CAMPER: curated annotations for profiling microbial polyphenol metabolic potential

Abstract

Summary: Polyphenols are diverse and abundant carbon sources across ecosystems-having important roles in host-associated and terrestrial systems alike. However, the microbial genes encoding polyphenol metabolic enzymes are poorly represented in commonly used annotation databases, limiting widespread surveying of this metabolism. Here we present CAMPER, a tool that combines custom annotation searches with database-derived searches to both annotate and summarize polyphenol metabolism genes for a wide audience. With CAMPER, users will identify potential polyphenol-active genes and genomes to more broadly understand microbial carbon cycling in their datasets.

Availability and implementation: CAMPER is implemented in Python and is published under the GNU General Public License Version 3. It is available as both a standalone tool and as a database in DRAM v.1.5+. The source code and full documentation is available on GitHub at https://github.com/WrightonLabCSU/CAMPER.

Figure 1.. CAMPER workflow and application.

(A) CAMPER annotation library is comprised of 12 custom hidden Markov models (HMMs), 32 custom Basic Local Alignment Search Tool (BLAST) searches, and 277 HMMs from other databases. (B) CAMPER takes as input one or multiple amino acid FASTA files, and using camper_annotate generates an annotations.tsv file and through camper_distill generates a summarized tsv file. (C) Examples of two CAMPER transformation pathways, Flavone/Flavanone degradation to phloroglucinol (orange arrows) and phloroglucinol degradation (pink arrows). (D) CAMPER annotated presence for seven genes in three isolate genomes, where green marks the presence of an A or B rank annotation. (E) The presence of the 7 example enzymes in other common or polyphenol-focused annotation databases, where grey indicates presence in the database.