Biology subjects

Oduwole, I.

Publications and source records attributed to Oduwole, I..

2 recordsLinked to original sources

bioRxiv2025

Functional genomic signatures predict microbial culturability across the tree of life

Most microbial taxa on Earth remain uncultivated, limiting our ability to study their physiology, ecology, and roles in environmental processes. Although metagenome-assembled genomes (MAGs) have expanded access to uncultured phylogenetic diversity, the functional basis for culturability remains poorly understood. Here, we analyze the 52,515 MAGs from the Genomes from Earths Microbiomes (GEM) catalog to test two hypotheses: 1) genomes from uncultured microbes encode more functionally novel genes than those from cultured taxa, and 2) specific genomic features are systematically associated with culturability across phyla. To assess functional novelty, we aligned predicted proteins to SwissProt and measured sequence dissimilarity to the nearest curated homolog. We find that uncultured MAGs, particularly among Archaea, harbor substantially more divergent proteins. To identify genomic traits predictive of culturability, we combined pathway-level enrichment with LASSO regression and permutation-based feature importance. Cultured MAGs were consistently enriched in Clusters of Orthologous Groups (COG) pathways related to vitamin and cofactor biosynthesis (e.g., thiamine, folate, B12), energy metabolism (e.g., TCA cycle), and CRISPR-Cas systems--functions often depleted in uncultured counterparts. LASSO models identified a subset of these pathways as strong predictors of cultured status even in poorly sampled phyla, suggesting conserved genomic signatures of culturability. In contrast, pathways such as purine biosynthesis and NADH dehydrogenase were associated with uncultured lineages, highlighting potential barriers to cultivation. These results 1) demonstrate the great functional novelty of uncultured microbes, potentially offering unprecedented opportunities for discoveries of novel function, and 2) identify metabolic traits associated with culturability to inform future cultivation strategies. ImportanceThe vast majority of microbes are uncultured, which means they have never been characterized under laboratory conditions. We showed that genomic sequences of uncultured microbes have less similarity to characterized proteins compared to cultured microbes, revealing that there may be fundamental biological reasons why they are not cultured. We also showed that certain metabolic pathways, such as those related to vitamin and cofactor biosynthesis, can predict the ability of microbes to grow under laboratory conditions, and these pathways are abundant in highly cultured phyla, indicating how metabolic pathways can influence cultivation strategies.

microbiology↗

bioRxiv2025

Thermophilic traits correlate with slow growth in permafrost soils

Permafrost soil is characterized by prolonged freezing conditions. Thermophilic microbes have been discovered in various permanently cold environments, including permafrost, where they can persist for extended periods. The reason for this apparent mismatch between microbial adaptations and environmental conditions is unclear. Here, we test the hypothesis that thermophilic traits provide selective advantage to extremely slow-growing microbes, even in cold temperatures. We used a computational approach to predict optimal growth rates and several measures of thermophilicity in metagenome-assembled genomes (MAGs) from permafrost and active layer soils in diverse cold regions. We find that in permafrost, where available energy is always low, measures of thermophilicity correlate positively with minimum doubling time, indicating that slow growers in permafrost have more thermophilic traits. This trend is reversed in microbes in active layer soil, in which seasonal thawing, temperature changes, and episodic rain events allow periodic fast growth. Similar trends were observed in the relationship between optimal growth rates and the optimal temperature of nucleoside diphosphate kinase (NDPK), an enzyme whose temperature optimum is known to be correlated to optimal growth temperatures of the host organism. Thermophilic traits within slow growers appear to be environmentally rather than phylogenetically constrained, and thermophilic slow growers share few horizontal gene transfers with other permafrost microbes. These findings suggest that the presence of thermophilic traits in slow-growers appears to be an adaptation to extreme slow growth in a persistently low-energy environment. ImportancePermanently cold environments, including permafrost soils, contain an active microbial community, which appears to include thermophilic, or heat-loving, microorganisms. This appears to be a paradox - how (and why) do microbes adapted to high temperatures live in permanently cold environments? We provide a potential answer: that the well-understood adaptations which allow microorganisms to survive high temperatures are similar to the poorly understood adaptations that allow microbes to persist over long timescales in very low-energy environments, including permafrost and the Earths deep subsurface. The latter environments represent 88% of the all biomass of bacteria and archaea on Earth, but the adaptations of deep subsurface microorganisms are poorly understood. This work is a step towards understanding how microorganisms persist in two different, challenging environments.

microbiology↗