A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling

Microbiome
Ari UgarteAlessandra Carbone

Abstract

Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism and one species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions. The new landscape we face requires the reconstruction of biochemical and regulatory pathways at the community level in a given environment. In order to understand how environmental factors affect the genetic material and the dynamics of the expression from one environment to another, we want to evaluate the quantity of gene protein sequences or transcripts associated to a given pathway by precisely estimating the abundance of protein domains, their weak presence or absence in environmental samples. MetaCLADE is a novel profile-based domain annotation pipeline based on a multi-source domain annotation strategy. It applies directly to reads and improves identification of the catalog of functions in microbiomes. MetaCLADE is applied to simulated data and to more than ten metagenomic and metatranscriptomic datasets from different environments where it outperforms InterProScan in the number of annotated domains. It i...Continue Reading

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Citations

Oct 15, 2019·Frontiers in Genetics·Migun ShakyaPatrick S G Chain
Feb 26, 2020·BMC Bioinformatics·Michelle L TreiberDanielle G Lemay
Apr 25, 2020·Bioinformatics·Laurent DavidAlessandra Carbone
Feb 6, 2020·Frontiers in Genetics·Rilquer MascarenhasPedro Milet Meirelles
Dec 15, 2020·Journal of Microbiological Methods·Caitlin S RomanisBrett A Neilan
Mar 9, 2021·Computational and Structural Biotechnology Journal·Yan WangZhidong Xue
Mar 25, 2021·Briefings in Bioinformatics·Masood Ur Rehman KayaniLei Chen
May 24, 2021·Nucleic Acids Research·Riccardo VicedominiAlessandra Carbone
Sep 2, 2021·Annual Review of Biomedical Data Science·Yancong ZhangCurtis Huttenhower

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Methods Mentioned

BETA
Illumina sequencing

Software Mentioned

wgsim
DAMA
HMM
HHblits
MOCAT2
MetaCLADE + UProC
InterProScan
GC
HMMER
MetaPath

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