ReviewThe ISME journal2024
Leveraging genomic information to predict environmental preferences of bacteria.
Review in The ISME journal, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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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.
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Who cites it
16 citing papers in PubMed.
- Genome-based predictions of metabolic preferences and substrate phenotypes in psychrotrophic bacteria from permafrost environments.Microbiology spectrum · 2026Article
- Article
- Catabolic Mechanism of 17β-Estradiol inJournal of microbiology and biotechnology · 2026Article
- Genomic traits associated with copiotrophy decouple from maximum growth rate predictions along temperature gradients.The ISME journal · 2026Article
- Constructing a "periodic table" of bacteria to map diversity in trait space.The ISME journal · 2026Article
- Genomic insights into adaptative traits of phyllosphere yeasts.Environmental microbiome · 2026Article
- A genomic view of Earth's biomes.Nature reviews. Genetics · 2026Review
- Fit for purpose: evaluation and evolution of agricultural bioinoculants across production landscapes.ISME communications · 2026Review
- National-scale biogeography and function of river and stream bacterial biofilm communities.Nature communications · 2025Article
- Comparative Analysis of Sponge-Associated, Seawater, and Sediment Microbial Communities from Site F Cold Seep in the South China Sea.Microorganisms · 2025Article
- Integrating Intermediate Traits in Phylogenetic Genotype-to-Phenotype Studies.Integrative and comparative biology · 2025Review
- Biodegradation of synthetic organic pollutants: principles, progress, problems, and perspectives.FEMS microbiology reviews · 2025Review
- Biodegradation of synthetic organic pollutants: principles, progress, problems, and perspectives.FEMS microbiology reviews · 2025Review
- Biodegradation of synthetic organic pollutants: principles, progress, problems, and perspectives.FEMS microbiology reviews · 2025Review
- Polyphasic taxonomy and genome mining ofCurrent research in microbial sciences · 2025Article
- Essential nucleic acid omics: a theoretical foundation for early-stage users.Frontiers in bioinformatics · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
Abstract
Genomic information is now available for a broad diversity of bacteria, including uncultivated taxa. However, we have corresponding knowledge on environmental preferences (i.e. bacterial growth responses across gradients in oxygen, pH, temperature, salinity, and other environmental conditions) for a relatively narrow swath of bacterial diversity. These limits to our understanding of bacterial ecologies constrain our ability to predict how assemblages will shift in response to global change factors, design effective probiotics, or guide cultivation efforts. We need innovative approaches that take advantage of expanding genome databases to accurately infer the environmental preferences of bacteria and validate the accuracy of these inferences. By doing so, we can broaden our quantitative understanding of the environmental preferences of the majority of bacterial taxa that remain uncharacterized. With this perspective, we highlight why it is important to infer environmental preferences from genomic information and discuss the range of potential strategies for doing so. In particular, we highlight concrete examples of how both cultivation-independent and cultivation-dependent approaches can be integrated with genomic data to develop predictive models. We also emphasize the limitations and pitfalls of these approaches and the specific knowledge gaps that need to be addressed to successfully expand our understanding of the environmental preferences of bacteria.
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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.