Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
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
_version_ 1783541416374304768
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
work_keys_str_mv AT majunli variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT shenglili variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT hongying variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT xichuchu variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT guyu variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT zhengningning variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT limengci variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT chenlinlin variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT wugaosong variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT liyue variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT yanjuan variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT hanruiting variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT libingbing variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT qiuhuihui variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT zhongjing variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT jiawei variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation
AT lihoukai variationsofgutmicrobiomeprofileunderdifferentstorageconditionsandpreservationperiodsamultidimensionalevaluation