Metagenomics: genomic analysis of microbial communities.

No abstract is available for this paper.

• Publication year

  2004

• Venue

  Annual Review of Genetics

• Publication date

  2004-11-29

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1146/ANNUREV.GENET.38.072902.091216PMID 15568985
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Targeting modular polyketide synthases with iteratively acting acyltransferases from metagenomes of uncultured bacterial consortia.

  2004cited by this paper
• Community structure and metabolism through reconstruction of microbial genomes from the environment

  2004influential reference
• Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a model.

  2004cited by this paper
• Environmental Genome Shotgun Sequencing of the Sargasso Sea

  2004influential reference
• Phylogenetic relationships ofBacteria based on comparative sequence analysis of elongation factor Tu and ATP-synthase β-subunit genes

  2004cited by this paper
• Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers.

  2004cited by this paper
• Environmental genomics, the big picture?

  2004cited by this paper
• Efficient molecular cloning of environmental DNA from geothermal sediments

  2004cited by this paper
• Metagenomic libraries from uncultured microorganisms

  2004cited by this paper
• Uncultured soil bacteria are a reservoir of new antibiotic resistance genes.

  2004cited by this paper
• Metagenome Survey of Biofilms in Drinking-Water Networks

  2003cited by this paper
• Diversification and spectral tuning in marine proteorhodopsins

  2003cited by this paper
• Extremely Acidophilic Protists from Acid Mine Drainage Host Rickettsiales-Lineage Endosymbionts That Have Intervening Sequences in Their 16S rRNA Genes

  2003cited by this paper
• Construction and Screening of Metagenomic Libraries Derived from Enrichment Cultures: Generation of a Gene Bank for Genes Conferring Alcohol Oxidoreductase Activity on Escherichia coli

  2003cited by this paper
• mRNA Differential Display in a Microbial Enrichment Culture: Simultaneous Identification of Three Cyclohexanone Monooxygenases from Three Species

  2003cited by this paper
• Synthesis of long-chain fatty acid enol esters isolated from an environmental DNA clone.

  2003cited by this paper
• Extracting phylogenetic information from whole-genome sequencing projects: the lactic acid bacteria as a test case.

  2003cited by this paper
• Molecular diversity among marine picophytoplankton as revealed by psbA analyses.

  2003cited by this paper
• Identification of Methyl Coenzyme M Reductase A (mcrA) Genes Associated with Methane-Oxidizing Archaea

  2003influential reference
• A Census of rRNA Genes and Linked Genomic Sequences within a Soil Metagenomic Library

  2003influential reference
• Prospecting for Novel Biocatalysts in a Soil Metagenome

  2003influential reference
• Metagenomic Analyses of an Uncultured Viral Community from Human Feces

  2003influential reference
• Recognition of individual genes in a single bacterial cell by fluorescence in situ hybridization – RING‐FISH

  2003influential reference
• Isolation of high molecular weight DNA from soil for cloning into BAC vectors.

  2003cited by this paper
• The uncultured microbial majority.

  2003influential reference
• Global phage diversity.

  2003cited by this paper
• Recombinant Environmental Libraries Provide Access to Microbial Diversity for Drug Discovery from Natural Products

  2003cited by this paper
• Efficient recovery of environmental DNA for expression cloning by indirect extraction methods.

  2003cited by this paper
• Metagenomic Profiling: Microarray Analysis of an Environmental Genomic Library

  2003cited by this paper
• Proteorhodopsin genes are distributed among divergent marine bacterial taxa

  2003cited by this paper
• Expanding functional spaces of enzymes by utilizing whole genome treasure for library construction

  2003cited by this paper
• Novel Proteorhodopsin variants from the Mediterranean and Red Seas.

  2003cited by this paper
• Novel Tetracycline Resistance Determinant from the Oral Metagenome

  2003cited by this paper
• Soil-based gene discovery: a new technology to accelerate and broaden biocatalytic applications.

