The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects

Research output: Contribution to journalArticleAcademicpeer-review

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Abstract

Large-scale cohort studies are currently being designed to investigate the human microbiome in health and disease. Adequate sampling strategies are required to limit bias due to shifts in microbial communities during sampling and storage. Therefore, we examined the impact of different sampling and storage conditions on the stability of fecal microbial communities in healthy and diseased subjects. Fecal samples from 10 healthy controls, 10 irritable bowel syndrome and 8 inflammatory bowel disease patients were collected on site, aliquoted immediately after defecation and stored at -80 degrees C, -20 degrees C for 1 week, at +4 degrees C or room temperature for 24 hours. Fecal transport swabs (FecalSwab, Copan) were collected and stored for 48-72 hours at room temperature. We used pyrosequencing of the 16S gene to investigate the stability of microbial communities. Alpha diversity did not differ between all storage methods and -80 degrees C, except for the fecal swabs. UPGMA clustering and principal coordinate analysis showed significant clustering by test subject (p<0.001) but not by storage method. Bray-Curtis dissimilarity and (un)weighted UniFrac showed a significant higher distance between fecal swabs and -80 degrees C versus the other methods and -80 degrees C samples (p<0.009). The relative abundance of Ruminococcus and Enterobacteriaceae did not differ between the storage methods versus -80 degrees C, but was higher in fecal swabs (p<0.05). Storage up to 24 hours (at +4 degrees C or room temperature) or freezing at -20 degrees C did not significantly alter the fecal microbial community structure compared to direct freezing of samples from healthy subjects and patients with gastrointestinal disorders.
Original languageEnglish
Article numbere0126685
Number of pages15
JournalPLOS ONE
Volume10
Issue number5
DOIs
Publication statusPublished - 29 May 2015

Keywords

  • INTESTINAL MICROBIOTA
  • COMMUNITIES
  • EFFICACY

Cite this

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title = "The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects",
abstract = "Large-scale cohort studies are currently being designed to investigate the human microbiome in health and disease. Adequate sampling strategies are required to limit bias due to shifts in microbial communities during sampling and storage. Therefore, we examined the impact of different sampling and storage conditions on the stability of fecal microbial communities in healthy and diseased subjects. Fecal samples from 10 healthy controls, 10 irritable bowel syndrome and 8 inflammatory bowel disease patients were collected on site, aliquoted immediately after defecation and stored at -80 degrees C, -20 degrees C for 1 week, at +4 degrees C or room temperature for 24 hours. Fecal transport swabs (FecalSwab, Copan) were collected and stored for 48-72 hours at room temperature. We used pyrosequencing of the 16S gene to investigate the stability of microbial communities. Alpha diversity did not differ between all storage methods and -80 degrees C, except for the fecal swabs. UPGMA clustering and principal coordinate analysis showed significant clustering by test subject (p<0.001) but not by storage method. Bray-Curtis dissimilarity and (un)weighted UniFrac showed a significant higher distance between fecal swabs and -80 degrees C versus the other methods and -80 degrees C samples (p<0.009). The relative abundance of Ruminococcus and Enterobacteriaceae did not differ between the storage methods versus -80 degrees C, but was higher in fecal swabs (p<0.05). Storage up to 24 hours (at +4 degrees C or room temperature) or freezing at -20 degrees C did not significantly alter the fecal microbial community structure compared to direct freezing of samples from healthy subjects and patients with gastrointestinal disorders.",
keywords = "INTESTINAL MICROBIOTA, COMMUNITIES, EFFICACY",
author = "D.I. Tedjo and D.M.A.E. Jonkers and P.H. Savelkoul and A.A. Masclee and {van Best}, N. and M.J. Pierik and J. Penders",
year = "2015",
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The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects. / Tedjo, D.I.; Jonkers, D.M.A.E.; Savelkoul, P.H.; Masclee, A.A.; van Best, N.; Pierik, M.J.; Penders, J.

