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

ABSTRACT 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 cla...

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Autores principales:	Amnon Amir, Daniel McDonald, Jose A. Navas-Molina, Justine Debelius, James T. Morton, Embriette Hyde, Adam Robbins-Pianka, Rob Knight
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	16S rRNA DNA sequencing bioinformatics Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/2c012213eb6846f487fefae97b198374
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spelling	oai:doaj.org-article:2c012213eb6846f487fefae97b1983742021-12-02T19:45:29ZCorrecting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping10.1128/mSystems.00199-162379-5077https://doaj.org/article/2c012213eb6846f487fefae97b1983742017-04-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00199-16https://doaj.org/toc/2379-5077ABSTRACT 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.Amnon AmirDaniel McDonaldJose A. Navas-MolinaJustine DebeliusJames T. MortonEmbriette HydeAdam Robbins-PiankaRob KnightAmerican Society for Microbiologyarticle16S rRNADNA sequencingbioinformaticsMicrobiologyQR1-502ENmSystems, Vol 2, Iss 2 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	16S rRNA DNA sequencing bioinformatics Microbiology QR1-502
spellingShingle	16S rRNA DNA sequencing bioinformatics Microbiology QR1-502 Amnon Amir Daniel McDonald Jose A. Navas-Molina Justine Debelius James T. Morton Embriette Hyde Adam Robbins-Pianka Rob Knight Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping
description	ABSTRACT 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.
format	article
author	Amnon Amir Daniel McDonald Jose A. Navas-Molina Justine Debelius James T. Morton Embriette Hyde Adam Robbins-Pianka Rob Knight
author_facet	Amnon Amir Daniel McDonald Jose A. Navas-Molina Justine Debelius James T. Morton Embriette Hyde Adam Robbins-Pianka Rob Knight
author_sort	Amnon Amir
title	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_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_sort	correcting for microbial blooms in fecal samples during room-temperature shipping
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/2c012213eb6846f487fefae97b198374
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Correcting for Microbial Blooms in Fecal Samples during Room-Temperature Shipping

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