ArticleNPJ biofilms and microbiomes2015
Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks.
Article in NPJ biofilms and microbiomes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Metagenomic insight into the diversity and biogeochemical functions of microbial communities in the maar tropical Lake Atexcac.Microbiology (Reading, England) · 2026Article
- Keystone concept revisited: insights into microbial community dynamics and control.Nature reviews. Microbiology · 2026Review
- Unknown Germany - An integrative biodiversity discovery program.npj biodiversity · 2025Review
- Integrated multi-omics highlights alterations of gut microbiome functions in prodromal and idiopathic Parkinson's disease.Microbiome · 2025Article
- Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson's disease.NPJ biofilms and microbiomes · 2025Article
- The Impact of the Skin Microbiome and Oxidative Stress on the Initiation and Development of Cutaneous Chronic Wounds.Antioxidants (Basel, Switzerland) · 2025Review
- Integrated metabolomics and metagenomics reveal plant-microbe interactions driving aroma differentiation in flue-cured tobacco leaves.Frontiers in plant science · 2025Article
- Diversity and interdomain networks of bacterial, pico-protist and nano-protist communities in a marine ranching.Frontiers in microbiology · 2025Article
- Flux sampling in genome-scale metabolic modeling of microbial communities.BMC bioinformatics · 2024Article
- Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling.Microbiome research reports · 2024Article
- Forecasting the dynamics of a complex microbial community using integrated meta-omics.Nature ecology & evolution · 2024Article
- Flux Sampling in Genome-scale Metabolic Modeling of Microbial Communities.bioRxiv : the preprint server for biology · 2023Article
- Regulatory Small RNAs for a Sustained Eco-Agriculture.International journal of molecular sciences · 2023Review
- Visualizing the next frontiers in wine yeast research.FEMS yeast research · 2022Article
- A Survey of Statistical Methods for Microbiome Data Analysis.Frontiers in applied mathematics and statistics · 2022Article
- Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics.ISME communications · 2021Article
- Multi-Omics Study of Keystone Species in a Cystic Fibrosis Microbiome.International journal of molecular sciences · 2021Article
- NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data.Microorganisms · 2021Article
- Mechanistic models of microbial community metabolism.Molecular omics · 2021Review
- Network analyses in microbiome based on high-throughput multi-omics data.Briefings in bioinformatics · 2021Review
Corrections and comments
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Authors and funding
17 authors.
Funding
Abstract
backgroundMixed microbial communities underpin important biotechnological processes such as biological wastewater treatment (BWWT). A detailed knowledge of community structure and function relationships is essential for ultimately driving these systems towards desired outcomes, e.g., the enrichment in organisms capable of accumulating valuable resources during BWWT.
methodsA comparative integrated omic analysis including metagenomics, metatranscriptomics and metaproteomics was carried out to elucidate functional differences between seasonally distinct oleaginous mixed microbial communities (OMMCs) sampled from an anoxic BWWT tank. A computational framework for the reconstruction of community-wide metabolic networks from multi-omic data was developed. These provide an overview of the functional capabilities by incorporating gene copy, transcript and protein abundances. To identify functional genes, which have a disproportionately important role in community function, we define a high relative gene expression and a high betweenness centrality relative to node degree as gene-centric and network topological features, respectively.
resultsGenes exhibiting high expression relative to gene copy abundance include genes involved in glycerolipid metabolism, particularly triacylglycerol lipase, encoded by known lipid accumulating populations, e.g.,
conclusionThe linking of key functionalities to community members through integrated omics opens up exciting possibilities for devising prediction and control strategies for microbial communities in the future.
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