  2003cited by this paper
• Evidence of Chemolithoautotrophy in the Bacterial Community Associated with Alvinella pompejana, a Hydrothermal Vent Polychaete

  2003cited by this paper
• Metagenomes of Complex Microbial Consortia Derived from Different Soils as Sources for Novel Genes Conferring Formation of Carbonyls from Short-Chain Polyols on Escherichia coli

  2003cited by this paper
• Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics

  2003influential reference
• Quantification of cell-specific substrate uptake by probe-defined bacteria under in situ conditions by microautoradiography and fluorescence in situ hybridization.

  2003cited by this paper
• Biotechnological prospects from metagenomics.

  2003cited by this paper
• The gene cassette metagenome is a basic resource for bacterial genome evolution.

  2003cited by this paper
• A novel, high performance enzyme for starch liquefaction. Discovery and optimization of a low pH, thermostable alpha-amylase.

  2002cited by this paper
• Genes Encoding TEM-4, SHV-2, and CTX-M-10 Extended-Spectrum β-Lactamases Are Carried by Multiple Klebsiella pneumoniae Clones in a Single Hospital (Madrid, 1989 to 2000)

  2002cited by this paper
• Cultivation of the ubiquitous SAR11 marine bacterioplankton clade

  2002cited by this paper
• Unsuspected diversity among marine aerobic anoxygenic phototrophs

  2002cited by this paper
• Approaches to prokaryotic biodiversity: a population genetics perspective.

  2002cited by this paper
• Isolation of Antibiotics Turbomycin A and B from a Metagenomic Library of Soil Microbial DNA

  2002cited by this paper
• RNA Stable Isotope Probing, a Novel Means of Linking Microbial Community Function to Phylogeny

  2002cited by this paper
• Genomic signature tags (GSTs): a system for profiling genomic DNA.

  2002cited by this paper
• Genomic analysis of uncultured marine viral communities

  2002influential reference
• A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles

  2002cited by this paper
• Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces

  2002cited by this paper
• New natural product families from an environmental DNA (eDNA) gene cluster.

  2002cited by this paper
• Identification of the Functionally Active Methanotroph Population in a Peat Soil Microcosm by Stable-Isotope Probing

  2002cited by this paper
• Exploring prokaryotic diversity in the genomic era

  2002influential reference
• First insight into the genome of an uncultivated crenarchaeote from soil.

  2002cited by this paper
• Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space.

  2002cited by this paper
• Stable isotope probing for detection of methanotrophs after enrichment with 13CH4.

  2002cited by this paper
• Improved Culturability of Soil Bacteria and Isolation in Pure Culture of Novel Members of the Divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia

  2002cited by this paper
• Metagenome—a challenging source of enzyme discovery

  2002cited by this paper
• Technical considerations for RNA-based stable isotope probing: an approach to associating microbial diversity with microbial community function.

  2002cited by this paper
• Identification of active methylotroph populations in an acidic forest soil by stable-isotope probing.

  2002cited by this paper
• Cultivating the uncultured

  2002cited by this paper
• 50 Million Years of Genomic Stasis in Endosymbiotic Bacteria

  2002cited by this paper
• A Novel, High Performance Enzyme for Starch Liquefaction

  2002cited by this paper
• Microbial population genomics and ecology.

  2002cited by this paper
• Cloning the metagenome: Culture-independent access to thediversity and functions of the uncultivated microbial world

  2002cited by this paper
• Microbial communities and their interactions in soil and rhizosphere ecosystems.

  2002cited by this paper
• Estimating prokaryotic diversity and its limits

  2002influential reference
• Ecology and industrial microbiology: Microbial diversity - sustaining the Earth and industry.

  2002cited by this paper
• Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys.

  2002cited by this paper
• The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga-Flavobacterium-Bacteroides division.

  2001cited by this paper
• Expression and isolation of antimicrobial small molecules from soil DNA libraries.

