Chapter 12: Human microbiome analysis
Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, archaeal, fungal, and viral. Under normal circumstances, these microbes help us to digest our food and to m...
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| Veröffentlicht in: | PLoS computational biology 2012-12, Vol.8 (12), p.e1002808-e1002808 |
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| description | Humans are essentially sterile during gestation, but during and after birth, every body surface, including the skin, mouth, and gut, becomes host to an enormous variety of microbes, bacterial, archaeal, fungal, and viral. Under normal circumstances, these microbes help us to digest our food and to maintain our immune systems, but dysfunction of the human microbiota has been linked to conditions ranging from inflammatory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioinformatic tools provide a powerful means of understanding the contribution of the human microbiome to health and its potential as a target for therapeutic interventions. This chapter will first discuss the historical origins of microbiome studies and methods for determining the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable microbiome analysis. Finally, it will conclude with examples of the functional genomics of the human microbiome and its influences upon health and disease. |
| doi_str_mv | 10.1371/journal.pcbi.1002808 |
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Under normal circumstances, these microbes help us to digest our food and to maintain our immune systems, but dysfunction of the human microbiota has been linked to conditions ranging from inflammatory bowel disease to antibiotic-resistant infections. Modern high-throughput sequencing and bioinformatic tools provide a powerful means of understanding the contribution of the human microbiome to health and its potential as a target for therapeutic interventions. This chapter will first discuss the historical origins of microbiome studies and methods for determining the ecological diversity of a microbial community. Next, it will introduce shotgun sequencing technologies such as metagenomics and metatranscriptomics, the computational challenges and methods associated with these data, and how they enable microbiome analysis. Finally, it will conclude with examples of the functional genomics of the human microbiome and its influences upon health and disease.</description><identifier>ISSN: 1553-7358</identifier><identifier>ISSN: 1553-734X</identifier><identifier>EISSN: 1553-7358</identifier><identifier>DOI: 10.1371/journal.pcbi.1002808</identifier><identifier>PMID: 23300406</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Antibiotics ; Bacteria - genetics ; Bacteria - isolation & purification ; Biology ; Computational biology ; Control ; Deoxyribonucleic acid ; DNA ; Education ; Genes, Bacterial ; Genomes ; Genomics ; Health aspects ; Host-parasite relationships ; Host-Pathogen Interactions ; Humans ; Inflammatory bowel disease ; Metagenome ; Metagenomics ; Microbial colonies ; Microbiology ; Organisms ; Phylogenetics ; Physiological aspects ; RNA, Ribosomal, 16S - genetics ; Studies ; Taxonomy</subject><ispartof>PLoS computational biology, 2012-12, Vol.8 (12), p.e1002808-e1002808</ispartof><rights>COPYRIGHT 2012 Public Library of Science</rights><rights>2012 Morgan, Huttenhower. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Morgan XC, Huttenhower C (2012) Chapter 12: Human Microbiome Analysis. 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genetics</topic><topic>Bacteria - isolation & purification</topic><topic>Biology</topic><topic>Computational biology</topic><topic>Control</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>Education</topic><topic>Genes, Bacterial</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Health aspects</topic><topic>Host-parasite relationships</topic><topic>Host-Pathogen Interactions</topic><topic>Humans</topic><topic>Inflammatory bowel disease</topic><topic>Metagenome</topic><topic>Metagenomics</topic><topic>Microbial colonies</topic><topic>Microbiology</topic><topic>Organisms</topic><topic>Phylogenetics</topic><topic>Physiological aspects</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Studies</topic><topic>Taxonomy</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Morgan, Xochitl C</creatorcontrib><creatorcontrib>Huttenhower, Curtis</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Canada</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Biotechnology Research Abstracts</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Computing Database (Alumni Edition)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Computer Science Collection</collection><collection>Computer Science Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Computing Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - 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| subjects | Antibiotics Bacteria - genetics Bacteria - isolation & purification Biology Computational biology Control Deoxyribonucleic acid DNA Education Genes, Bacterial Genomes Genomics Health aspects Host-parasite relationships Host-Pathogen Interactions Humans Inflammatory bowel disease Metagenome Metagenomics Microbial colonies Microbiology Organisms Phylogenetics Physiological aspects RNA, Ribosomal, 16S - genetics Studies Taxonomy |
| title | Chapter 12: Human microbiome analysis |
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