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Gastroenterology DOI:10.1053/j.gastro.2014.01.049

Meta'omic analytic techniques for studying the intestinal microbiome.

Publication TypeJournal Article
Year of Publication2014
AuthorsMorgan, XC, Huttenhower, C
JournalGastroenterology
Volume146
Issue6
Pages1437-1448.e1
Date Published2014 May
ISSN1528-0012
KeywordsAnimals, Bacteria, DNA, Bacterial, Gene Expression Profiling, Gene Expression Regulation, Bacterial, Genotype, High-Throughput Nucleotide Sequencing, Host-Pathogen Interactions, Humans, Inflammatory Bowel Diseases, Intestines, Metagenome, Metagenomics, Microbiota, Models, Statistical, Phenotype, Phylogeny, Ribotyping, RNA, Bacterial, RNA, Ribosomal, 16S, Transcriptome
Abstract

Nucleotide sequencing has become increasingly common and affordable, and is now a vital tool for studies of the human microbiome. Comprehensive microbial community surveys such as MetaHit and the Human Microbiome Project have described the composition and molecular functional profile of the healthy (normal) intestinal microbiome. This knowledge will increase our ability to analyze host and microbial DNA (genome) and RNA (transcriptome) sequences. Bioinformatic and statistical tools then can be used to identify dysbioses that might cause disease, and potential treatments. Analyses that identify perturbations in specific molecules can leverage thousands of culture-based isolate genomes to contextualize culture-independent sequences, or may integrate sequence data with whole-community functional assays such as metaproteomic or metabolomic analyses. We review the state of available systems-level models for studies of the intestinal microbiome, along with analytic techniques and tools that can be used to determine its functional capabilities in healthy and unhealthy individuals.

URLhttp://linkinghub.elsevier.com/retrieve/pii/S0016-5085(14)00140-1
DOI10.1053/j.gastro.2014.01.049
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/24486053?dopt=Abstract

Alternate JournalGastroenterology
PubMed ID24486053
Grant ListR01HG005969 / HG / NHGRI NIH HHS / United States