Predicting oxygen levels in microbial habitats using a metagenome-based approach

ABSTRACT Oxygen is a primary driver of the distribution and activity of microbial life. Since oxygen levels are often difficult to measure in situ , one potential solution is to use bacteria as bioindicators of oxygen levels. As bacteria range from obligate aerobes to obligate anaerobes, quantification of bacterial community oxygen preferences could be used to infer variation in oxygen levels and bacterial metabolic strategies. After using ensemble machine learning to select the 20 most important genes that predict oxygen tolerances in individual bacteria, we established a relationship between the abundance ratio of aerobic:anaerobic indicator genes and the proportional abundance of aerobic bacteria using simulated metagenomes with varying ratios of known aerobes and anaerobes. We developed a tool, OxyMetaG, that takes metagenomic reads as input, extracts bacterial reads, maps reads to the 20 genes, and predicts oxygen availability in any sample on a scale from 0% to 100% (completely anoxic to completely oxic). We tested OxyMetaG on a suite of metagenomes with measured or inferred oxygen levels across a variety of environmental and host-associated samples. To demonstrate its utility, we applied OxyMetaG to 540 surface soils, showing that surface soils are predominantly oxic, but wetter sites with finer textures have relatively less oxygen. Finally, we applied OxyMetaG to 73 human gut samples, showing that in the first 3 years of life, human guts progress from oxygen levels as high as 61% down to 0%. We expect OxyMetaG to have broad utility for characterizing oxygen levels in both modern and ancient microbial habitats. IMPORTANCE Oxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ . We developed a tool, OxyMetaG, that leverages differences in bacterial gene content across known aerobic and anaerobic taxa to predict the oxygen level of a given sample directly from shotgun metagenomic reads. OxyMetaG works on samples with low sequencing depth and avoids computationally expensive genome assembly, which often captures only a fraction of the microbial community in a given environment. With OxyMetaG, bacteria can be used as bioindicators of oxygen availability over broader time scales than just a single measurement and provide crucial environmental context in cases where oxygen has not been or cannot be measured. OxyMetaG is publicly available and can be used to answer a wide variety of ecological questions in both environmental and host-associated systems.