Predicting microbial growth conditions from amino acid composition

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 22, 2024

The ability to grow a microbe in the laboratory enables reproducible study and engineering of its genetics. Unfortunately, majority microbes tree life remain uncultivated because effort required identify culturing conditions. Predictions viable growth conditions guide experimental testing would be highly desirable. While carbon energy sources can computationally predicted with annotated genes, it is harder predict other requirements for such as oxygen, temperature, salinity, pH. Here, we developed genome-based computational models capable predicting oxygen tolerance (92% balanced accuracy), optimum temperature (R2=0.73), salinity (R2=0.81) pH (R2=0.48) novel taxonomic microbial families without requiring functional gene annotations. Using genome sequences 15,596 bacteria archaea, found that amino acid frequencies are predictive requirements. As little two acids 88% accuracy. cellular localization proteins compute improved prediction (R2 increase 0.36). Because these do not rely on presence or absence specific they applied incomplete genomes, 10% completeness. We our all 85,205 species sequenced archaea enriched thermophiles, anaerobes, acidophiles. Finally, 3,349 environmental samples metagenome-assembled genomes showed individual within community have differing This work guides identification constraints cultivation diverse microbes.

Language: Английский

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Comparative genomic analysis of Planctomycetota potential for polysaccharide degradation identifies biotechnologically relevant microbes

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: May 27, 2024

Abstract Background Members of the Planctomycetota phylum harbour an outstanding potential for carbohydrate degradation given abundance and diversity carbohydrate-active enzymes (CAZymes) encoded in their genomes. However, mainly members Planctomycetia class have been characterised up to now, little is known about degrading capacities other . Here, we present a comprehensive comparative analysis all available planctomycetotal genome representatives detail carbohydrolytic across phylogenetic groups different habitats. Results Our in-depth characterisation genomic resources increases our knowledge We show that this single encompasses wide variety currently CAZyme assigned glycoside hydrolase families many encode versatile enzymatic machinery towards complex degradation, including lignocellulose. highlight Isosphaerales, Pirellulales, Sedimentisphaerales Tepidisphaerales orders as having highest hydrolytic Furthermore, yet uncultivated group affiliated Phycisphaerales order could represent interesting source novel lytic polysaccharide monooxygenases boost lignocellulose degradation. Surprisingly, from anaerobic digestion reactors CAZymes targeting algal polysaccharides – opens new perspectives biomass valorisation biogas processes. Conclusions study provides perspective on potential, highlighting distinct which provide wealth diverse, potentially industrial interest.

Language: Английский

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Microbial functional guilds respond cohesively to rapidly fluctuating environments

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 30, 2025

Microbial communities experience environmental fluctuations across timescales from rapid changes in moisture, temperature, or light levels to long-term seasonal climactic variations. Understanding how microbial populations respond these is critical for predicting the impact of perturbations, interventions, and climate change on communities. Since typically harbor tens hundreds distinct taxa, response abundances perturbations potentially complex. However, while taxonomic diversity high, many taxa can be grouped into functional guilds strains with similar metabolic traits. These effectively reduce complexity system by providing a physiologically motivated coarse-graining. Here, using combination simulations, theory, experiments, we show that nutrient depends timescale those fluctuations. Rapid drive cohesive, positively correlated abundance dynamics within guilds. For slower variation, members guild begin compete due resource preferences, driving negative correlations between same guild. Our results provide route understanding relationship community changing environments, as well an experimental approach discovering via designed

Language: Английский

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Inferring resource competition in microbial communities from time series

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 12, 2025

The competition for resources is a defining feature of microbial communities. In many contexts, from soils to host-associated communities, highly diverse microbes are organized into metabolic groups or guilds with similar resource preferences. preferences individual taxa that give rise these critical understanding fluxes through the community and structure diversity in system. However, inferring capabilities taxa, their other within challenging unresolved. Here we address this gap knowledge by leveraging dynamic measurements abundances We show simple correlations often misleading predicting competition. spectral methods such as cross-power density (CPSD) coherence account time-delayed effects superior metrics first demonstrate fact on synthetic data generated consumer-resource models time-dependent availability, where By applying oceanic plankton time-series data, detect interaction structures among species genomic sequences. Our results indicate analyzing temporal across multiple timescales can reveal underlying

Language: Английский

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‘Goldilocks’-size extensively annotated model for Escherichia coli metabolism

Peer Community In Mathematical and Computational Biology, Journal Year: 2025, Volume and Issue: unknown

Published: April 22, 2025

Language: Английский

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Comparative genomic analysis ofPlanctomycetotapotential towards complex polysaccharide degradation identifies phylogenetically distinct groups of biotechnologically relevant microbes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 10, 2024

ABSTRACT The outstanding hydrolytic potential of the Planctomycetota phylum for complex polysaccharide degradation has recently been acknowledged based on numerous carbohydrate-active enzymes (CAZymes) encoded in their genomes. However, mainly members Planctomycetia class have characterised up to now, and little is known about degrading capacities other . Our in-depth characterisation available planctomycetotal genomic resources increased our knowledge carbohydrolytic We showed that this single encompasses a wide variety currently CAZyme diversity assigned glycoside hydrolase families, many are by high versatility towards carbohydrate degradation, including lignocellulose. also highlighted Isosphaerales, Pirellulales, Sedimentisphaerales Tepidisphaerales orders as having highest Furthermore, yet uncultivated group affiliated Phycisphaerales were identified an interesting source novel, lytic monooxygenases could boost lignocellulose degradation. Surprisingly, from anaerobic digestion reactors shown encode CAZymes targeting algal polysaccharides – opens new perspectives biomass valorisation biogas processes. study provides perspective potential, highlighting distinct phylogenetic groups which provide wealth diverse, potentially novel industrial interest.

Language: Английский

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MICROPHERRET: MICRObial PHEnotypic tRait ClassifieR using Machine lEarning Techniques

Environmental Microbiome, Journal Year: 2024, Volume and Issue: 19(1)

Published: Aug. 8, 2024

In recent years, there has been a rapid increase in the number of microbial genomes reconstructed through shotgun sequencing, and obtained by newly developed approaches including metagenomic binning single-cell sequencing. However, our ability to functionally characterize these experimental assays is orders magnitude less efficient. Consequently, pressing need for development swift automated strategies functional classification genomes.

Language: Английский

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