ArticleFrontiers in microbiology2014
Demonstrating microbial co-occurrence pattern analyses within and between ecosystems.
Article in Frontiers in microbiology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 131 papers, 1 of them a synthesis that pooled it.
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Who cites it
131 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Testing for Consistency in Co-occurrence Patterns Among Bacterial Taxa Across the Microbiomes of Four Different Trematode Parasites.Microbial ecology · 2025Article
- Integrating network analysis with in vivo-in situ manipulation to elucidate microbiome dynamics in Aedes albopictus.FEMS microbiology letters · 2025Article
- Exploring the Diversity and Ecological Dynamics of Palm Leaf Spotting Fungi-A Case Study on Ornamental Palms in Portugal.Journal of fungi (Basel, Switzerland) · 2025Article
- Characteristics of gut microbiota inFrontiers in microbiology · 2025Article
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- Root zone microbial communities ofFrontiers in microbiology · 2025Article
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- Link between gut microbiota dysbiosis and childhood asthma: Insights from a systematic review.The journal of allergy and clinical immunology. Global · 2024Review
- Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology.Heliyon · 2024Review
- Seasonal dynamics of intestinal microbiota in juvenile Chinese mitten crab (Frontiers in cellular and infection microbiology · 2024Article
- Water masses influence the variation of microbial communities in the Yangtze River Estuary and its adjacent waters.Frontiers in microbiology · 2024Article
71 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Co-occurrence patterns are used in ecology to explore interactions between organisms and environmental effects on coexistence within biological communities. Analysis of co-occurrence patterns among microbial communities has ranged from simple pairwise comparisons between all community members to direct hypothesis testing between focal species. However, co-occurrence patterns are rarely studied across multiple ecosystems or multiple scales of biological organization within the same study. Here we outline an approach to produce co-occurrence analyses that are focused at three different scales: co-occurrence patterns between ecosystems at the community scale, modules of co-occurring microorganisms within communities, and co-occurring pairs within modules that are nested within microbial communities. To demonstrate our co-occurrence analysis approach, we gathered publicly available 16S rRNA amplicon datasets to compare and contrast microbial co-occurrence at different taxonomic levels across different ecosystems. We found differences in community composition and co-occurrence that reflect environmental filtering at the community scale and consistent pairwise occurrences that may be used to infer ecological traits about poorly understood microbial taxa. However, we also found that conclusions derived from applying network statistics to microbial relationships can vary depending on the taxonomic level chosen and criteria used to build co-occurrence networks. We present our statistical analysis and code for public use in analysis of co-occurrence patterns across microbial communities.
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