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Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes

Kathryn Kananen,Iva A. Veseli,Christian J. Quiles Pérez,Samuel E. Miller,A. M. Eren,Patrick H. Bradley

Published 2025 in Bioinformatics Advances

ABSTRACT

Abstract Motivation Gene function annotation in microbial genomes and metagenomes is a fundamental in silico first step toward understanding metabolic potential and determinants of fitness. The Kyoto Encyclopedia of Genes and Genomes publishes a curated list of profile hidden Markov models to identify orthologous gene families (KOfams) with roles in metabolism. However, the computational tools that rely upon KOfams yield different annotations for the same set of genomes, leading to different downstream biological inferences. Results Here, we apply three open-source software tools that can annotate KOfams to genomes of phylogenetically diverse bacterial families from host-associated and free-living biomes. We use multiple computational approaches to benchmark these methods and investigate individual case studies where they differ. Our results show that despite their fundamental similarities, these methods have different annotation rates and quality. In particular, a method that adaptively tunes sequence similarity thresholds substantially improves sensitivity while maintaining high accuracy. We observe particularly large improvements for protein families with few reference sequences, or when annotating genomes from nonmodel organisms (such as gut-dwelling Lachnospiraceae). Our findings show that small improvements in annotation workflows can maximize the utility of existing databases and meaningfully improve in silico characterizations of microbial metabolism. Availability and implementation Anvi’o is available at https://anvio.org under the GNU GPL license. Scripts and workflow are available at https://github.com/pbradleylab/2023-anvio-comparison under the MIT license.

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