ArticleGenomics, proteomics & bioinformatics2019
How Microbes Shape Their Communities? A Microbial Community Model Based on Functional Genes.
Article in Genomics, proteomics & bioinformatics, 2019. 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, 33 citations in OpenAlex.
- Global Meta-analysis of Airborne Bacterial Communities and Associations with Anthropogenic Activities.Environmental science & technology · 2022Pooled it
- The mycobiome in human cancer: analytical challenges, molecular mechanisms, and therapeutic implications.Molecular cancer · 2025Review
- Hidden Places for Foodborne Bacterial Pathogens and Novel Approaches to Control Biofilms in the Meat Industry.Foods (Basel, Switzerland) · 2024Review
- Exploring and exploiting the rice phytobiome to tackle climate change challenges.Plant communications · 2024Review
- Continuous cropping of Patchouli alters soil physiochemical properties and rhizosphere microecology revealed by metagenomic sequencing.Frontiers in microbiology · 2024Article
- Evolutionary patterns of archaea predominant in acidic environment.Environmental microbiome · 2023Article
- Machine learning and deep learning applications in microbiome research.ISME communications · 2022Review
- Dietary Goji Shapes the Gut Microbiota to Prevent the Liver Injury Induced by Acute Alcohol Intake.Frontiers in nutrition · 2022Article
- Persistence of functional microbiota composition across generations.Scientific reports · 2021Article
- Interactions betweenCurrent opinion in physiology · 2021Article
- A practical guide to amplicon and metagenomic analysis of microbiome data.Protein & cell · 2021Review
- Predicting Microbiome Function Across Space Is Confounded by Strain-Level Differences and Functional Redundancy Across Taxa.Frontiers in microbiology · 2020Article
- The Fast Track for Microbiome Research.Genomics, proteomics & bioinformatics · 2019Article
Corrections and comments
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Authors and funding
7 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Exploring the mechanisms of maintaining microbial community structure is important to understand biofilm development or microbiota dysbiosis. In this paper, we propose a functional gene-based composition prediction (FCP) model to predict the population structure composition within a microbial community. The model predicts the community composition well in both a low-complexity community as acid mine drainage (AMD) microbiota, and a complex community as human gut microbiota. Furthermore, we define community structure shaping (CSS) genes as functional genes crucial for shaping the microbial community. We have identified CSS genes in AMD and human gut microbiota samples with FCP model and find that CSS genes change with the conditions. Compared to essential genes for microbes, CSS genes are significantly enriched in the genes involved in mobile genetic elements, cell motility, and defense mechanisms, indicating that the functions of CSS genes are focused on communication and strategies in response to the environment factors. We further find that it is the minority, rather than the majority, which contributes to maintaining community structure. Compared to health control samples, we find that some functional genes associated with metabolism of amino acids, nucleotides, and lipopolysaccharide are more likely to be CSS genes in the disease group. CSS genes may help us to understand critical cellular processes and be useful in seeking addable gene circuitries to maintain artificial self-sustainable communities. Our study suggests that functional genes are important to the assembly 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.