ArticleScientific reports2022
Higher-order interactions shape microbial interactions as microbial community complexity increases.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
22 citing papers in PubMed.
- Specificity and longevity of a bacterial interspecies mutual cooperation benefiting organic micropollutant biodegradation.Applied and environmental microbiology · 2026Article
- Diverse Microbial Communities Assemble on Both Recalcitrant and Labile Carbon Sources.Environmental microbiology · 2026Article
- Higher-Order Interactions Can Promote Coexistence by Rewiring Intransitivities Into Competitive Networks.Ecology letters · 2026Article
- Article
- Subinhibitory concentrations of antibiotics mediate primary metabolism and shape diverse species interactions among coevolved soil Streptomyces.The ISME journal · 2026Article
- Transitive interactions among rhizobia determine their symbiotic fitness.ISME communications · 2026Article
- Community state shifts driven by total carbon availability over resource complexity in a synthetic microbial community.ISME communications · 2026Article
- Statistical design of a synthetic microbiome that suppresses diverse gut pathogens.bioRxiv : the preprint server for biology · 2025Article
- Cobamide-based interactions between soil bacteria can be predicted based on monoculture growth.bioRxiv : the preprint server for biology · 2025Article
- Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Microbial community interactions on a chip.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation.Signal transduction and targeted therapy · 2024Review
- Metabolic interdependencies in thermophilic communities are revealed using co-occurrence and complementarity networks.Nature communications · 2024Article
- Higher-order interactions and emergent properties of microbial communities: The power of synthetic ecology.Heliyon · 2024Review
- High-throughput sequencing-based analysis of the composition and diversity of the endophytic bacterial community in the roots of3 Biotech · 2024Article
- Phage resistance mutations affecting the bacterial cell surface increase susceptibility to fungi in a model cheese community.ISME communications · 2024Article
- Predicting bacterial interaction outcomes from monoculture growth and supernatant assays.ISME communications · 2024Article
- Competition for shared resources increases dependence on initial population size during coalescence of gut microbial communities.bioRxiv : the preprint server for biology · 2023Article
- Mutualism reduces the severity of gene disruptions in predictable ways across microbial communities.The ISME journal · 2023Article
- Sparsity of higher-order landscape interactions enables learning and prediction for microbiomes.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Non-pairwise interactions, or higher-order interactions (HOIs), in microbial communities have been described as significant drivers of emergent features in microbiomes. Yet, the re-organization of microbial interactions between pairwise cultures and larger communities remains largely unexplored from a molecular perspective but is central to our understanding and further manipulation of microbial communities. Here, we used a bottom-up approach to investigate microbial interaction mechanisms from pairwise cultures up to 4-species communities from a simple microbiome (Hafnia alvei, Geotrichum candidum, Pencillium camemberti and Escherichia coli). Specifically, we characterized the interaction landscape for each species combination involving E. coli by identifying E. coli's interaction-associated mutants using an RB-TnSeq-based interaction assay. We observed a deep reorganization of the interaction-associated mutants, with very few 2-species interactions conserved all the way up to a 4-species community and the emergence of multiple HOIs. We further used a quantitative genetics strategy to decipher how 2-species interactions were quantitatively conserved in higher community compositions. Epistasis-based analysis revealed that, of the interactions that are conserved at all levels of complexity, 82% follow an additive pattern. Altogether, we demonstrate the complex architecture of microbial interactions even within a simple microbiome, and provide a mechanistic and molecular explanation of HOIs.
Indexed as
Identifiers
What OpenQuestion holds
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.