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Molecular eco-systems biology: towards an understanding of community function
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Microarray Applications in Microbial Ecology Research
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Towards Cellular Systems in 4D
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Integrating ecology into biotechnology
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Protein function space: viewing the limits or limited by our view?
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iPath: interactive exploration of biochemical pathways and networks
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Microbial diversity and function in soil: from genes to ecosystems
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Synergistic interactions in the microbial world
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A marine microbial consortium apparently mediating anaerobic oxidation of methane
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GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
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What's the ‘meta’ with metagenomics?
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Witnessing the last supper of uncultivated microbial cells with Raman-FISH
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Soil eukaryotic functional diversity, a metatranscriptomic approach
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Millimeter‐scale genetic gradients and community‐level molecular convergence in a hypersaline microbial mat
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Is there biological research beyond Systems Biology? A comparative analysis of terms
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Metabolic modeling of a mutualistic microbial community
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Community structure and metabolism through reconstruction of microbial genomes from the environment
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Spatial scaling of microbial eukaryote diversity
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A taxa–area relationship for bacteria
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Symbiosis insights through metagenomic analysis of a microbial consortium
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Strain-resolved community proteomics reveals recombining genomes of acidophilic bacteria
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Two-dimensional annotation of genomes
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Sequencing genomes from single cells by polymerase cloning
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The minimum information about a genome sequence (MIGS) specification
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Sequence census methods for functional genomics
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Metagenomics: DNA sequencing of environmental samples
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High-throughput fluorescence microscopy for systems biology
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Microbial biogeography: putting microorganisms on the map
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Communication in bacteria: an ecological and evolutionary perspective
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Social evolution theory for microorganisms
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Microbial landscapes: new paths to biofilm research
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Global patterns in bacterial diversity
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Quantitative assessment of protein function prediction from metagenomics shotgun sequences
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An experimental metagenome data management and analysis system
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From genomics to chemical genomics: new developments in KEGG
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The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide
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STITCH: interaction networks of chemicals and proteins
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Rapid quantitative profiling of complex microbial populations
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Application of a nifH oligonucleotide microarray for profiling diversity of N 2 ‐fixing microorganisms in marine microbial mats
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The future of single‐cell environmental microbiology
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Single‐cell genomics
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The importance of individuals and scale: moving towards single cell microbiology
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Design and testing of ‘genome‐proxy’ microarrays to profile marine microbial communities
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Recent advances in molecular techniques for the detection of phylogenetic markers and functional genes in microbial communities
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Methane-Consuming Archaea Revealed by Directly Coupled Isotopic and Phylogenetic Analysis
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Systems Biology: A Brief Overview
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Environmental Genome Shotgun Sequencing of the Sargasso Sea
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Microbes, Molecules, and Marine Ecosystems
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Comparative Metagenomics of Microbial Communities
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Community Proteomics of a Natural Microbial Biofilm
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Larger Islands House More Bacterial Taxa
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In Situ Stable Isotope Probing of Methanogenic Archaea in the Rice Rhizosphere
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Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior
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Microfluidic Digital PCR Enables Multigene Analysis of Individual Environmental Bacteria
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Emergent Biogeography of Microbial Communities in a Model Ocean
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Signals from chloroplasts converge to regulate nuclear gene expression.
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A Molecular View of Microbial Diversity and the Biosphere
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Bacterial Rhodopsin: Evidence for a New Type of Phototrophy in the Sea
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The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function
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Metagenomics: Application of Genomics to Uncultured Microorganisms
inferredcites →https://doi.org/10.1146/annurev.micro.52.1.81openalex-snapshot
THINKING ABOUT BACTERIAL POPULATIONS AS MULTICELLULAR ORGANISMS
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Biofilm Formation as Microbial Development
inferredcites →https://doi.org/10.1186/1471-2105-6-41openalex-snapshot
PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information
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Prediction of effective genome size in metagenomic samples
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Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters
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Cooperation among Microorganisms
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CAMERA: A Community Resource for Metagenomics
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The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific
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Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes
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Development of the Human Infant Intestinal Microbiota
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SPECIES CO-OCCURRENCE: A META-ANALYSIS OF J. M. DIAMOND'S ASSEMBLY RULES MODEL
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A(r)Ray of Hope in Analysis of the Function and Diversity of Microbial Communities
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Heterogeneity in bacterioplankton abundance from 4.5 millimetre resolution sampling
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Application of Metagenomic Technologies for Antimicrobial Resistance and Food Safety Research and Beyond☆☆CYC and XY contributed equally to this review. The opinions expressed in this review are entirely those of the authors and do not represent those of the USDA.