  2001influential reference
• Soil DNA and the microbial metagenome. An annotated selection of World Wide Web sites relevant to the topics in Environmental Microbiology Web alert.

  2001cited by this paper
• Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton.

  2001cited by this paper
• Screening of Environmental DNA Libraries for the Presence of Genes Conferring Na+(Li+)/H+Antiporter Activity on Escherichia coli: Characterization of the Recovered Genes and the Corresponding Gene Products

  2001cited by this paper
• Direct Cloning from Enrichment Cultures, a Reliable Strategy for Isolation of Complete Operons and Genes from Microbial Consortia

  2001cited by this paper
• Proteorhodopsin phototrophy in the ocean

  2001cited by this paper
• Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA.

  2001cited by this paper
• DNA from Uncultured Organisms as a Source of 2,5-Diketo-d-Gluconic Acid Reductases

  2001cited by this paper
• Structure and functional analysis of the microbial community in an aerobic: anaerobic sequencing batch reactor (SBR) with no phosphorus removal.

  2001cited by this paper
• Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage.

  2000cited by this paper
• Cloning the Soil Metagenome: a Strategy for Accessing the Genetic and Functional Diversity of Uncultured Microorganisms

  2000influential reference
• Novel natural products from soil DNA libraries in a streptomycete host.

  2000cited by this paper
• Geochemical and biological aspects of sulfide mineral dissolution: lessons from Iron Mountain, California

  2000cited by this paper
• Cultivation-independent techniques for studying methanotroph ecology.

  2000cited by this paper
• Use of Combined Microautoradiography and Fluorescence In Situ Hybridization To Determine Carbon Metabolism in Mixed Natural Communities of Uncultured Bacteria from the GenusAchromatium

  2000cited by this paper
• Screening of Environmental DNA Libraries for the Presence of Genes Conferring Lipolytic Activity onEscherichia coli

  2000cited by this paper
• Long-Chain N-Acyl Amino Acid Antibiotics Isolated from Heterologously Expressed Environmental DNA

  2000influential reference
• rpoB-Based Microbial Community Analysis Avoids Limitations Inherent in 16S rRNA Gene Intraspecies Heterogeneity

  2000cited by this paper
• Bacterial rhodopsin: evidence for a new type of phototrophy in the sea.

  2000cited by this paper
• Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process

  2000cited by this paper
• Identification of Enterococcus Species and Phenotypically Similar Lactococcus andVagococcus Species by Reverse Checkerboard Hybridization to Chaperonin 60 Gene Sequences

  2000cited by this paper
• Stable-isotope probing as a tool in microbial ecology

  2000cited by this paper
• rRNA Operon Copy Number Reflects Ecological Strategies of Bacteria

  2000cited by this paper
• Virioplankton: Viruses in Aquatic Ecosystems

  2000cited by this paper
• Phylogenetic structures of the genus Acinetobacter based on gyrB sequences: comparison with the grouping by DNA-DNA hybridization.

  1999cited by this paper
• Construction of Environmental DNA Libraries inEscherichia coli and Screening for the Presence of Genes Conferring Utilization of 4-Hydroxybutyrate

  1999cited by this paper
• Chitinases from Uncultured Marine Microorganisms

  1999cited by this paper
• Diversity of radA Genes from Cultured and UnculturedArchaea: Comparative Analysis of Putative RadA Proteins and Their Use as a Phylogenetic Marker

  1999cited by this paper
• The Earth's bounty: assessing and accessing soil microbial diversity.

