Data from: Tetranucleotide frequencies and ratios of frequencies

Microbiomes are constrained by physicochemical conditions, nutrient
regimes, and community interactions across diverse environments, yet
genomic signatures of this adaptation remain unclear. Metagenome
sequencing is a powerful technique to analyze genomic content in the
context of natural environments, establishing concepts of microbial
ecological trends. Here, we developed a data discovery tool - a
tetranucleotide-informed metagenome stability diagram - that is publicly
available in the Integrated Microbial Genomes and Microbiomes (IMG/M)
platform for metagenome-ecosystem analyses. We analyzed the
tetranucleotide frequencies from quality-filtered and unassembled sequence
data of over 12,000 metagenomes to assess ecosystem-specific microbial
community composition and function. We found that tetranucleotide
frequencies can differentiate communities across various natural
environments, and that specific functional and metabolic trends can be
observed in this structuring. Our tool places metagenomes sampled from
diverse environments into clusters and along gradients of tetranucleotide
frequency similarity, suggesting microbiome community compositions
specific to gradient conditions. Within the resulting metagenome clusters,
we identify protein-coding gene identifiers that are most differentiated
between ecosystem classifications. We plan for annual updates to the
metagenome stability diagram in IMG/M with new data, allowing for
refinement of the ecosystem classifications delineated here. This
framework has the potential to inform future studies on microbiome
engineering, bioremediation, and the prediction of microbial community
responses to environmental change.