The phenotype and genotype of fermentative microbes

Hackmann, Timothy J.

doi:10.1101/2023.01.12.523810

Cited by 1 publication

(2 citation statements)

References 139 publications

(117 reference statements)

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“…Aerobes, however, are different from anaerobes, and these differences — though subtle — are legible in their genomes. Aerobes tend to have larger genomes (4) with more O 2 utilizing enzymes (2, 5) and usually belong to specific phylogenetic groups (4). Conversely, anaerobes make use of diverse fermentation pathways to conserve energy in low O 2 settings (3, 5).…”

Section: Introductionmentioning

confidence: 99%

“…Aerobes tend to have larger genomes (4) with more O 2 utilizing enzymes (2, 5) and usually belong to specific phylogenetic groups (4). Conversely, anaerobes make use of diverse fermentation pathways to conserve energy in low O 2 settings (3, 5). These differences have been used to predict O 2 utilization from the genome with reasonable accuracy (2, 6, 7).…”

Section: Introductionmentioning

confidence: 99%

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Annotation-free prediction of microbial dioxygen utilization

Flamholz,

Goldford,

Larsson

et al. 2024

Preprint

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Aerobes require dioxygen (O2) to grow; anaerobes do not. But nearly all microbes — aerobes, anaerobes, and facultative organisms alike — express enzymes whose substrates include O2, if only for detoxification. This presents a challenge when trying to assess which organisms are aerobic from genomic data alone. This challenge can be overcome by noting that O2 utilization has wide-ranging effects on microbes: aerobes typically have larger genomes, encode more O2-utilizing enzymes, and tend to use different amino acids in their proteins. Here we show that these effects permit high-quality prediction of O2 utilization from genome sequences, with several models displaying >70% balanced accuracy on a ternary classification task wherein blind guessing is only 33.3% accurate. Since genome annotation is compute-intensive and relies on many assumptions, we asked if annotation-free methods also perform well. We discovered that simple and efficient models based entirely on genome sequence content — e.g. triplets of amino acids —perform about as well as intensive annotation-based algorithms, enabling the rapid processing of global-scale sequence data to predict aerobic physiology. To demonstrate the utility of efficient physiological predictions we estimated the prevalence of aerobes and anaerobes along a well-studied O2 gradient in the Black Sea, finding strong quantitative correspondence between local chemistry (O2:sulfide concentration ratio) and the composition of microbial communities. We therefore suggest that statistical methods like ours can be used to estimate, or “sense,” pivotal features of the environment from DNA sequencing data.

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