Published in mSystems

Mutagenic processes drive evolutionary progress, with ultraviolet (UV) radiation significantly affec

Ruminants play an important part in global food security, but also emit methane which contributes to

Differential culturable bacteria grow in liquid culture medium but are unable to form colonies on so

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 Earth’s 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.

Municipal wastewater treatment plants (WWTPs) are recognized as the significant source of fungal aerosols, which pose a significant threat to human health globally. Herein, the occurrences characterization, community structure, and health risk assessment of airborne fungi were investigated from a semiunderground WWTP. The concentrations of culturable fungi emitted into the air from the WWTP ranged from 30.6 to 1431.1 colony forming units (CFU)/m3, with primary and biochemical treatments constituting the principal sources of emission (P < 0.05). Diversity analysis revealed seasonal and facility-dependent fluctuations in culturable fungal communities. Approximately 13.5% of the total airborne fungal genera detected in the WWTP were culturable. Some airborne fungi in the WWTP with relatively low abundance but high cultivability, such as Cladosporium, Trichoderma, Neurospora, Filobasidium, and Hannaella, tended to be overlooked because of their limited presence in airborne environments. We also developed a health risk assessment method for fungi, utilizing seven indicators to characterize the risk posed by fungal pathogens from multiple perspectives, providing a comprehensive evaluation of potential health impacts. The simulated risk values of the air outlet and biochemical treatment exceeded those of other treatment facilities, with median risks of 2.2 × 102 and 1.4 × 102, respectively. Consequently, management strategies should prioritize enhanced controls for fungal aerosols to mitigate the risk of disease transmission.

Campylobacter is the leading bacterial cause of foodborne illness in the United States with chicken as the primary source of infections. It can enter …

Mutagenic processes drive evolutionary progress, with ultraviolet (UV) radiation significantly affec

Ruminants play an important part in global food security, but also emit methane which contributes to

Differential culturable bacteria grow in liquid culture medium but are unable to form colonies on so

The phylum Atribacterota is ubiquitous in anoxic environments where it plays important roles in syntrophic carbon and hydrogen metabolism; however, only two species have been isolated. Here, we report...

Author Summary The relative importance of direct and indirect contact, large droplet spray, and aerosols as modes of influenza transmission is not known but is important in devising effective interven...

Few halophilic strains have been examined in detail for their culturability and metabolic activity at subzero temperatures, within the ice matrix, over the longer term. Here, we examine three Arctic s...