Absolute quantification of microbial taxon abundances View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-09-09

AUTHORS

Ruben Props, Frederiek-Maarten Kerckhof, Peter Rubbens, Jo De Vrieze, Emma Hernandez Sanabria, Willem Waegeman, Pieter Monsieurs, Frederik Hammes, Nico Boon

ABSTRACT

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. More... »

PAGES

584-587

References to SciGraph publications

  • 2013-08-25. Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences in NATURE BIOTECHNOLOGY
  • 2015-03-02. Ecology and exploration of the rare biosphere in NATURE REVIEWS MICROBIOLOGY
  • 2013-02-14. Robust estimation of microbial diversity in theory and in practice in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2008-05. Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques in NATURE REVIEWS MICROBIOLOGY
  • 2015-05-15. Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2016-03-29. Challenges in microbial ecology: building predictive understanding of community function and dynamics in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2015-04-27. Sequencing and beyond: integrating molecular 'omics' for microbial community profiling in NATURE REVIEWS MICROBIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/ismej.2016.117

    DOI

    http://dx.doi.org/10.1038/ismej.2016.117

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1036110439

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/27612291


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