Comparative Microbial Diversity in the Gastrointestinal Tracts of Food Animal Species1
Molecular tools based on small subunit (SSU) rDNA gene sequences offer a powerful and rapid tool for the analysis of complex microbial communities found in the gastrointestinal tracts (GIT) of food animal species. Extensive comparative sequence analysis of SSU rRNA molecules representing a wide dive...
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ftbioone:10.1093/icb/42.2.327 2024-06-02T08:03:42+00:00 Comparative Microbial Diversity in the Gastrointestinal Tracts of Food Animal Species1 Joyce M. Simpson Svetlana A. Kocherginskaya Roustam I. Aminov Laura T. Skerlos Terence M. Bradley Roderick I. Mackie Bryan A. White Joyce M. Simpson Svetlana A. Kocherginskaya Roustam I. Aminov Laura T. Skerlos Terence M. Bradley Roderick I. Mackie Bryan A. White world 2002-04-01 text/HTML https://doi.org/10.1093/icb/42.2.327 en eng The Society for Integrative and Comparative Biology doi:10.1093/icb/42.2.327 All rights reserved. https://doi.org/10.1093/icb/42.2.327 Text 2002 ftbioone https://doi.org/10.1093/icb/42.2.327 2024-05-07T00:53:24Z Molecular tools based on small subunit (SSU) rDNA gene sequences offer a powerful and rapid tool for the analysis of complex microbial communities found in the gastrointestinal tracts (GIT) of food animal species. Extensive comparative sequence analysis of SSU rRNA molecules representing a wide diversity of organisms shows that different regions of the molecule vary in sequence conservation. Oligonucleotides complementing regions of universally conversed SSU rRNA sequences are used as universal probes, while those complementing more variable regions of sequence are useful as selective probes targeting species, genus, or phylogenetic groups. Different approaches derive different information and this is highly dependent on the type of target nucleic acid employed and the conceptual and technical basis used for nucleic acid probe design. Generally these approaches can be divided into DNA-based methods employing empirically characterized probes and rRNA-based methods based on comparative sequence analysis for design and interpretation of “rational” probes. Polymerase chain reaction (PCR) based techniques can also be applied to the analysis of microbial communities in the GIT. Direct cloning of SSU rDNA genes amplified from these complex communities can be used to determine the extent of diversity in these GIT communities. Denaturing gradient gel electrophoresis (DGGE) is another powerful tool for profiling microbial diversity of microbial communities in GI tracts. Sequence analysis of the excised DGGE amplicons can then be used to presumptively identify predominant bacterial species. Examples of how these molecular approaches are being used to study the microbial diversity of communities from steers fed different diets, swine fed probiotics, and Atlantic salmon fed aquaculture diets are presented. Text Atlantic salmon BioOne Online Journals Integrative and Comparative Biology 42 2 327 331 |
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Molecular tools based on small subunit (SSU) rDNA gene sequences offer a powerful and rapid tool for the analysis of complex microbial communities found in the gastrointestinal tracts (GIT) of food animal species. Extensive comparative sequence analysis of SSU rRNA molecules representing a wide diversity of organisms shows that different regions of the molecule vary in sequence conservation. Oligonucleotides complementing regions of universally conversed SSU rRNA sequences are used as universal probes, while those complementing more variable regions of sequence are useful as selective probes targeting species, genus, or phylogenetic groups. Different approaches derive different information and this is highly dependent on the type of target nucleic acid employed and the conceptual and technical basis used for nucleic acid probe design. Generally these approaches can be divided into DNA-based methods employing empirically characterized probes and rRNA-based methods based on comparative sequence analysis for design and interpretation of “rational” probes. Polymerase chain reaction (PCR) based techniques can also be applied to the analysis of microbial communities in the GIT. Direct cloning of SSU rDNA genes amplified from these complex communities can be used to determine the extent of diversity in these GIT communities. Denaturing gradient gel electrophoresis (DGGE) is another powerful tool for profiling microbial diversity of microbial communities in GI tracts. Sequence analysis of the excised DGGE amplicons can then be used to presumptively identify predominant bacterial species. Examples of how these molecular approaches are being used to study the microbial diversity of communities from steers fed different diets, swine fed probiotics, and Atlantic salmon fed aquaculture diets are presented. |
author2 |
Joyce M. Simpson Svetlana A. Kocherginskaya Roustam I. Aminov Laura T. Skerlos Terence M. Bradley Roderick I. Mackie Bryan A. White |
format |
Text |
author |
Joyce M. Simpson Svetlana A. Kocherginskaya Roustam I. Aminov Laura T. Skerlos Terence M. Bradley Roderick I. Mackie Bryan A. White |
spellingShingle |
Joyce M. Simpson Svetlana A. Kocherginskaya Roustam I. Aminov Laura T. Skerlos Terence M. Bradley Roderick I. Mackie Bryan A. White Comparative Microbial Diversity in the Gastrointestinal Tracts of Food Animal Species1 |
author_facet |
Joyce M. Simpson Svetlana A. Kocherginskaya Roustam I. Aminov Laura T. Skerlos Terence M. Bradley Roderick I. Mackie Bryan A. White |
author_sort |
Joyce M. Simpson |
title |
Comparative Microbial Diversity in the Gastrointestinal Tracts of Food Animal Species1 |
title_short |
Comparative Microbial Diversity in the Gastrointestinal Tracts of Food Animal Species1 |
title_full |
Comparative Microbial Diversity in the Gastrointestinal Tracts of Food Animal Species1 |
title_fullStr |
Comparative Microbial Diversity in the Gastrointestinal Tracts of Food Animal Species1 |
title_full_unstemmed |
Comparative Microbial Diversity in the Gastrointestinal Tracts of Food Animal Species1 |
title_sort |
comparative microbial diversity in the gastrointestinal tracts of food animal species1 |
publisher |
The Society for Integrative and Comparative Biology |
publishDate |
2002 |
url |
https://doi.org/10.1093/icb/42.2.327 |
op_coverage |
world |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
https://doi.org/10.1093/icb/42.2.327 |
op_relation |
doi:10.1093/icb/42.2.327 |
op_rights |
All rights reserved. |
op_doi |
https://doi.org/10.1093/icb/42.2.327 |
container_title |
Integrative and Comparative Biology |
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42 |
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2 |
container_start_page |
327 |
op_container_end_page |
331 |
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1800748300847022080 |