ArticleISME communications2024
Quantifying microbial guilds.
Article in ISME communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pooled it
- Nicotinamide modulates gut microbial metabolic potential and accelerates recovery in mild-to-moderate COVID-19.Nature metabolism · 2025Trial
- Microbiome varies by body site in the yellow mud turtle,Microbiology spectrum · 2026Article
- The island biology of the host microbiome.Trends in microbiology · 2026Review
- Defining metabolic niches for marine microbial heterotrophs.Science advances · 2026Article
- Gut dysbiosis in oncology: a risk factor for immunoresistance.Cell research · 2026Review
- Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities.The ISME journal · 2026Article
- Xenometabolomics reveals metabolic functional guilds unique to specific inulin subtypes in human gut microbiota cultures.mSystems · 2025Article
- Article
- Metagenomic analysis of heavy water-adapted bacterial communities.Microbial genomics · 2025Article
- Microbial functional guilds respond cohesively to rapidly fluctuating environments.bioRxiv : the preprint server for biology · 2025Article
- Timescale of environmental change modulates metabolic guild cohesion in microbial communities.The ISME journal · 2025Article
- Picoplankton nitrogen guilds in the tropical and subtropical oceans: From the surface to the deep.PloS one · 2025Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The ecological role of microorganisms is of utmost importance due to their multiple interactions with the environment. However, assessing the contribution of individual taxonomic groups has proven difficult despite the availability of high throughput data, hindering our understanding of such complex systems. Here, we propose a quantitative definition of guild that is readily applicable to metagenomic data. Our framework focuses on the functional character of protein sequences, as well as their diversifying nature. First, we discriminate functional sequences from the whole sequence space corresponding to a gene annotation to then quantify their contribution to the guild composition across environments. In addition, we identify and distinguish functional implementations, which are sequence spaces that have different ways of carrying out the function. In contrast, we found that orthology delineation did not consistently align with ecologically (or functionally) distinct implementations of the function. We demonstrate the value of our approach with two case studies: the ammonia oxidation and polyamine uptake guilds from the Malaspina circumnavigation cruise, revealing novel ecological dynamics of the latter in marine ecosystems. Thus, the quantification of guilds helps us to assess the functional role of different taxonomic groups with profound implications on the study of microbial communities.
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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.