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Plasticity of the adult human small intestinal stoma microbiota
inferred← citeshttps://doi.org/10.1016/j.copbio.2010.01.012openalex-snapshot
Application of Fourier-transform ion cyclotron resonance mass spectrometry to metabolic profiling and metabolite identification
inferred← citeshttps://doi.org/10.1016/j.copbio.2010.06.007openalex-snapshot
Systems approaches to microbial communities and their functioning
inferred← citeshttps://doi.org/10.1016/j.copbio.2010.08.003openalex-snapshot
Systems biology of the gut: the interplay of food, microbiota and host at the mucosal interface
inferred← citeshttps://doi.org/10.1016/j.copbio.2011.11.025openalex-snapshot
Low-temperature anaerobic digestion for wastewater treatment
inferred← citeshttps://doi.org/10.1016/j.copbio.2013.04.001openalex-snapshot
Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities
inferred← citeshttps://doi.org/10.1016/j.copbio.2015.02.002openalex-snapshot
A methodological framework for linking bioreactor function to microbial communities and environmental conditions
inferred← citeshttps://doi.org/10.1016/j.copbio.2015.03.012openalex-snapshot
Deciphering microbial community robustness through synthetic ecology and molecular systems synecology
inferred← citeshttps://doi.org/10.1016/j.csbj.2020.06.028openalex-snapshot
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes
inferred← citeshttps://doi.org/10.1016/j.csbj.2024.05.047openalex-snapshot
Biotic interactions and environmental modifications determine symbiotic microbial diversity and stability
inferred← citeshttps://doi.org/10.1016/j.ecoenv.2019.109733openalex-snapshot
Evaluating genotoxicity of metal oxide nanoparticles: Application of advanced supervised and unsupervised machine learning techniques
inferred← citeshttps://doi.org/10.1016/j.ecoinf.2012.07.003openalex-snapshot
Poseidon: An information retrieval and extraction system for metagenomic marine science
inferred← citeshttps://doi.org/10.1016/j.ecolind.2024.112532openalex-snapshot
Quantifying the functional genes of C, N, P, and S cycling in a deep lake: Depth patterns and drivers
inferred← citeshttps://doi.org/10.1016/j.ecolmodel.2015.01.024openalex-snapshot
From protein damage to cell aging to population fitness in E. coli: Insights from a multi-level agent-based model
inferred← citeshttps://doi.org/10.1016/j.envpol.2017.08.057openalex-snapshot
Response of soil microbial communities and microbial interactions to long-term heavy metal contamination
inferred← citeshttps://doi.org/10.1016/j.envpol.2018.04.087openalex-snapshot
Responses of microbial tolerance to heavy metals along a century-old metal ore pollution gradient in a subarctic birch forest
inferred← citeshttps://doi.org/10.1016/j.envres.2023.115242openalex-snapshot
Microbial community structure and denitrification responses to cascade low-head dams and their contribution to eutrophication in urban rivers
inferred← citeshttps://doi.org/10.1016/j.envres.2024.120602openalex-snapshot
Functional characteristics and mechanisms of microbial community succession and assembly in a long-term moving bed biofilm reactor treating real municipal wastewater
inferred← citeshttps://doi.org/10.1016/j.fm.2018.11.005openalex-snapshot
The use of next generation sequencing for improving food safety: Translation into practice
inferred← citeshttps://doi.org/10.1016/j.funbio.2010.11.002openalex-snapshot
From pattern to process: species and functional diversity in fungal endophytes of Abies beshanzuensis
inferred← citeshttps://doi.org/10.1016/j.jclepro.2025.146022openalex-snapshot
Potential of ozone-ultraviolet combined technology on mitigating the aquatic risks of receiving river: The significance of dissolved organic matter
