ArticleBMC bioinformatics2016
MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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33 citing papers in PubMed.
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- BSocial Tool Deciphers Highly Functional Plant Growth-Promoting Bacterial Consortia.Microbial biotechnology · 2025Article
- A survey of computational approaches for characterizing microbial interactions in microbial mats.Genome biology · 2025Review
- Exploring interspecific interaction variability in microbiota: A review.Engineering microbiology · 2024Review
- The MTIST platform: a microbiome time series inference standardized test.Research square · 2024Article
- Formation of a constructed microbial community in a nutrient-rich environment indicates bacterial interspecific competition.mSystems · 2024Article
- Methodological Considerations in Longitudinal Analyses of Microbiome Data: A Comprehensive Review.Genes · 2023Review
- Microbiome distribution modeling using gradient descent strategies for mock, in vitro and clinical community distributions.PloS one · 2023Article
- Article
- ARZIMM: A Novel Analytic Platform for the Inference of Microbial Interactions and Community Stability from Longitudinal Microbiome Study.Frontiers in genetics · 2022Article
- Modeling Microbial Community Networks: Methods and Tools.Current genomics · 2021Review
- Shrimp AHPND Causing Vibrio anguillarum Infection: Quantitative Diagnosis and Identifying Antagonistic Bacteria.Marine biotechnology (New York, N.Y.) · 2021Article
- Diversity and Interactomics of Bacterial Communities Associated with Dominant Trees During Tropical Forest Recovery.Current microbiology · 2021Article
- The Interplay between Campylobacter and the Caecal Microbial Community of Commercial Broiler Chickens over Time.Microorganisms · 2021Article
- Exploring the Microbiome Analysis and Visualization Landscape.Frontiers in bioinformatics · 2021Review
- A network-based approach to deciphering a dynamic microbiome's response to a subtle perturbation.Scientific reports · 2020Article
- Article
- A network approach to investigating the key microbes and stability of gut microbial communities in a mouse neuropathic pain model.BMC microbiology · 2020Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe complexity and dynamics of microbial communities are major factors in the ecology of a system. With the NGS technique, metagenomics data provides a new way to explore microbial interactions. Lotka-Volterra models, which have been widely used to infer animal interactions in dynamic systems, have recently been applied to the analysis of metagenomic data.
resultsIn this paper, we present the Lotka-Volterra model based tool, the Metagenomic Microbial Interacticon Simulator (MetaMIS), which is designed to analyze the time series data of microbial community profiles. MetaMIS first infers underlying microbial interactions from abundance tables for operational taxonomic units (OTUs) and then interprets interaction networks using the Lotka-Volterra model. We also embed a Bray-Curtis dissimilarity method in MetaMIS in order to evaluate the similarity to biological reality. MetaMIS is designed to tolerate a high level of missing data, and can estimate interaction information without the influence of rare microbes. For each interaction network, MetaMIS systematically examines interaction patterns (such as mutualism or competition) and refines the biotic role within microbes. As a case study, we collect a human male fecal microbiome and show that Micrococcaceae, a relatively low abundance OTU, is highly connected with 13 dominant OTUs and seems to play a critical role. MetaMIS is able to organize multiple interaction networks into a consensus network for comparative studies; thus we as a case study have also identified a consensus interaction network between female and male fecal microbiomes.
conclusionsMetaMIS provides an efficient and user-friendly platform that may reveal new insights into metagenomics data. MetaMIS is freely available at: https://sourceforge.net/projects/metamis/ .
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