FAPROTAX

Predict the likely functional potential of bacterial and archaeal taxa in one or more microbiome samples. The client provides taxonomic identities of queried OTUs and an optional OTU abundance table.

High-throughput sequencing of 16S rRNA gene amplicons, also known as 16S metabarcoding, has revealed a vast array of new microbial diversity, with the majority of bacterial and archaeal (aka. prokaryotic) species that are found in natural environments lacking a cultured representative. This means that the metabolic functions and ecological strategies of most detected prokaryotes must be estimated indirectly, for example based on their evolutionary relationships with other better known species.

FAPROTAX (Functional Annotation of Prokaryotic Taxa) is a well-established bioinformatics tool for making such inferences, thus facilitating the ecological interpretation of microbiome surveys. FAPROTAX uses a custom database of experimentally confirmed microbial phenotypes, covering over 80 functions of ecological interest, and a custom algorithm for determining the likely functional capabilities of novel prokaryotic taxa. This analysis applies FAPROTAX to a user-provided list of prokaryotic taxa to generate "microbial functional profiles" for your samples.

Caveats and limitations: When using FAPROTAX, keep in mind the following caveats and limitations:

• Functional predictions by FAPROTAX can be erroneous, especially for species with no cultured close relatives, or for functions with low evel of phylogenetic conservatism (i.e., varying between sister species or even between conspecific strains).
• FAPROTAX largely focuses on microbial biochemical functions of particular ecological/geochemical importance, and only covers bacteria and archaea (no eukaryotes).

Our analysis starts with a list of Operational Taxonomic Units (OTUs) with known taxonomic identities, and optionally an OTU abundance table across one or more microbiome samples. Note that your OTUs may represent individual strains, species (most common scenario), genera etc, and FAPROTAX is agnostic with regards to that. We then apply the FAPROTAX annotation pipeline to predict likely functional capabilities for each OTU, and to estimate the overall proportions of various functional groups in your samples. Covered functions mostly cover metabolisms of ecological importance, such as methanogenesis, denitrification, fermentation, photosynthesis etc.

Main deliverables:

• A table specifying for each OTU and each function whether the OTU is predicted to exhibit that function.
• If an OTU abundance table was provided, we also generate a corresponding function abundance table (aka. "functional profiles") and overview visualizations.

In addition, we provide a Materials & Methods writeup for use in your publications.

• Taxonomic identities of OTUs, either as part of the optional OTU abundance table (see below) or as a separate CSV or TSV file. FAPROTAX works best if taxonomic identities are known down to species level.
• Optional OTU abundance table in CSV, TSV or BIOM file format, specifying OTU abundances in various samples. This table may include the taxonomic identities of OTUs.

Main databases and software used in this analysis:

• FAPROTAX

• Louca, S., Parfrey, L. W., Doebeli, M. (2016). Decoupling function and taxonomy in the global ocean microbiome. Science 353:1272-1277
• Louca, S., Jacques, S. M. S., Pires, A. P. F., Leal, J. S., Srivastava, D. S., Parfrey, L. W. et al. (2016). High taxonomic variability despite stable functional structure across microbial communities. Nature Ecology & Evolution 1:0015

Price $50 base + $0.01 per OTU. A preview of results is released and payment becomes due upon completion of computations. Payment must be received within 30 days thereafter, and full results become available upon payment.