inferred← citeshttps://doi.org/10.1016/j.jembe.2024.152047openalex-snapshot
Temporal dynamics of microbial communities in the water of polyculture pond system for Chinese swimming crab Portunus trituberculatus
inferred← citeshttps://doi.org/10.1016/j.jenvman.2021.114380openalex-snapshot
Pollution gradients shape the co-occurrence networks and interactions of sedimentary bacterial communities in Taihu Lake, a shallow eutrophic lake
inferred← citeshttps://doi.org/10.1016/j.jenvman.2024.122339openalex-snapshot
Soil and stone terraces offset the negative impacts of sloping cultivation on soil microbial diversity and functioning by protecting soil carbon
inferred← citeshttps://doi.org/10.1016/j.jes.2024.05.032openalex-snapshot
Phyllosphere microbiome assists the hyperaccumulating plant in resisting heavy metal stress
inferred← citeshttps://doi.org/10.1016/j.jhazmat.2020.122068openalex-snapshot
Interactions of PAH-degradation and nitrate-/sulfate-reducing assemblages in anaerobic sediment microbial community
inferred← citeshttps://doi.org/10.1016/j.jhazmat.2025.138553openalex-snapshot
Metal pollution-induced alterations in soil fungal community structure and functional adaptations across regional scales
inferred← citeshttps://doi.org/10.1016/j.jinsphys.2014.05.016openalex-snapshot
Towards an integrated understanding of gut microbiota using insects as model systems
inferred← citeshttps://doi.org/10.1016/j.jmb.2010.02.005openalex-snapshot
Unfinished Stories on Viral Quasispecies and Darwinian Views of Evolution
inferred← citeshttps://doi.org/10.1016/j.jprot.2011.07.010openalex-snapshot
Green systems biology — From single genomes, proteomes and metabolomes to ecosystems research and biotechnology
inferred← citeshttps://doi.org/10.1016/j.jwpe.2023.103600openalex-snapshot
Achievement and microbial profiles of non-aerated partial nitrification in photo sequencing batch and continuous flow reactors
inferred← citeshttps://doi.org/10.1016/j.jwpe.2024.106841openalex-snapshot
Bio-wax carriers exhibit a competitive edge in developing biofilms under varying shear stresses: Integrating growth models and biological information
inferred← citeshttps://doi.org/10.1016/j.margen.2016.02.003openalex-snapshot
Molecular trophic markers in marine food webs and their potential use for coral ecology
inferred← citeshttps://doi.org/10.1016/j.mib.2014.02.002openalex-snapshot
Synthetic microbial communities
inferred← citeshttps://doi.org/10.1016/j.micres.2015.10.006openalex-snapshot
Bacterial diversity indicates dietary overlap among bats of different feeding habits
inferred← citeshttps://doi.org/10.1016/j.mimet.2016.10.018openalex-snapshot
Methodologies for probing the metatranscriptome of grassland soil
inferred← citeshttps://doi.org/10.1016/j.nbt.2017.07.001openalex-snapshot
The microbiome as engineering tool: Manufacturing and trading between microorganisms
inferred← citeshttps://doi.org/10.1016/j.pedsph.2025.04.001openalex-snapshot
Cropping alfalfa for 18 years increases importance of fungi in multi-kingdom networks in saline-alkali soils
inferred← citeshttps://doi.org/10.1016/j.pisc.2014.02.003openalex-snapshot
Predictive genomic and metabolomic analysis for the standardization of enzyme data
inferred← citeshttps://doi.org/10.1016/j.plantsci.2026.113182openalex-snapshot
Unveiling the plant growth-promoting and antifungal potential of Melissa officinalis endophytes: The integrative culture-dependent and metagenomic approaches
inferred← citeshttps://doi.org/10.1016/j.plaphy.2026.111626openalex-snapshot
Wheat microbiome interactions under climate change: Mechanisms of abiotic stress tolerance and sustainable crop resilience
inferred← citeshttps://doi.org/10.1016/j.plasmid.2013.05.001openalex-snapshot
