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Absolute quantification of microbial taxon abundances

(2017) ISME JOURNAL. 11(2). p.584-587
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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.
Keywords
microbiology, flow cytometry, microbiome, microbial ecology, IN-SITU HYBRIDIZATION, COMMUNITIES, DIVERSITY, BACTERIA, ECOLOGY, SAMPLES

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Chicago
Props, Ruben, Frederiek-Maarten Kerckhof, Peter Rubbens, Jo De Vrieze, Emma Hernandez Sanabria, Willem Waegeman, Pieter Monsieurs, Frederik Hammes, and Nico Boon. 2017. “Absolute Quantification of Microbial Taxon Abundances.” Isme Journal 11 (2): 584–587.
APA
Props, R., Kerckhof, F.-M., Rubbens, P., De Vrieze, J., Hernandez Sanabria, E., Waegeman, W., Monsieurs, P., et al. (2017). Absolute quantification of microbial taxon abundances. ISME JOURNAL, 11(2), 584–587.
Vancouver
1.
Props R, Kerckhof F-M, Rubbens P, De Vrieze J, Hernandez Sanabria E, Waegeman W, et al. Absolute quantification of microbial taxon abundances. ISME JOURNAL. 2017;11(2):584–7.
MLA
Props, Ruben et al. “Absolute Quantification of Microbial Taxon Abundances.” ISME JOURNAL 11.2 (2017): 584–587. Print.
@article{8071166,
  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.},
  author       = {Props, Ruben and Kerckhof, Frederiek-Maarten and Rubbens, Peter and De Vrieze, Jo and Hernandez Sanabria, Emma and Waegeman, Willem and Monsieurs, Pieter and Hammes, Frederik and Boon, Nico},
  issn         = {1751-7362},
  journal      = {ISME JOURNAL},
  language     = {eng},
  number       = {2},
  pages        = {584--587},
  title        = {Absolute quantification of microbial taxon abundances},
  url          = {http://dx.doi.org/10.1038/ismej.2016.117},
  volume       = {11},
  year         = {2017},
}

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