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

Abstract

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. 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 methodmore » 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. 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".« less

Authors:
ORCiD logo [1];  [1];  [2];  [3];  [4];  [4];  [3];  [1];  [5]
  1. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
  2. Univ. of Tennessee, Knoxville, TN (United States)
  3. Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  4. Masdar Institute of Science and Technology, Abu Dhabi (United Arab Emirates)
  5. INRA (France)
Publication Date:
Research Org.:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1327714
Alternate Identifier(s):
OSTI ID: 1480721
Grant/Contract Number:  
AC05-00OR22725; AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 11; Journal Issue: 5; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; oils; microbial ecology; probability distribution; community ecology; crude oil; oceans; sequence databases; sequence alignment

Citation Formats

Olesen, Scott W., Vora, Suhani, Techtmann, Stephen M., Fortney, Julian L., Bastidas-Oyanedel, Juan R., Rodriguez, Jorge, Hazen, Terry C., Alm, Eric J., and Humbert, Jean -Francois. A novel analysis method for paired-sample microbial ecology experiments. United States: N. p., 2016. Web. doi:10.1371/journal.pone.0154804.
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. A novel analysis method for paired-sample microbial ecology experiments. United States. https://doi.org/10.1371/journal.pone.0154804
Olesen, Scott W., Vora, Suhani, Techtmann, Stephen M., Fortney, Julian L., Bastidas-Oyanedel, Juan R., Rodriguez, Jorge, Hazen, Terry C., Alm, Eric J., and Humbert, Jean -Francois. 2016. "A novel analysis method for paired-sample microbial ecology experiments". United States. https://doi.org/10.1371/journal.pone.0154804. https://www.osti.gov/servlets/purl/1327714.
@article{osti_1327714,
title = {A novel analysis method for paired-sample microbial ecology experiments},
author = {Olesen, Scott W. and Vora, Suhani and Techtmann, Stephen M. and Fortney, Julian L. and Bastidas-Oyanedel, Juan R. and Rodriguez, Jorge and Hazen, Terry C. and Alm, Eric J. and Humbert, Jean -Francois},
abstractNote = {This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. 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. 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".},
doi = {10.1371/journal.pone.0154804},
url = {https://www.osti.gov/biblio/1327714}, journal = {PLoS ONE},
issn = {1932-6203},
number = 5,
volume = 11,
place = {United States},
year = {Fri May 06 00:00:00 EDT 2016},
month = {Fri May 06 00:00:00 EDT 2016}
}

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Cited by: 5 works
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Works referenced in this record:

Associations between species and groups of sites: indices and statistical inference
journal, December 2009


Maricurvus nonylphenolicus gen. nov., sp. nov., a nonylphenol-degrading bacterium isolated from seawater
journal, December 2011


Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB
journal, July 2006


Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data
journal, December 2012


Development of membrane inlet mass spectrometry for examination of fermentation processes
journal, December 2010


PyNAST: a flexible tool for aligning sequences to a template alignment
journal, November 2009


DNA-based stable isotope probing coupled with cultivation methods implicates Methylophaga in hydrocarbon degradation
journal, January 2014


Effects of crude oil on marine microbial communities in short term outdoor microcosms
journal, October 2010


Database indexing for production MegaBLAST searches
journal, June 2008


Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework
journal, October 2007


Aestuariicella hydrocarbonica gen. nov., sp. nov., an aliphatic hydrocarbon-degrading bacterium isolated from a sea tidal flat
journal, June 2015


Estimating prokaryotic diversity and its limits
journal, July 2002


The lognormal distribution is not an appropriate null hypothesis for the species-abundance distribution
journal, May 2005


The Unique Chemistry of Eastern Mediterranean Water Masses Selects for Distinct Microbial Communities by Depth
journal, March 2015


Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill
journal, August 2013


Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance
journal, October 2012


FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010


APE: Analyses of Phylogenetics and Evolution in R language
journal, January 2004


Analyzing Spatial Structure of Communities Using the Two‐Dimensional Poisson Lognormal Species Abundance Model
journal, July 2002


Search and clustering orders of magnitude faster than BLAST
journal, August 2010


Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
journal, January 2011


Patterns of relative species abundance in rainforests and coral reefs
journal, November 2007


UPARSE: highly accurate OTU sequences from microbial amplicon reads
journal, August 2013


Inferring Correlation Networks from Genomic Survey Data
journal, September 2012


Effects of crude oil on marine microbial communities in short term outdoor microcosms
journal, October 2010


Development of membrane inlet mass spectrometry for examination of fermentation processes
journal, December 2010


Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill
journal, August 2013


Patterns of relative species abundance in rainforests and coral reefs
journal, November 2007


Site-specific molecular analysis of the bacteriota on worn spectacles
journal, March 2020


Comparative analysis of racial differences in breast tumor microbiome
journal, August 2020


Analyzing Spatial Structure of Communities Using the Two‐Dimensional Poisson Lognormal Species Abundance Model
journal, July 2002


APE: Analyses of Phylogenetics and Evolution in R language
journal, January 2004


Database indexing for production MegaBLAST searches
journal, June 2008


PyNAST: a flexible tool for aligning sequences to a template alignment
journal, November 2009


Search and clustering orders of magnitude faster than BLAST
journal, August 2010


Error filtering, pair assembly and error correction for next-generation sequencing reads
journal, July 2015


Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons
journal, January 2011


Species abundance distributions: moving beyond single prediction theories to integration within an ecological framework
journal, October 2007


Maricurvus nonylphenolicus gen. nov., sp. nov., a nonylphenol-degrading bacterium isolated from seawater
journal, December 2011


Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
journal, June 2007


Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit
journal, August 2013


Critical Evaluation of the Volumetric "Bottle Effect" on Microbial Batch Growth
journal, December 2009


Inferring Correlation Networks from Genomic Survey Data
journal, September 2012


Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data
journal, December 2012


Species Assemblages and Indicator Species: The Need for a Flexible Asymmetrical Approach
journal, August 1997


DNA-based stable isotope probing coupled with cultivation methods implicates Methylophaga in hydrocarbon degradation
journal, January 2014


Works referencing / citing this record:

Generalized Hotelling's test for paired compositional data with application to human microbiome studies
journal, May 2018


Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations
journal, January 2017


Oil Hydrocarbon Degradation by Caspian Sea Microbial Communities
journal, May 2019


Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations
journal, January 2017