A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments
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 samp...
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| Format: | Article |
| Language: | en_US |
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Public Library of Science
2017
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| Online Access: | http://hdl.handle.net/1721.1/109394 https://orcid.org/0000-0001-8294-9364 https://orcid.org/0000-0001-5400-4945 |
| _version_ | 1826215950627635200 |
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| author | Techtmann, Stephen M. Fortney, Julian L. Bastidas-Oyanedel, Juan R. Rodríguez, Jorge Hazen, Terry C. Alm, Eric J Olesen, Scott Wilder Vora, Suhani Deepak |
| author2 | Massachusetts Institute of Technology. Department of Biological Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Biological Engineering Techtmann, Stephen M. Fortney, Julian L. Bastidas-Oyanedel, Juan R. Rodríguez, Jorge Hazen, Terry C. Alm, Eric J Olesen, Scott Wilder Vora, Suhani Deepak |
| author_sort | Techtmann, Stephen M. |
| collection | MIT |
| description | 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”. |
| first_indexed | 2024-09-23T16:40:04Z |
| format | Article |
| id | mit-1721.1/109394 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T16:40:04Z |
| publishDate | 2017 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | mit-1721.1/1093942022-09-29T20:38:51Z A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments Techtmann, Stephen M. Fortney, Julian L. Bastidas-Oyanedel, Juan R. Rodríguez, Jorge Hazen, Terry C. Alm, Eric J Olesen, Scott Wilder Vora, Suhani Deepak Massachusetts Institute of Technology. Department of Biological Engineering Alm, Eric J Olesen, Scott Wilder Vora, Suhani Deepak 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”. BP (Firm) (MIT Energy Initiative Grant No. 6926835) National Science Foundation (U.S.) (Grant No. 0821391) National Science Foundation (U.S.). Graduate Research Fellowship Program (Grant No. 1122374) 2017-05-26T21:25:00Z 2017-05-26T21:25:00Z 2016-05 2015-10 Article http://purl.org/eprint/type/JournalArticle 1932-6203 http://hdl.handle.net/1721.1/109394 Olesen, Scott W., Suhani Vora, Stephen M. Techtmann, Julian L. Fortney, Juan R. Bastidas-Oyanedel, Jorge Rodríguez, Terry C. Hazen, and Eric J. Alm. “A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.” Edited by Jean-François Humbert. PLoS ONE 11, no. 5 (May 6, 2016): e0154804. https://orcid.org/0000-0001-8294-9364 https://orcid.org/0000-0001-5400-4945 en_US http://dx.doi.org/10.1371/journal.pone.0154804 PLoS ONE Creative Commons CC0 https://creativecommons.org/publicdomain/zero/1.0/ application/pdf Public Library of Science PLOS |
| spellingShingle | Techtmann, Stephen M. Fortney, Julian L. Bastidas-Oyanedel, Juan R. Rodríguez, Jorge Hazen, Terry C. Alm, Eric J Olesen, Scott Wilder Vora, Suhani Deepak A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments |
| title | A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments |
| title_full | A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments |
| title_fullStr | A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments |
| title_full_unstemmed | A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments |
| title_short | A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments |
| title_sort | novel analysis method for paired sample microbial ecology experiments |
| url | http://hdl.handle.net/1721.1/109394 https://orcid.org/0000-0001-8294-9364 https://orcid.org/0000-0001-5400-4945 |
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