  1999cited by this paper

• Antibiotic Resistance Patterns of Escherichia coli from Children’s Sandpits in Durban, South Africa: A Point Prevalence Study

  2026cites this paper
• Microbial mechanisms as tools for monitoring and treating emerging contaminants in urban pollution: an overview

  2026influential citation
• Metagenomic insights into the interactions between Chaetomium , tomato and the Fusarium–Meloidogyne complex

  2026cites this paper
• Cultivation and genomic characterization of novel methanogens from arid desert biocrust

  2026cites this paper
• MOSMAP: Mosquito metagenome analysis pipeline

  2025cites this paper
• Metagenomics-assembled genomes reveal microbial metabolic adaptation to athalassohaline environment, the case Lake Barkol, China

  2025cites this paper
• Modern Molecular-Genetic Tools of Personalized Biomedicine

  2025cites this paper
• Anti-Dirt Hand Sanitizer: A Zeolite-Enhanced Approach to Hygiene and Microbial Protection

  2025cites this paper
• LorBin: efficient binning of long-read metagenomes by multiscale adaptive clustering and evaluation

  2025cites this paper
• Metagenomic and metatranscriptomic analysis reveals the enzymatic mechanism of plant polysaccharide degradation through gut microbiome in plateau model animal (Ochotona curzoniae).

  2025cites this paper
• A collection of metagenome-assembled genomes from platinum mine tailings in South Africa

  2025cites this paper
• MetaflowX: a scalable and resource-efficient workflow for multi-strategy metagenomic analysis

  2025cites this paper
• Microbial Solutions in Agriculture: Enhancing Soil Health and Resilience Through Bio-Inoculants and Bioremediation

  2025cites this paper
• Next generation DNA sequencing data analysis and its application in clinical genomics.

  2025cites this paper
• On-site microbial community analysis in rivers: integrating autonomous sampling with a portable sequencing workflow

  2025cites this paper
• Structure of fungal community and culturable fungi on the discolored surfaces of pine storage boxes in the tropical region in Dong Nai, Vietnam.

  2025cites this paper
• Exploring genetic adaptation and microbial dynamics in engineered anaerobic ecosystems via strain-level metagenomics

  2025cites this paper
• Role of the Plant–Microbiome Partnership in Environmentally Harmonious 21st Century Agriculture

  2025cites this paper
• Large-scale classification of metagenomic samples: a comparative analysis of classical machine learning techniques vs a novel brain-inspired hyperdimensional computing approach

  2025cites this paper
• Sea cucumbers as bioindicators of pollution and sea cucumber microbiomes as markers of environmental stress: A review

  2025cites this paper
• Metagenomic analysis’ rhizomicrobiome’ Prunus mahaleb based on 16S RNA gene sequencing on the Illumina MiSeq

  2025cites this paper
• Metagenomics Insights into the Role of Microbial Communities in Mycotoxin Accumulation During Maize Ripening and Storage

  2025cites this paper
• Microfluidics based exploration for quorum quenching genes in Antarctic microbiomes

  2025cites this paper
• Biodegradable polylactic acid plastic can aid to achieve partial nitrification/denitrification for low carbon to nitrogen ratio wastewater treatment: Performance and microbial mechanism.

  2025cites this paper
• Advanced computational tools, artificial intelligence and machine-learning approaches in gut microbiota and biomarker identification

  2025cites this paper
• Modeled Rates Explain a Significant Amount of Variation in Abundance for Several Key Genes in an Important Estuarine Ecosystem

  2025cites this paper
• Repurposing and reusing aquaculture wastes through a biosecure microfloc technology.

  2025cites this paper
• Microbes as Teachers: Rethinking Knowledge in the Anthropocene

  2025cites this paper
• Analysis of metagenomic data

  2025cites this paper
• Allelopathy as a Strategy for Biological Invasion: Calotropis procera and Its Impact on Plant Succession

  2025cites this paper
• Metagenomic driven isolation of poorly culturable species in food.

