A novel analysis method for paired-sample microbial ecology experiments

Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.; Fortney, Julian L.; Bastidas-Oyanedel, Juan R.; Rodriguez, Jorge; Hazen, Terry C.; Alm, Eric J.; Humbert, Jean -Francois

doi:10.1371/journal.pone.0154804

Title: A novel analysis method for paired-sample microbial ecology experiments

Journal Article · Fri May 06 04:00:00 UTC 2016 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0154804 · OSTI ID:1327714

^[1]; Vora, Suhani ^[1]; Techtmann, Stephen M. ^[2]; Fortney, Julian L. ^[3]; Bastidas-Oyanedel, Juan R. ^[4]; Rodriguez, Jorge ^[4]; Hazen, Terry C. ^[3]; Alm, Eric J. ^[1]; Humbert, Jean -Francois ^[5]

Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
Univ. of Tennessee, Knoxville, TN (United States)
Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Masdar Institute of Science and Technology, Abu Dhabi (United Arab Emirates)
INRA (France)

Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1327714

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 5 Vol. 11; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
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Title: A novel analysis method for paired-sample microbial ecology experiments

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