Indigenous plasmids of Bacillus megaterium WSH-002 involved in mutualism with Ketogulonicigenium vulgare WSH-001
inferred← citeshttps://doi.org/10.1016/j.prevetmed.2010.07.003openalex-snapshot
From “one medicine” to “one health” and systemic approaches to health and well-being
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2016.08.150openalex-snapshot
Network analysis reveals seasonal variation of co-occurrence correlations between Cyanobacteria and other bacterioplankton
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2021.152565openalex-snapshot
Soil microbial co-occurrence networks become less connected with soil development in a high Arctic glacier foreland succession
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2023.162818openalex-snapshot
Effects of combining flow intermittency and exposure to emerging contaminants on the composition and metabolic response of streambed biofilm bacterial communities
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2023.166372openalex-snapshot
Cd contamination determined assembly processes and network stability of AM fungal communities in an urban green space ecosystem
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2024.174322openalex-snapshot
Heavy metals and nutrients mediate the distribution of soil microbial community in a typical contaminated farmland of South China
inferred← citeshttps://doi.org/10.1016/j.soilbio.2012.11.009openalex-snapshot
Soil enzymes in a changing environment: Current knowledge and future directions
inferred← citeshttps://doi.org/10.1016/j.soilbio.2014.07.020openalex-snapshot
Land-use and management practices affect soil ammonia oxidiser community structure, activity and connectedness
inferred← citeshttps://doi.org/10.1016/j.soilbio.2016.01.007openalex-snapshot
Crop rotations alter bacterial and fungal diversity in paddy soils across East Asia
inferred← citeshttps://doi.org/10.1016/j.soilbio.2017.05.004openalex-snapshot
Using community trait-distributions to assign microbial responses to pH changes and Cd in forest soils treated with wood ash
inferred← citeshttps://doi.org/10.1016/j.soilbio.2020.108120openalex-snapshot
Succession of the composition and co-occurrence networks of rhizosphere microbiota is linked to Cd/Zn hyperaccumulation
inferred← citeshttps://doi.org/10.1016/j.soilbio.2025.109909openalex-snapshot
Wetland restoration following agricultural abandonment supports diversity and reduces stochasticity in soil fungal communities due to anaerobic-induced interspecific associations
inferred← citeshttps://doi.org/10.1016/j.still.2025.106605openalex-snapshot
Ecological niche differentiation of detritivores dominates soil mesofaunal community assembly in a 33-year fertilized cropland
inferred← citeshttps://doi.org/10.1016/j.syapm.2012.03.004openalex-snapshot
CLASI-FISH: Principles of combinatorial labeling and spectral imaging
inferred← citeshttps://doi.org/10.1016/j.tig.2012.09.005openalex-snapshot
Biodiversity and functional genomics in the human microbiome
inferred← citeshttps://doi.org/10.1016/j.tim.2009.05.010openalex-snapshot
Infrequent marine–freshwater transitions in the microbial world
inferred← citeshttps://doi.org/10.1016/j.tim.2013.04.009openalex-snapshot
Condensing the omics fog of microbial communities
inferred← citeshttps://doi.org/10.1016/j.tplants.2010.07.004openalex-snapshot
Genomic insights into photosynthesis in eukaryotic phytoplankton
inferred← citeshttps://doi.org/10.1016/j.watres.2019.115307openalex-snapshot
Large-sized planktonic bioaggregates possess high biofilm formation potentials: Bacterial succession and assembly in the biofilm metacommunity
inferred← citeshttps://doi.org/10.1016/j.watres.2023.120403openalex-snapshot
