Long‐term stability of microbiome diversity and composition in fecal samples stored in eNAT medium
Abstract Fecal samples collected for microbiome analyses are typically frozen to avoid postcollection changes in microbial composition. eNAT is a guanidine thiocyanate‐based medium that stabilizes microbial DNA and allows safe specimen handling and shipping by inactivating microorganisms. We collect...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2020-07-01
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| Series: | MicrobiologyOpen |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/mbo3.1046 |
| _version_ | 1818293932075778048 |
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| author | Rebecca R. Young Kirsten Jenkins Felix Araujo‐Perez Patrick C. Seed Matthew S. Kelly |
| author_facet | Rebecca R. Young Kirsten Jenkins Felix Araujo‐Perez Patrick C. Seed Matthew S. Kelly |
| author_sort | Rebecca R. Young |
| collection | DOAJ |
| description | Abstract Fecal samples collected for microbiome analyses are typically frozen to avoid postcollection changes in microbial composition. eNAT is a guanidine thiocyanate‐based medium that stabilizes microbial DNA and allows safe specimen handling and shipping by inactivating microorganisms. We collected fecal samples (n = 50) from children undergoing hematopoietic stem cell transplantation. We divided samples into three aliquots: (a) stored in RNAlater and immediately transferred to −80°C; (b) stored in eNAT medium and immediately transferred to −80°C; and (c) stored in eNAT medium at ambient temperature (~20°C) for 30 days prior to transfer to −80°C. Mean (standard deviation) Shannon diversity and Chao1 indices in sample aliquots were 2.05 (0.62) and 23.8 (16.6), respectively. Comparing samples frozen immediately in RNAlater to samples frozen immediately in eNAT, there were no differences in Shannon diversity (p = .51), Chao1 richness (p = .66), and overall microbiome composition (p = .99). Comparing eNAT samples frozen immediately to samples stored at ambient temperature, we identified no differences in Shannon diversity (p = .65), Chao1 richness (p = .87), and overall microbiome composition (p = .99). Storage of fecal samples in eNAT at ambient temperature for 30 days did not alter microbiome richness, diversity, or composition. eNAT may be a useful medium for fecal microbiome studies, particularly when cold chain storage is unavailable. |
| first_indexed | 2024-12-13T03:23:42Z |
| format | Article |
| id | doaj.art-bcff646b1ce8417389bcade08c81de2f |
| institution | Directory Open Access Journal |
| issn | 2045-8827 |
| language | English |
| last_indexed | 2024-12-13T03:23:42Z |
| publishDate | 2020-07-01 |
| publisher | Wiley |
| record_format | Article |
| series | MicrobiologyOpen |
| spelling | doaj.art-bcff646b1ce8417389bcade08c81de2f2022-12-22T00:01:18ZengWileyMicrobiologyOpen2045-88272020-07-0197n/an/a10.1002/mbo3.1046Long‐term stability of microbiome diversity and composition in fecal samples stored in eNAT mediumRebecca R. Young0Kirsten Jenkins1Felix Araujo‐Perez2Patrick C. Seed3Matthew S. Kelly4Division of Pediatric Infectious Diseases Duke University Durham NC USADivision of Pediatric Infectious Diseases Duke University Durham NC USADepartment of Pediatrics Feinberg School of Medicine Northwestern University Chicago IL USADepartment of Pediatrics Feinberg School of Medicine Northwestern University Chicago IL USADivision of Pediatric Infectious Diseases Duke University Durham NC USAAbstract Fecal samples collected for microbiome analyses are typically frozen to avoid postcollection changes in microbial composition. eNAT is a guanidine thiocyanate‐based medium that stabilizes microbial DNA and allows safe specimen handling and shipping by inactivating microorganisms. We collected fecal samples (n = 50) from children undergoing hematopoietic stem cell transplantation. We divided samples into three aliquots: (a) stored in RNAlater and immediately transferred to −80°C; (b) stored in eNAT medium and immediately transferred to −80°C; and (c) stored in eNAT medium at ambient temperature (~20°C) for 30 days prior to transfer to −80°C. Mean (standard deviation) Shannon diversity and Chao1 indices in sample aliquots were 2.05 (0.62) and 23.8 (16.6), respectively. Comparing samples frozen immediately in RNAlater to samples frozen immediately in eNAT, there were no differences in Shannon diversity (p = .51), Chao1 richness (p = .66), and overall microbiome composition (p = .99). Comparing eNAT samples frozen immediately to samples stored at ambient temperature, we identified no differences in Shannon diversity (p = .65), Chao1 richness (p = .87), and overall microbiome composition (p = .99). Storage of fecal samples in eNAT at ambient temperature for 30 days did not alter microbiome richness, diversity, or composition. eNAT may be a useful medium for fecal microbiome studies, particularly when cold chain storage is unavailable.https://doi.org/10.1002/mbo3.104616S rRNA sequencingbacterial inactivationbiological sample shippingstabilization media |
| spellingShingle | Rebecca R. Young Kirsten Jenkins Felix Araujo‐Perez Patrick C. Seed Matthew S. Kelly Long‐term stability of microbiome diversity and composition in fecal samples stored in eNAT medium MicrobiologyOpen 16S rRNA sequencing bacterial inactivation biological sample shipping stabilization media |
| title | Long‐term stability of microbiome diversity and composition in fecal samples stored in eNAT medium |
| title_full | Long‐term stability of microbiome diversity and composition in fecal samples stored in eNAT medium |
| title_fullStr | Long‐term stability of microbiome diversity and composition in fecal samples stored in eNAT medium |
| title_full_unstemmed | Long‐term stability of microbiome diversity and composition in fecal samples stored in eNAT medium |
| title_short | Long‐term stability of microbiome diversity and composition in fecal samples stored in eNAT medium |
| title_sort | long term stability of microbiome diversity and composition in fecal samples stored in enat medium |
| topic | 16S rRNA sequencing bacterial inactivation biological sample shipping stabilization media |
| url | https://doi.org/10.1002/mbo3.1046 |
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