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Variations of Gut Microbiome Profile Under Different Storage Conditions and Preservation Periods: A Multi-Dimensional Evaluation
Gut dysbiosis is heavily involved in the development of various human diseases. There are thousands of publications per year for investigating the role of gut microbiota in diseases. However, emerging evidence has indicated the frequent data inconsistency between different studies, which is largely...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267014/ https://www.ncbi.nlm.nih.gov/pubmed/32536906 http://dx.doi.org/10.3389/fmicb.2020.00972 |
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author | Ma, Junli Sheng, Lili Hong, Ying Xi, Chuchu Gu, Yu Zheng, Ningning Li, Mengci Chen, Linlin Wu, Gaosong Li, Yue Yan, Juan Han, Ruiting Li, Bingbing Qiu, Huihui Zhong, Jing Jia, Wei Li, Houkai |
author_facet | Ma, Junli Sheng, Lili Hong, Ying Xi, Chuchu Gu, Yu Zheng, Ningning Li, Mengci Chen, Linlin Wu, Gaosong Li, Yue Yan, Juan Han, Ruiting Li, Bingbing Qiu, Huihui Zhong, Jing Jia, Wei Li, Houkai |
author_sort | Ma, Junli |
collection | PubMed |
description | Gut dysbiosis is heavily involved in the development of various human diseases. There are thousands of publications per year for investigating the role of gut microbiota in diseases. However, emerging evidence has indicated the frequent data inconsistency between different studies, which is largely overlooked. There are many factors that can cause data variation and inconsistency during the process of microbiota study, in particular, sample storage conditions and sequencing process. Here, we systemically evaluated the impacts of six fecal sample storage conditions (three non-commercial storage protocols, −80°C, −80°C with 70% ethanol (ET_−80°C), 4°C with 70% ethanol (ET_4°C), and three commercial storage reagents, OMNIgeneGUT OMR-200 (GT) and MGIEasy (MGIE) at room temperature, and Longsee at 4°C (LS) on gut microbiome profile based on 16S rRNA gene sequencing. In addition, we also investigated the impacts of storage periods (1 and 2 weeks, or 6 months) and sequencing platform on microbiome profile. The efficacy of storage conditions was evaluated by DNA yield and quality, α and β diversity, relative abundance of the dominant and functional bacteria associated with short-chain fatty acid (SCFA) production, and BAs metabolism. Our current study suggested that −80°C was acceptable for fecal sample storage, and the addition of 70% ethanol had some benefits in maintaining the microbial community structure. Meanwhile, we found that samples in ET_4°C and GT reagents were comparable, both of them introduced some biases in α or β diversity, and the relative abundance of functional bacteria. Samples stored in MGIE reagent resulted in the least variation, whereas the most obvious variations were introduced by LS reagents. In addition, our results indicated that variations caused by storage condition were larger than that of storage time and sequencing platform. Collectively, our study provided a multi-dimensional evaluation on the impacts of storage conditions, storage time periods, and sequencing platform on gut microbial profile. |
format | Online Article Text |
id | pubmed-7267014 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-72670142020-06-12 Variations of Gut Microbiome Profile Under Different Storage Conditions and Preservation Periods: A Multi-Dimensional Evaluation Ma, Junli Sheng, Lili Hong, Ying Xi, Chuchu Gu, Yu Zheng, Ningning Li, Mengci Chen, Linlin Wu, Gaosong Li, Yue Yan, Juan Han, Ruiting Li, Bingbing Qiu, Huihui Zhong, Jing Jia, Wei Li, Houkai Front Microbiol Microbiology Gut dysbiosis is heavily involved in the development of various human diseases. There are thousands of publications per year for investigating the role of gut microbiota in diseases. However, emerging evidence has indicated the frequent data inconsistency between different studies, which is largely overlooked. There are many factors that can cause data variation and inconsistency during the process of microbiota study, in particular, sample storage conditions and sequencing process. Here, we systemically evaluated the impacts of six fecal sample storage conditions (three non-commercial storage protocols, −80°C, −80°C with 70% ethanol (ET_−80°C), 4°C with 70% ethanol (ET_4°C), and three commercial storage reagents, OMNIgeneGUT OMR-200 (GT) and MGIEasy (MGIE) at room temperature, and Longsee at 4°C (LS) on gut microbiome profile based on 16S rRNA gene sequencing. In addition, we also investigated the impacts of storage periods (1 and 2 weeks, or 6 months) and sequencing platform on microbiome profile. The efficacy of storage conditions was evaluated by DNA yield and quality, α and β diversity, relative abundance of the dominant and functional bacteria associated with short-chain fatty acid (SCFA) production, and BAs metabolism. Our current study suggested that −80°C was acceptable for fecal sample storage, and the addition of 70% ethanol had some benefits in maintaining the microbial community structure. Meanwhile, we found that samples in ET_4°C and GT reagents were comparable, both of them introduced some biases in α or β diversity, and the relative abundance of functional bacteria. Samples stored in MGIE reagent resulted in the least variation, whereas the most obvious variations were introduced by LS reagents. In addition, our results indicated that variations caused by storage condition were larger than that of storage time and sequencing platform. Collectively, our study provided a multi-dimensional evaluation on the impacts of storage conditions, storage time periods, and sequencing platform on gut microbial profile. Frontiers Media S.A. 2020-05-27 /pmc/articles/PMC7267014/ /pubmed/32536906 http://dx.doi.org/10.3389/fmicb.2020.00972 Text en Copyright © 2020 Ma, Sheng, Hong, Xi, Gu, Zheng, Li, Chen, Wu, Li, Yan, Han, Li, Qiu, Zhong, Jia and Li. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Ma, Junli Sheng, Lili Hong, Ying Xi, Chuchu Gu, Yu Zheng, Ningning Li, Mengci Chen, Linlin Wu, Gaosong Li, Yue Yan, Juan Han, Ruiting Li, Bingbing Qiu, Huihui Zhong, Jing Jia, Wei Li, Houkai Variations of Gut Microbiome Profile Under Different Storage Conditions and Preservation Periods: A Multi-Dimensional Evaluation |
title | Variations of Gut Microbiome Profile Under Different Storage Conditions and Preservation Periods: A Multi-Dimensional Evaluation |
title_full | Variations of Gut Microbiome Profile Under Different Storage Conditions and Preservation Periods: A Multi-Dimensional Evaluation |
title_fullStr | Variations of Gut Microbiome Profile Under Different Storage Conditions and Preservation Periods: A Multi-Dimensional Evaluation |
title_full_unstemmed | Variations of Gut Microbiome Profile Under Different Storage Conditions and Preservation Periods: A Multi-Dimensional Evaluation |
title_short | Variations of Gut Microbiome Profile Under Different Storage Conditions and Preservation Periods: A Multi-Dimensional Evaluation |
title_sort | variations of gut microbiome profile under different storage conditions and preservation periods: a multi-dimensional evaluation |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7267014/ https://www.ncbi.nlm.nih.gov/pubmed/32536906 http://dx.doi.org/10.3389/fmicb.2020.00972 |
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