Antibiotic resistome associated with inhalable bioaerosols from wastewater to atmosphere: Mobility, bacterial hosts, source contributions and resistome risk
inferred← citeshttps://doi.org/10.1016/s0065-2164(10)70005-8openalex-snapshot
Shining Light on the Microbial World
inferred← citeshttps://doi.org/10.1017/cbo9780511675751.015openalex-snapshot
From genes to ecosystems
inferred← citeshttps://doi.org/10.1017/s0007114511006970openalex-snapshot
New insights into the impact of the intestinal microbiota on health and disease: a symposium report
inferred← citeshttps://doi.org/10.1017/s1751731110002120openalex-snapshot
The integration of ‘omic’ disciplines and systems biology in cattle breeding
inferred← citeshttps://doi.org/10.1017/s1751731112000419openalex-snapshot
Rumen microbial (meta)genomics and its application to ruminant production
inferred← citeshttps://doi.org/10.1021/acs.est.0c07891openalex-snapshot
Overlooked Ecological Roles of Influent Wastewater Microflora in Improving Biological Phosphorus Removal in an Anoxic/Aerobic MBR Process
inferred← citeshttps://doi.org/10.1021/acs.est.4c07901openalex-snapshot
Recycled Phosphorus Bioamendments from Wastewater Impact Rhizomicrobiome and Benefit Crop Growth: Sustainability Implications at Water-Food Nexus
inferred← citeshttps://doi.org/10.1021/cr100311qopenalex-snapshot
Chemical Challenges to Bacterial AHL Signaling in the Environment
inferred← citeshttps://doi.org/10.1021/es803616kopenalex-snapshot
Microbial Architecture of Environmental Sulfur Processes: A Novel Syntrophic Sulfur-Metabolizing Consortia
inferred← citeshttps://doi.org/10.1021/pr100989copenalex-snapshot
Dynamic Omics Approach Identifies Nutrition-Mediated Microbial Interactions
inferred← citeshttps://doi.org/10.1038/ismej.2011.212openalex-snapshot
The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates
inferred← citeshttps://doi.org/10.1038/ismej.2011.78openalex-snapshot
De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities
inferred← citeshttps://doi.org/10.1038/ismej.2012.72openalex-snapshot
A biomolecular isolation framework for eco-systems biology
inferred← citeshttps://doi.org/10.1038/ismej.2012.85openalex-snapshot
Taming the smallest predators of the oceans
inferred← citeshttps://doi.org/10.1038/ismej.2014.64openalex-snapshot
Reprograming of gut microbiome energy metabolism by the FUT2 Crohn’s disease risk polymorphism
inferred← citeshttps://doi.org/10.1038/ismej.2015.66openalex-snapshot
Metagenomic and lipid analyses reveal a diel cycle in a hypersaline microbial ecosystem
inferred← citeshttps://doi.org/10.1038/msb.2010.30openalex-snapshot
Ecological distribution and population physiology defined by proteomics in a natural microbial community
inferred← citeshttps://doi.org/10.1038/msb.2011.6openalex-snapshot
Toward molecular trait‐based ecology through integration of biogeochemical, geographical and metagenomic data
inferred← citeshttps://doi.org/10.1038/nature09944openalex-snapshot
Enterotypes of the human gut microbiome
inferred← citeshttps://doi.org/10.1038/nature10386openalex-snapshot
Persistence of soil organic matter as an ecosystem property
inferred← citeshttps://doi.org/10.1038/nbt.2939openalex-snapshot
Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
inferred← citeshttps://doi.org/10.1038/nbt.3960openalex-snapshot
Towards standards for human fecal sample processing in metagenomic studies
inferred← citeshttps://doi.org/10.1038/ncomms2203openalex-snapshot
Virtual metagenome reconstruction from 16S rRNA gene sequences
inferred← citeshttps://doi.org/10.1038/nrmicro2107openalex-snapshot
The role of predictive modelling in rationally re-engineering biological systems
inferred← citeshttps://doi.org/10.1038/nrmicro2119-c2openalex-snapshot
To sequence or not to sequence the whole-soil metagenome?
