ArticleNature communications2014
Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage.
Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multi-omics time-series analysis in microbiome research: a systematic review.Briefings in bioinformatics · 2025Pooled it
- Forecasting the dynamics of a complex microbial community using integrated meta-omics.Nature ecology & evolution · 2024Article
- High speciation rate of niche specialists in hot springs.The ISME journal · 2023Article
- Revealing the role of microalgae-bacteria niche for boosting wastewater treatment and energy reclamation in response to temperature.Environmental science and ecotechnology · 2023Article
- MetaProD: A Highly-Configurable Mass Spectrometry Analyzer for Multiplexed Proteomic and Metaproteomic Data.Journal of proteome research · 2023Article
- Low-energy adsorptive separation by zeolites.National science review · 2022Review
- Undervalued Pseudo-mSphere · 2021Article
- Influence of Extraction Solvent on Nontargeted Metabolomics Analysis of Enrichment Reactor Cultures Performing Enhanced Biological Phosphorus Removal (EBPR).Metabolites · 2021Article
- A multi-omic screening approach for the discovery of thermoactive glycoside hydrolases.Extremophiles : life under extreme conditions · 2021Article
- Low Global Diversity ofFrontiers in microbiology · 2021Article
- Challenges, Strategies, and Perspectives for Reference-Independent Longitudinal Multi-Omic Microbiome Studies.Frontiers in genetics · 2021Article
- Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics.Nature microbiology · 2021Article
- Integration of time-series meta-omics data reveals how microbial ecosystems respond to disturbance.Nature communications · 2020Article
- The role of probiotics on the roadmap to a healthy microbiota: a symposium report.Gut microbiome (Cambridge, England) · 2020Review
- A Meta-proteogenomic Approach to Peptide Identification Incorporating Assembly Uncertainty and Genomic Variation.Molecular & cellular proteomics : MCP · 2019Article
- Determining Microbial Niche Breadth in the Environment for Better Ecosystem Fate Predictions.mSystems · 2019Article
- An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community.Microbiome · 2019Article
- Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities UsingFrontiers in microbiology · 2019Article
- The Gut Microbiota and Hematopoietic Stem Cell Transplantation: Challenges and Potentials.Journal of innate immunity · 2019Review
- ProteoStorm: An Ultrafast Metaproteomics Database Search Framework.Cell systems · 2018Article
Corrections and comments
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Authors and funding
22 authors.
Funding
Abstract
Microbial communities are complex and dynamic systems that are primarily structured according to their members' ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.