The vast majority of microorganisms on Earth reside in often-inseparable environment-specific communities – microbiomes. Meta-genomic/-transcriptomic sequencing could reveal the otherwise inaccessible functionality of microbiomes. However, existing analysis approaches focus on attributing sequencing reads to known genes/genomes and, thus, often fail to make maximal use of available data.
We created faser (functional annotation of sequencing reads), an algorithm that is instead optimised to map reads to molecular functions encoded by the read-correspondent genes. The mi-faser microbiome analysis pipeline, combining faser with our manually curated reference database of protein functions, accurately annotates each microbiome as a set of molecular functions.
mi-faser's "20 minutes per microbiome" processing speed is significantly faster than the state of the art annotation methods, allowing for large scale comparisons. Microbiome function vectors can be compared between different conditions to highlight environment-specific and/or time-dependent changes in functionality.
With mi-faser, we identified previously unseen oil degradation-specific functions in BP oil-spill data. Our method also revealed variability in microbiome functionality between Crohn’s Disease (CD) patients and clearly distinguished patient microbiomes from those of related healthy individuals. We highlight the role of the microbiome in CD pathogenicity by showing that the patient microbiomes are enriched in both the functions that promote inflammation and those that help bacteria survive it.
Citing mi-faser. If you use mi-faser in published research, please cite:
Zhu, C., Miller, M., Marpaka, S., Vaysberg, P., Rühlemann, M. C., Wu, G. H. F.-A., . . . Bromberg, Y. (2017). Functional sequencing read annotation for high precision microbiome analysis. Nucleic Acids Res. doi:10.1093/nar/gkx1209
Read this publication at Nucleic Acids Research (doi:10.1093).