{"id":8801,"date":"2014-05-23T20:46:56","date_gmt":"2014-05-23T20:46:56","guid":{"rendered":"http:\/\/admin.acceleratingscience.com\/behindthebench\/?p=8801"},"modified":"2016-12-01T22:32:16","modified_gmt":"2016-12-01T22:32:16","slug":"microbial-community-analysis-via-16s-rrna-profiling","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/microbial-community-analysis-via-16s-rrna-profiling\/","title":{"rendered":"Microbial Community Analysis Via 16S rRNA Profiling"},"content":{"rendered":"

Understanding the diversity of microbial communities, in almost any conceivable environment, has been greatly facilitated by rapid advances in\u00a0next-generation sequencing<\/a>\u00a0(NGS) technologies and associated bioinformatics approaches.\u00a016S rRNA sequencing<\/a>\u00a0is a fast, inexpensive research profiling technique based on variation in the bacterial 16S ribosomal RNA (rRNA) gene.<\/p>\n

\"RNA<\/a>Sequencing the 16S rRNA gene<\/a>\u00a0can be used to identify bacterial species, characterize bacteria populations, and perform grouping by shared sequence characteristics (taxonomical assignment). The 16S rRNA gene is highly conserved across domains of Bacteria and Archaea, and taxonomical assignment is possible due to the presence of nine hypervariable regions (V1\u2013V9) that contain sufficient sequence diversity to classify microbes. Moreover, since these variable regions are flanked by conserved regions, PCR amplification using universal primers is possible.<\/p>\n

Universal primers targeting the 16S rRNA gene allow a single, or a few, PCR reactions to be used when amplifying bacterial communities as a whole. Due to the clonal nature of massively parallel NGS workflows, each PCR reaction and subsequent sequencing read can be considered to be representative of a single bacterium within a mixed population. This approach has allowed characterization of bacterial communities without isolation and culturing. Through a deep sequencing approach, 16S rRNA research profiling has fundamentally changed our understanding of countless microbial communities and has proven to be an important discovery tool, revealing what is called the \u201cmicrobial dark matter\u201d of our planet due to the difficulty of culturing most bacterial species.<\/p>\n

The Ion PGM\u2122 System has been used to characterize an incredible array of bacterial communities, including microbial populations important for research into human health in diverse sites such as the\u00a0mouth<\/a>,\u00a0airway<\/a>,\u00a0complex bacterial infections<\/a>,\u00a0diabetic mycetoma<\/a>\u00a0(or \u201cMadura foot\u201d), during\u00a0stool substitute transplants,<\/a>\u00a0and the\u00a0human<\/a>\u00a0and\u00a0murine<\/a>\u00a0intestinal tract.<\/p>\n

Semiconductor sequencing has also revealed the composition of bacterial populations in a wide variety of environmental sources: such as waterways in response to\u00a0oil<\/a>\u00a0sands <\/a>mining and\u00a0sewage<\/a>; the\u00a0northern Gulf of Mexico<\/a>\u00a0and the\u00a0English Channel<\/a>; soil and rhizosphere of a\u00a0cactus<\/a>\u00a0and\u00a0willow<\/a>; uranium mine\u00a0tailings<\/a>\u00a0and the\u00a0tailings-water interface<\/a>; contaminated\u00a0arctic soils<\/a>;\u00a0aquaculture systems<\/a>;\u00a0biowaste reservoirs<\/a>; bioproduction settings [1<\/a>,\u00a02<\/a>,\u00a03<\/a>]; and during the life cycle of the\u00a0Lone Star tick<\/a>.<\/p>\n

To learn more about the possibilities of 16S rRNA profiling and\u00a0bacterial typing<\/a>\u00a0research,\u00a0Dr. Joe Petrosino<\/a>\u00a0of Baylor College of Medicine discusses in a series of videos using the Ion PGM\u2122 Sequencer and 16S rRNA sequencing to study microbial associations with\u00a0Type 1 Diabetes<\/a>,\u00a0fecal transplants<\/a>, and for forensic use, the\u00a0decomposition of corpses<\/a>.\u00a0Here’s a video<\/a>\u00a0of David Visi of University of North Texas describing the use of the Ion PGM Sequencer for 16S rRNA analysis of a kenaf microbial retting community (kenaf is valuable fiber plant used in cultivation, and retting is a stage in its processing).\u00a0\u00a0Dr. Antonius Suwanto<\/a>\u00a0of Bogor Agricultural University in Indonesia) describes his study evaluating the\u00a0bacterial composition of tempeh samples<\/a>\u00a0(a type of soybean) using 16s rRNA sequencing on the Ion PGM\u2122 Sequencer.<\/p>\n

See also an application note (PDF) about the collaboration between\u00a0Dr. George Watts<\/a>\u00a0(Genomics Shared Service at the University of Arizona Cancer Center, Tucson, Arizona) and Ion Torrent researchers\u00a0to optimize the amplicon region targeted in the 16S rRNA gene<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"

Understanding the diversity of microbial communities, in almost any conceivable environment, has been greatly facilitated by rapid advances in\u00a0next-generation sequencing\u00a0(NGS) technologies and associated bioinformatics approaches.\u00a016S rRNA sequencing\u00a0is a fast, inexpensive research profiling technique based on variation in the bacterial 16S ribosomal RNA (rRNA) gene. Sequencing the 16S rRNA gene\u00a0can be used to identify bacterial species,<\/p>\n","protected":false},"author":111,"featured_media":8805,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[84],"tags":[103,11,6],"division":[],"class_list":{"0":"post-8801","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-metagenomics","8":"tag-16s-rrna-microbial","9":"tag-ion-torrent","10":"tag-next-generation-sequencing","11":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"\nMicrobial Community Analysis Via 16S rRNA Profiling - Behind the Bench<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/microbial-community-analysis-via-16s-rrna-profiling\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Microbial Community Analysis Via 16S rRNA Profiling\" \/>\n<meta property=\"og:description\" content=\"Understanding the diversity of microbial communities, in almost any conceivable environment, has been greatly facilitated by rapid advances in\u00a0next-generation sequencing\u00a0(NGS) technologies and associated bioinformatics approaches.\u00a016S rRNA sequencing\u00a0is a fast, inexpensive research profiling technique based on variation in the bacterial 16S ribosomal RNA (rRNA) gene. 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