title: Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome.
abstract: The advances in experimental methods and the development of high performance bioinformatic tools have substantially improved our understanding of microbial communities associated with human niches. Many studies have documented that changes in microbial abundance and composition of the human microbiome is associated with human health and diseased state. The majority of research on human microbiome is typically focused in the analysis of one level of biological information, i.e., metagenomics or metatranscriptomics. In this review, we describe some of the different experimental and bioinformatic strategies applied to analyze the 16S rRNA gene profiling and shotgun sequencing data of the human microbiome. We also discuss how some of the recent insights in the combination of metagenomics, metatranscriptomics and viromics can provide more detailed description on the interactions between microorganisms and viruses in oral and gut microbiomes. Recent studies on viromics have begun to gain importance due to the potential involvement of viruses in microbial dysbiosis. In addition, metatranscriptomic combined with metagenomic analysis have shown that a substantial fraction of microbial transcripts can be differentially regulated relative to their microbial genomic abundances. Thus, understanding the molecular interactions in the microbiome using the combination of metagenomics, metatranscriptomics and viromics is one of the main challenges towards a system level understanding of human microbiome.
authors.affiliation: Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico.
authors.forename: Shirley
authors.initials: S
authors.lastname: Bikel
authors.affiliation: Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico.
authors.forename: Alejandra
authors.initials: A
authors.lastname: Valdez-Lara
authors.affiliation: Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico.
authors.forename: Fernanda
authors.initials: F
authors.lastname: Cornejo-Granados
authors.affiliation: Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico.
authors.forename: Karina
authors.initials: K
authors.lastname: Rico
authors.affiliation: Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico.
authors.forename: Samuel
authors.initials: S
authors.lastname: Canizales-Quinteros
authors.affiliation: Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F., Mexico.
authors.forename: Xavier
authors.initials: X
authors.lastname: Soberón
authors.affiliation: Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F., Mexico.
authors.forename: Luis
authors.initials: L
authors.lastname: Del Pozo-Yauner
authors.affiliation: Unidad de Genómica de Poblaciones Aplicada la Salud, Facultad de Química, UNAM, Instituto Nacional de Medicina Genómica (INMEGEN), México, D.F. 14610, Mexico ; Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Avenida Universidad 2001, Cuernavaca C.P. 62210, Mexico.
authors.forename: Adrián
authors.initials: A
authors.lastname: Ochoa-Leyva
keywords: Bioinformatics; Human microbiome; Metagenomics; Metatranscriptomics; Systems-level; Viromics