https://doi.org/10.7554/elife.46923openalex-snapshot
Consistent and correctable bias in metagenomic sequencing experiments
inferredcites →https://doi.org/10.7717/peerj.7359openalex-snapshot
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation
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Characterization of microbial communities in urban subway: connotation for indoor environment quality and public health
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Bacterial diversity and biomarkers screening of station and carriage surface in Shanghai metro system, China
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Buffering updates enables efficient dynamic de Bruijn graphs
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Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
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Exploring the antibiotic resistance of Listeria monocytogenes in food environments – a review
inferred← citeshttps://doi.org/10.1080/13102818.2022.2151378openalex-snapshot
In silico discovering relationship between bacteriophages and antimicrobial resistance
inferred← citeshttps://doi.org/10.1093/nar/gkz1010openalex-snapshot
MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data
inferred← citeshttps://doi.org/10.1101/2019.12.20.860569openalex-snapshot
The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes
inferred← citeshttps://doi.org/10.1101/2020.10.01.322164openalex-snapshot
Indexing All Life’s Known Biological Sequences
inferred← citeshttps://doi.org/10.1101/2020.11.10.376954openalex-snapshot
Genetic and Immunological Evidence for Microbial Transfer Between the International Space Station and an Astronaut
inferred← citeshttps://doi.org/10.1128/msystems.00771-20openalex-snapshot
End-to-End Protocol for the Detection of SARS-CoV-2 from Built Environments
inferred← citeshttps://doi.org/10.1186/s13059-023-03033-5openalex-snapshot
Ariadne: synthetic long read deconvolution using assembly graphs
inferred← citeshttps://doi.org/10.1186/s13062-020-00287-yopenalex-snapshot
Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data
inferred← citeshttps://doi.org/10.1186/s40168-019-0772-9openalex-snapshot
The subway microbiome: seasonal dynamics and direct comparison of air and surface bacterial communities
inferred← citeshttps://doi.org/10.1186/s40168-021-01020-1openalex-snapshot
A comprehensive metagenomics framework to characterize organisms relevant for planetary protection
inferred← citeshttps://doi.org/10.1186/s40168-021-01082-1openalex-snapshot
Diurnal variation in the human skin microbiome affects accuracy of forensic microbiome matching
inferred← citeshttps://doi.org/10.1186/s40168-021-01166-yopenalex-snapshot
Metagenomic insights into the microbial communities of inert and oligotrophic outdoor pier surfaces of a coastal city
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Global analysis of the metaplasmidome: ecological drivers and spread of antibiotic resistance genes across ecosystems
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Performance evaluation of high-volume electret filter air samplers in aerosol microbiome research
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Characterization of Spacesuit Associated Microbial Communities and Their Implications for NASA Missions
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Metagenomic Approaches to Analyze Antimicrobial Resistance: An Overview
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Origin Sample Prediction and Spatial Modeling of Antimicrobial Resistance in Metagenomic Sequencing Data
inferred← citeshttps://doi.org/10.3389/fmicb.2020.608101openalex-snapshot
Forensic Applications of Microbiomics: A Review
inferred← citeshttps://doi.org/10.3389/fmicb.2021.608478openalex-snapshot
Characterization of Spacesuit Associated Microbial Communities and Their Implications for NASA Missions
inferred← citeshttps://doi.org/10.3389/fmicb.2022.874236openalex-snapshot
Antimicrobial Coating Efficacy for Prevention of Pseudomonas aeruginosa Biofilm Growth on ISS Water System Materials
inferred← citeshttps://doi.org/10.3390/life11121322openalex-snapshot
Usefulness of Microbiome for Forensic Geolocation: A Review
inferred← citeshttps://doi.org/10.3791/62379openalex-snapshot
Swabbing the Urban Environment - A Pipeline for Sampling and Detection of SARS-CoV-2 From Environmental Reservoirs
inferred← citeshttps://doi.org/10.3791/62379-vopenalex-snapshot
Swabbing the Urban Environment - A Pipeline for Sampling and Detection of SARS-CoV-2 From Environmental Reservoirs
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A Review of Forensic Microbes in Crime Investigations
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META$^\mathbf{2}$: Memory-efficient taxonomic classification and abundance estimation for metagenomics with deep learning
inferred← citeshttps://doi.org/10.6084/m9.figshare.12731715openalex-snapshot
Additional file 1 of Performance evaluation of high-volume electret filter air samplers in aerosol microbiome research
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