inferred← citeshttps://doi.org/10.1038/nrmicro2167openalex-snapshot
Unravelling ancient microbial history with community proteogenomics and lipid geochemistry
inferred← citeshttps://doi.org/10.1038/nrmicro2778openalex-snapshot
Microbial ecology of expanding oxygen minimum zones
inferred← citeshttps://doi.org/10.1038/nrmicro2832openalex-snapshot
Microbial interactions: from networks to models
inferred← citeshttps://doi.org/10.1038/s41396-019-0427-7openalex-snapshot
Resource heterogeneity structures aquatic bacterial communities
inferred← citeshttps://doi.org/10.1038/s41559-020-1099-4openalex-snapshot
Strength of species interactions determines biodiversity and stability in microbial communities
inferred← citeshttps://doi.org/10.1038/s41579-020-0364-5openalex-snapshot
Tara Oceans: towards global ocean ecosystems biology
inferred← citeshttps://doi.org/10.1038/s41598-018-27172-zopenalex-snapshot
Heterogeneity of interactions of microbial communities in regions of Taihu Lake with different nutrient loadings: A network analysis
inferred← citeshttps://doi.org/10.1038/s41598-023-36221-1openalex-snapshot
Eco-evolutionary dynamics in microbial interactions
inferred← citeshttps://doi.org/10.1038/s41598-023-41401-0openalex-snapshot
Pedogenesis of typical zonal soil drives belowground bacterial communities of arable land in the Northeast China Plain
inferred← citeshttps://doi.org/10.1038/s41598-025-05106-wopenalex-snapshot
Environmental DNA analysis at multiple taxonomic levels highlights geographic variation in subtropical coastal marine communities
inferred← citeshttps://doi.org/10.1038/s42003-020-01159-xopenalex-snapshot
Biohydrogen production beyond the Thauer limit by precision design of artificial microbial consortia
inferred← citeshttps://doi.org/10.1038/s44185-024-00063-5openalex-snapshot
pH Adaptation stabilizes bacterial communities
inferred← citeshttps://doi.org/10.1038/srep10007openalex-snapshot
Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession
inferred← citeshttps://doi.org/10.1038/srep14266openalex-snapshot
An integrated insight into the response of sedimentary microbial communities to heavy metal contamination
inferred← citeshttps://doi.org/10.1038/srep14345openalex-snapshot
Planting increases the abundance and structure complexity of soil core functional genes relevant to carbon and nitrogen cycling
inferred← citeshttps://doi.org/10.1038/srep33350openalex-snapshot
Effects of captivity and artificial breeding on microbiota in feces of the red-crowned crane (Grus japonensis)
inferred← citeshttps://doi.org/10.1039/b913876popenalex-snapshot
Meta-analysis of genome regulation and expression variability across hundreds of environmental and genetic perturbations in fission yeast
inferred← citeshttps://doi.org/10.1039/c2mb25133gopenalex-snapshot
Engineering ecosystems and synthetic ecologies
inferred← citeshttps://doi.org/10.1053/j.gastro.2009.02.075openalex-snapshot
Patterns and Scales in Gastrointestinal Microbial Ecology
inferred← citeshttps://doi.org/10.1073/pnas.1101134108openalex-snapshot
Systems-level analysis of microbial community organization through combinatorial labeling and spectral imaging
inferred← citeshttps://doi.org/10.1073/pnas.1116053109openalex-snapshot
Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
inferred← citeshttps://doi.org/10.1080/10408398.2014.983591openalex-snapshot
Wine microbiome: A dynamic world of microbial interactions
inferred← citeshttps://doi.org/10.1080/10408398.2018.1512471openalex-snapshot
Cheesomics: the future pathway to understanding cheese flavour and quality
inferred← citeshttps://doi.org/10.1080/1040841x.2016.1208146openalex-snapshot
Critical review on biofilm methods
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