Annotation-free prediction of microbial dioxygen utilization

Abstract

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.

Predicting microbial growth conditions from amino acid composition

“…9C ) and similar overall gene content 12 . A recent effort was unable to accurately predict obligate aerobes, facultative anaerobes, and obligate anaerobes using amino acid frequencies (balanced accuracy 55%) 21 . The similarity between facultative anaerobes and aerobes is evidence of the strong selective pressure that oxic conditions exert on amino acid usage.…”

“…For example, while some bacterial species can evolve to grow faster through the loss of many different genes 19 , maximum growth rate across diverse phyla is consistently correlated with bias in codon usage 20 . For oxygen sensitivity, aerobic organisms tend to have higher G+C content compared to anaerobic relatives, and amino acid frequencies have been linked to oxygen use 16,[21][22][23] . For temperature, proteins tend to contain more aromatic and hydrophobic residues at higher temperatures [24][25][26] .…”