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Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping

The use of sterile swabs is a convenient and common way to collect microbiome samples, and many studies have shown that the effects of room-temperature storage are smaller than physiologically relevant differences between subjects. However, several bacterial taxa, notably members of the class Gammap...

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Autores principales: Amir, Amnon, McDonald, Daniel, Navas-Molina, Jose A., Debelius, Justine, Morton, James T., Hyde, Embriette, Robbins-Pianka, Adam, Knight, Rob
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340865/
https://www.ncbi.nlm.nih.gov/pubmed/28289733
http://dx.doi.org/10.1128/mSystems.00199-16
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author Amir, Amnon
McDonald, Daniel
Navas-Molina, Jose A.
Debelius, Justine
Morton, James T.
Hyde, Embriette
Robbins-Pianka, Adam
Knight, Rob
author_facet Amir, Amnon
McDonald, Daniel
Navas-Molina, Jose A.
Debelius, Justine
Morton, James T.
Hyde, Embriette
Robbins-Pianka, Adam
Knight, Rob
author_sort Amir, Amnon
collection PubMed
description The use of sterile swabs is a convenient and common way to collect microbiome samples, and many studies have shown that the effects of room-temperature storage are smaller than physiologically relevant differences between subjects. However, several bacterial taxa, notably members of the class Gammaproteobacteria, grow at room temperature, sometimes confusing microbiome results, particularly when stability is assumed. Although comparative benchmarking has shown that several preservation methods, including the use of 95% ethanol, fecal occult blood test (FOBT) and FTA cards, and Omnigene-GUT kits, reduce changes in taxon abundance during room-temperature storage, these techniques all have drawbacks and cannot be applied retrospectively to samples that have already been collected. Here we performed a meta-analysis using several different microbiome sample storage condition studies, showing consistent trends in which specific bacteria grew (i.e., “bloomed”) at room temperature, and introduce a procedure for removing the sequences that most distort analyses. In contrast to similarity-based clustering using operational taxonomic units (OTUs), we use a new technique called “Deblur” to identify the exact sequences corresponding to blooming taxa, greatly reducing false positives and also dramatically decreasing runtime. We show that applying this technique to samples collected for the American Gut Project (AGP), for which participants simply mail samples back without the use of ice packs or other preservatives, yields results consistent with published microbiome studies performed with frozen or otherwise preserved samples. IMPORTANCE In many microbiome studies, the necessity to store samples at room temperature (i.e., remote fieldwork) and the ability to ship samples without hazardous materials that require special handling training, such as ethanol (i.e., citizen science efforts), is paramount. However, although room-temperature storage for a few days has been shown not to obscure physiologically relevant microbiome differences between comparison groups, there are still changes in specific bacterial taxa, notably, in members of the class Gammaproteobacteria, that can make microbiome profiles difficult to interpret. Here we identify the most problematic taxa and show that removing sequences from just a few fast-growing taxa is sufficient to correct microbiome profiles.
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spelling pubmed-53408652017-03-13 Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping Amir, Amnon McDonald, Daniel Navas-Molina, Jose A. Debelius, Justine Morton, James T. Hyde, Embriette Robbins-Pianka, Adam Knight, Rob mSystems Observation The use of sterile swabs is a convenient and common way to collect microbiome samples, and many studies have shown that the effects of room-temperature storage are smaller than physiologically relevant differences between subjects. However, several bacterial taxa, notably members of the class Gammaproteobacteria, grow at room temperature, sometimes confusing microbiome results, particularly when stability is assumed. Although comparative benchmarking has shown that several preservation methods, including the use of 95% ethanol, fecal occult blood test (FOBT) and FTA cards, and Omnigene-GUT kits, reduce changes in taxon abundance during room-temperature storage, these techniques all have drawbacks and cannot be applied retrospectively to samples that have already been collected. Here we performed a meta-analysis using several different microbiome sample storage condition studies, showing consistent trends in which specific bacteria grew (i.e., “bloomed”) at room temperature, and introduce a procedure for removing the sequences that most distort analyses. In contrast to similarity-based clustering using operational taxonomic units (OTUs), we use a new technique called “Deblur” to identify the exact sequences corresponding to blooming taxa, greatly reducing false positives and also dramatically decreasing runtime. We show that applying this technique to samples collected for the American Gut Project (AGP), for which participants simply mail samples back without the use of ice packs or other preservatives, yields results consistent with published microbiome studies performed with frozen or otherwise preserved samples. IMPORTANCE In many microbiome studies, the necessity to store samples at room temperature (i.e., remote fieldwork) and the ability to ship samples without hazardous materials that require special handling training, such as ethanol (i.e., citizen science efforts), is paramount. However, although room-temperature storage for a few days has been shown not to obscure physiologically relevant microbiome differences between comparison groups, there are still changes in specific bacterial taxa, notably, in members of the class Gammaproteobacteria, that can make microbiome profiles difficult to interpret. Here we identify the most problematic taxa and show that removing sequences from just a few fast-growing taxa is sufficient to correct microbiome profiles. American Society for Microbiology 2017-03-07 /pmc/articles/PMC5340865/ /pubmed/28289733 http://dx.doi.org/10.1128/mSystems.00199-16 Text en Copyright © 2017 Amir et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/) .
spellingShingle Observation
Amir, Amnon
McDonald, Daniel
Navas-Molina, Jose A.
Debelius, Justine
Morton, James T.
Hyde, Embriette
Robbins-Pianka, Adam
Knight, Rob
Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping
title Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping
title_full Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping
title_fullStr Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping
title_full_unstemmed Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping
title_short Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping
title_sort correcting for microbial blooms in fecal samples during room-temperature shipping
topic Observation
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340865/
https://www.ncbi.nlm.nih.gov/pubmed/28289733
http://dx.doi.org/10.1128/mSystems.00199-16
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