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Absolute quantification of microbial taxon abundances
High-throughput amplicon sequencing has become a well-established approach for microbial community profiling. Correlating shifts in the relative abundances of bacterial taxa with environmental gradients is the goal of many microbiome surveys. As the abundances generated by this technology are semi-q...
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| Published in: | The ISME Journal 2017-02, Vol.11 (2), p.584-587 |
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| Main Authors: | , , , , , , , , |
| Format: | Article |
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| container_end_page | 587 |
| container_issue | 2 |
| container_start_page | 584 |
| container_title | The ISME Journal |
| container_volume | 11 |
| creator | Props, Ruben Kerckhof, Frederiek-Maarten Rubbens, Peter De Vrieze, Jo Hernandez Sanabria, Emma Waegeman, Willem Monsieurs, Pieter Hammes, Frederik Boon, Nico |
| description | High-throughput amplicon sequencing has become a well-established approach for microbial community profiling. Correlating shifts in the relative abundances of bacterial taxa with environmental gradients is the goal of many microbiome surveys. As the abundances generated by this technology are semi-quantitative by definition, the observed dynamics may not accurately reflect those of the actual taxon densities. We combined the sequencing approach (16S rRNA gene) with robust single-cell enumeration technologies (flow cytometry) to quantify the absolute taxon abundances. A detailed longitudinal analysis of the absolute abundances resulted in distinct abundance profiles that were less ambiguous and expressed in units that can be directly compared across studies. We further provide evidence that the enrichment of taxa (increase in relative abundance) does not necessarily relate to the outgrowth of taxa (increase in absolute abundance). Our results highlight that both relative and absolute abundances should be considered for a comprehensive biological interpretation of microbiome surveys. |
| doi_str_mv | 10.1038/ismej.2016.117 |
| format | article |
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Correlating shifts in the relative abundances of bacterial taxa with environmental gradients is the goal of many microbiome surveys. As the abundances generated by this technology are semi-quantitative by definition, the observed dynamics may not accurately reflect those of the actual taxon densities. We combined the sequencing approach (16S rRNA gene) with robust single-cell enumeration technologies (flow cytometry) to quantify the absolute taxon abundances. A detailed longitudinal analysis of the absolute abundances resulted in distinct abundance profiles that were less ambiguous and expressed in units that can be directly compared across studies. We further provide evidence that the enrichment of taxa (increase in relative abundance) does not necessarily relate to the outgrowth of taxa (increase in absolute abundance). 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Correlating shifts in the relative abundances of bacterial taxa with environmental gradients is the goal of many microbiome surveys. As the abundances generated by this technology are semi-quantitative by definition, the observed dynamics may not accurately reflect those of the actual taxon densities. We combined the sequencing approach (16S rRNA gene) with robust single-cell enumeration technologies (flow cytometry) to quantify the absolute taxon abundances. A detailed longitudinal analysis of the absolute abundances resulted in distinct abundance profiles that were less ambiguous and expressed in units that can be directly compared across studies. We further provide evidence that the enrichment of taxa (increase in relative abundance) does not necessarily relate to the outgrowth of taxa (increase in absolute abundance). 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>The ISME Journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Props, Ruben</au><au>Kerckhof, Frederiek-Maarten</au><au>Rubbens, Peter</au><au>De Vrieze, Jo</au><au>Hernandez Sanabria, Emma</au><au>Waegeman, Willem</au><au>Monsieurs, Pieter</au><au>Hammes, Frederik</au><au>Boon, Nico</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Absolute quantification of microbial taxon abundances</atitle><jtitle>The ISME Journal</jtitle><stitle>ISME J</stitle><addtitle>ISME J</addtitle><date>2017-02-01</date><risdate>2017</risdate><volume>11</volume><issue>2</issue><spage>584</spage><epage>587</epage><pages>584-587</pages><issn>1751-7362</issn><eissn>1751-7370</eissn><abstract>High-throughput amplicon sequencing has become a well-established approach for microbial community profiling. 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| ispartof | The ISME Journal, 2017-02, Vol.11 (2), p.584-587 |
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| source | Oxford Journals Open Access Collection; PubMed Central |
| subjects | 45/47 631/158/855 631/326/2522 631/326/2565/855 Bacteria - classification Bacteria - genetics Bacteria - growth & development Bacteria - isolation & purification Biodiversity Biomedical and Life Sciences DNA, Bacterial - chemistry DNA, Bacterial - genetics DNA, Ribosomal - chemistry DNA, Ribosomal - genetics Ecology Environmental gradient Evolutionary Biology Flow Cytometry Life Sciences Microbial Ecology Microbial Genetics and Genomics Microbiology Microbiota Relative abundance Sequence Analysis, DNA Short Communication |
| title | Absolute quantification of microbial taxon abundances |
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