  2025cites this paper
• Recent advances in characterization and diagnosis of stone fruit tree viruses

  2025cites this paper
• A Review on the Current and Future State of Urinary Tract Infection Diagnostics

  2025cites this paper
• The Ocular Microbiome: Micro-Steps Towards Macro-Shift in Targeted Treatment? A Comprehensive Review

  2024cites this paper
• Metagenomic Analysis of Microbial Diversity in the Moroccan Coastal Water of the Gibraltar Strait

  2024cites this paper
• Rapid identification of antibiotic resistance gene hosts by prescreening ARG-like reads

  2024cites this paper
• The choice of 16S rRNA gene sequence analysis impacted characterization of highly variable surface microbiota in dairy processing environments

  2024cites this paper
• Binning Metagenomic Contigs Using Contig Embedding and Decomposed Tetranucleotide Frequency

  2024cites this paper
• SPLANG—a synthetic poisson-lognormal-based abundance and network generative model for microbial interaction inference algorithms

  2024cites this paper
• TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs

  2024cites this paper
• Bullseye: shotgun metagenomics taking aim at the microbial diversity associated with tubes of Ceriantharia

  2024cites this paper
• Genomic Face-off: An In Silico Comparison of the Probiotic Potential of Lactobacillus spp. and Akkermansia muciniphila

  2024cites this paper
• Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2

  2024cites this paper
• The underground network: facilitation in soil bacteria

  2024cites this paper
• AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides

  2024cites this paper
• 16S amplicon sequencing of the gastrointestinal microbiota of Cirrhinus reba and isolation of an autochthonous probiotic using culture based approaches

  2024cites this paper
• Synergistic impact of bioavailable PHEs and alkalinity on microbial diversity and traits in agricultural soil adjacent to chromium-asbestos mines.

  2024cites this paper
• Research progress on volatile compounds and microbial metabolism of traditional fermented soybean products in China

  2024cites this paper
• Microbial diagnostics in periodontal diseases.

  2024cites this paper
• Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security

  2024cites this paper
• Enhancing the efficiency of anaerobic sulfate-reducing bacteria for biohydrogen production through gradual acclimation

  2024cites this paper
• Metagenomic approaches and opportunities in arid soil research.

  2024cites this paper
• Metagenomic analysis of pathogenic bacteria and virulence factor genes in coastal sediments from highly urbanized cities of India.

  2024cites this paper
• Integrating Quantitative Trait Loci (QTLs) through Meta-QTL (MQTL) Analysis to Facilitate Identification of Relationships between Phenotype and Genotype

  2024cites this paper
• Metagenomic analysis reveals the effect of revegetation types on the function of soil microorganisms in carbon and nitrogen metabolism in the open-cast mining area

  2024cites this paper
• Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities

  2024cites this paper
• The contribution of microorganisms to sustainable development: towards a green future through synthetic biology and systems biology

  2024cites this paper
• Application of infrared spectroscopy to study carbon-deuterium kinetics and isotopic spectral shifts at the single-cell level.

  2024cites this paper
• Optimizing electrochemically active microorganisms as a key player in the bioelectrochemical system: Identification methods and pathways to large-scale implementation.

  2024cites this paper
• Solving genomic puzzles: computational methods for metagenomic binning

  2024cites this paper
• Skin Microbial Composition and Genetic Mutation Analysis in Precision Medicine for Epidermolysis Bullosa.

  2024cites this paper
• Removal of organic matter from food wastewater using anaerobic digestion at low temperatures enhanced by exogenous signaling molecule N-hexanoyl-homoserine lactone enhancement: Insight to extracellular polymeric substances and key functional genes.

  2024cites this paper
• Effective binning of metagenomic contigs using contrastive multi-view representation learning

  2024cites this paper
• Trade-off between microbial ecophysiological features regulated by soil fertility governs plant residue decomposition

  2023cites this paper
• The bidirectional relationship between endometriosis and microbiome

  2023cites this paper
• Unlocking the microbial studies through computational approaches: how far have we reached?

