title: FCMM: A comparative metagenomic approach for functional characterization of multiple metagenome samples.
abstract: Next-generation sequencing (NGS) technologies make it possible to obtain the entire genomic content of microorganisms in metagenome samples. Thus, many studies have developed methods for the processing and analysis of metagenomic NGS reads, including analyses for predicting functions and their enrichments in environmental metagenome samples. Especially, comparative functional studies by using multi-metagenome samples are essential for identifying and comparing different characteristics of multiple environmental samples. In this paper, we introduce a pipeline for functional characterization of multiple metagenome samples to infer major functions as well as their quantitative scores in a comparative metagenomics manner. The pipeline performs the annotation of functions related to expected proteins in the metagenome samples, calculates their enrichment scores based on the reads per kilobase per million reads (RPKM) measure, and predicts the relative abundance of associated functions by a statistical test. The results from single sample analysis are then used to find common and sample-specific major functions. By applying the pipeline to six different environmental metagenome samples, including two ocean (Antarctica aquatic and Baltic Sea) and four terrestrial (Acid mine drainage, human gut microbiome, Amazon River, and Wasca soil) samples, we were able to predict common functions as well as environment-specific functions. Our pipeline is available at http://bioinfo.konkuk.ac.kr/FCMM/.
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea.
authors.forename: Jongin
authors.initials: J
authors.lastname: Lee
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea.
authors.forename: Hoon Taek
authors.initials: HT
authors.lastname: Lee
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea.
authors.forename: Woon-young
authors.initials: WY
authors.lastname: Hong
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea.
authors.forename: Eunji
authors.initials: E
authors.lastname: Jang
authors.affiliation: Department of Animal Biotechnology, Konkuk University, Seoul 143-701, Republic of Korea. Electronic address: jbkim@konkuk.ac.kr.
authors.forename: Jaebum
authors.initials: J
authors.lastname: Kim
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D019015:Geologic Sediments / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D054892:Metagenome; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota; D012988:Soil Microbiology; D014871:Water Microbiology
keywords: Comparative metagenomics; Functional characterization; Multiple samples