Sequencing and beyond: integrating molecular 'omics' for microbial community profiling.
High-throughput DNA sequencing has proven invaluable for investigating diverse environmental and host-associated microbial communities. In this Review, we discuss emerging strategies for microbial community analysis that complement and expand traditional metagenomic profiling. These include novel DNA sequencing strategies for identifying strain-level microbial variation and community temporal dynamics; measuring multiple 'omic' data types that better capture community functional activity, such as transcriptomics, proteomics and metabolomics; and combining multiple forms of omic data in an integrated framework. We highlight studies in which the 'multi-omics' approach has led to improved mechanistic models of microbial community structure and function.
1] Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts 02115, USA. [2] The Broad Institute, Cambridge, Massachusetts 02142, USA.
Eric A
EA
Franzosa
1] Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts 02115, USA. [2] The Broad Institute, Cambridge, Massachusetts 02142, USA.
Tiffany
T
Hsu
1] The Broad Institute, Cambridge, Massachusetts 02142, USA. [2] Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.
Alexandra
A
Sirota-Madi
Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts 02115, USA.
Afrah
A
Shafquat
Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts 02115, USA.
Galeb
G
Abu-Ali
1] Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts 02115, USA. [2] The Broad Institute, Cambridge, Massachusetts 02142, USA.
Xochitl C
XC
Morgan
1] Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts 02115, USA. [2] The Broad Institute, Cambridge, Massachusetts 02142, USA.
Curtis
C
Huttenhower
D020869:Gene Expression Profiling / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D055432:Metabolomics / Q000379:methods*; D056186:Metagenomics / Q000379:methods*; D064307:Microbiota / Q000235:genetics / Q000502:physiology*; D040901:Proteomics / Q000379:methods*; D049490:Systems Biology / Q000379:methods*