  2023cites this paper
• Microbiome in Lower Urinary Tract Symptoms (LUTSs): Mapping the State of the Art with Bibliometric Analysis

  2023cites this paper
• Transcriptional Interplay between Malassezia restricta and Staphylococcus Species Co-Existing in the Skin Environment

  2023cites this paper
• Classical-to-Quantum Sequence Encoding in Genomics

  2023cites this paper
• The Evolving Nature of Semi-passive Mine Water Treatment

  2023cites this paper
• Investigating the Ocular Surface Microbiome: What Can It Tell Us?

  2023cites this paper
• Decoding the microbial universe with metagenomics: a brief insight

  2023cites this paper
• Structure and Metabolic Potential of the Microbiome of Lake Baikal Upper Sediment Layers Determined by Metagenome Analysis

  2023cites this paper
• Unfolding and De-confounding: Biologically meaningful causal inference from longitudinal multi-omic networks using METALICA

  2023cites this paper
• Bioaerosols in the atmosphere: A comprehensive review on detection methods, concentration and influencing factors.

  2023cites this paper
• Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil

  2023cites this paper
• Assembly strategies for rubber-degrading microbial consortia based on omics tools

  2023cites this paper
• Application of Microorganisms in Biotransformation and Bioremediation of Environmental Contaminant: A Review

  2023cites this paper
• Carotenoids in Health as Studied by Omics-Related Endpoints

  2023cites this paper
• Bioremediation Techniques: Harnessing the Power of Microorganisms for Environmental Restoration

  2023cites this paper
• Bacteriophage-based biosensors for detection of pathogenic microbes in wastewater.

  2023cites this paper
• Dominant influence of plants on soil microbial carbon cycling functions during natural restoration of degraded karst vegetation.

  2023cites this paper
• Abakus: Accelerating k-mer Counting with Storage Technology

  2023cites this paper
• Identification of Oral Microbiome with full-length 16S Sequencing Using Nanopore Technology

  2023cites this paper
• Viabin: A novel method for Overlapped Binning of Metagenomic Contigs using ZINB-autodecoder and Assembly Graphs: Viabin: a metagenomic contigs binning tool

  2023cites this paper
• Identifying Microbiome Dynamics in Pediatric IBD: More than a Family Matter

  2023cites this paper
• Sustainable Fish Feeds with Insects and Probiotics Positively Affect Freshwater and Marine Fish Gut Microbiota

  2023cites this paper
• Composition and transcriptional activity of oil reservoir microorganisms under different gas/liquid ratios

  2023cites this paper
• Microbial community composition analysis to decipher the possible role of inherent bacteria for in-situ arsenic (As) bioremediation

  2023cites this paper
• Perspectives on Using a Competitive Exclusion Approach to Control Listeria monocytogenes in Biological Soil Amendments of Animal Origin (BSAAO): A Review

  2023cites this paper
• Microbiome Analysis of Sugarcane Juices and Biofilms from Louisiana Raw Sugar Factories

  2023cites this paper
• Gut Microbiome–Brain Alliance: A Landscape View into Mental and Gastrointestinal Health and Disorders

  2023cites this paper
• Fine-scale mapping of the microbiome on phylloplane and spermoplane of aromatic and non-aromatic rice genotypes

  2023cites this paper
• Quantification of Microbial Communities in Activated Sludge Containing Lignin and Chlorophenol from the Pulp and Paper Industry as Determined by 16s Rrna Analysis

  2023cites this paper
• Microfluidics: Insights into Intestinal Microorganisms

  2023cites this paper
• Molecular technologies ending with ‘omics’: The driving force toward sustainable plant production and protection

  2023cites this paper
• A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome

  2023cites this paper
• The Impact of Different Inoculation Schemes on the Microbiota, Physicochemical and Sensory Characteristics of Greek Kopanisti Cheese throughout Production and Ripening

  2022cites this paper
• Metabarcoding Approach for Evaluation of Bacterial Diversity in Soft Rotting Potato Tubers and Corresponding Geocaulospheres

  2022cites this paper
• A case for investment in clinical metagenomics in low-income and middle-income countries.

  2022cites this paper