In: PLOS ONE, Vol. 10, No. 5, e0126685, 29.05.2015.

Research output: Contribution to journalArticleAcademicpeer-review

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T1 - The Effect of Sampling and Storage on the Fecal Microbiota Composition in Healthy and Diseased Subjects

AU - Tedjo, D.I.

AU - Jonkers, D.M.A.E.

AU - Savelkoul, P.H.

AU - Masclee, A.A.

AU - van Best, N.

AU - Pierik, M.J.

AU - Penders, J.

PY - 2015/5/29

Y1 - 2015/5/29

N2 - Large-scale cohort studies are currently being designed to investigate the human microbiome in health and disease. Adequate sampling strategies are required to limit bias due to shifts in microbial communities during sampling and storage. Therefore, we examined the impact of different sampling and storage conditions on the stability of fecal microbial communities in healthy and diseased subjects. Fecal samples from 10 healthy controls, 10 irritable bowel syndrome and 8 inflammatory bowel disease patients were collected on site, aliquoted immediately after defecation and stored at -80 degrees C, -20 degrees C for 1 week, at +4 degrees C or room temperature for 24 hours. Fecal transport swabs (FecalSwab, Copan) were collected and stored for 48-72 hours at room temperature. We used pyrosequencing of the 16S gene to investigate the stability of microbial communities. Alpha diversity did not differ between all storage methods and -80 degrees C, except for the fecal swabs. UPGMA clustering and principal coordinate analysis showed significant clustering by test subject (p<0.001) but not by storage method. Bray-Curtis dissimilarity and (un)weighted UniFrac showed a significant higher distance between fecal swabs and -80 degrees C versus the other methods and -80 degrees C samples (p<0.009). The relative abundance of Ruminococcus and Enterobacteriaceae did not differ between the storage methods versus -80 degrees C, but was higher in fecal swabs (p<0.05). Storage up to 24 hours (at +4 degrees C or room temperature) or freezing at -20 degrees C did not significantly alter the fecal microbial community structure compared to direct freezing of samples from healthy subjects and patients with gastrointestinal disorders.

AB - Large-scale cohort studies are currently being designed to investigate the human microbiome in health and disease. Adequate sampling strategies are required to limit bias due to shifts in microbial communities during sampling and storage. Therefore, we examined the impact of different sampling and storage conditions on the stability of fecal microbial communities in healthy and diseased subjects. Fecal samples from 10 healthy controls, 10 irritable bowel syndrome and 8 inflammatory bowel disease patients were collected on site, aliquoted immediately after defecation and stored at -80 degrees C, -20 degrees C for 1 week, at +4 degrees C or room temperature for 24 hours. Fecal transport swabs (FecalSwab, Copan) were collected and stored for 48-72 hours at room temperature. We used pyrosequencing of the 16S gene to investigate the stability of microbial communities. Alpha diversity did not differ between all storage methods and -80 degrees C, except for the fecal swabs. UPGMA clustering and principal coordinate analysis showed significant clustering by test subject (p<0.001) but not by storage method. Bray-Curtis dissimilarity and (un)weighted UniFrac showed a significant higher distance between fecal swabs and -80 degrees C versus the other methods and -80 degrees C samples (p<0.009). The relative abundance of Ruminococcus and Enterobacteriaceae did not differ between the storage methods versus -80 degrees C, but was higher in fecal swabs (p<0.05). Storage up to 24 hours (at +4 degrees C or room temperature) or freezing at -20 degrees C did not significantly alter the fecal microbial community structure compared to direct freezing of samples from healthy subjects and patients with gastrointestinal disorders.

KW - INTESTINAL MICROBIOTA

KW - COMMUNITIES

KW - EFFICACY

U2 - 10.1371/journal.pone.0126685

DO - 10.1371/journal.pone.0126685

M3 - Article

VL - 10

JO - PLOS ONE

JF - PLOS ONE

SN - 1932-6203

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M1 - e0126685

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