1
|
Elie C, Perret M, Hage H, Sentausa E, Hesketh A, Louis K, Fritah-Lafont A, Leissner P, Vachon C, Rostaing H, Reynier F, Gervasi G, Saliou A. Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome. Sci Rep 2023; 13:10279. [PMID: 37355726 PMCID: PMC10290636 DOI: 10.1038/s41598-023-33959-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/21/2023] [Indexed: 06/26/2023] Open
Abstract
The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to compare DNA extraction protocols for 16S sequencing. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) upstream DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and 16S sequenced. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates. SPD improved overall efficiency of three of the four tested protocols compared with their commercial version, in terms of DNA extraction yield, sample alpha-diversity, and recovery of Gram-positive bacteria. The best overall performance was obtained for the S-DQ protocol, SPD combined with the DNeasy PowerLyser PowerSoil protocol from QIAGEN. Based on this evaluation, we strongly believe that the use of such stool preprocessing device improves both the standardization and the quality of the DNA extraction in the human gut microbiome studies.
Collapse
Affiliation(s)
- Céline Elie
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Magali Perret
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Hayat Hage
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Erwin Sentausa
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Amy Hesketh
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Karen Louis
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Asmaà Fritah-Lafont
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Philippe Leissner
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Carole Vachon
- bioMérieux, 5 Rue des Berges, 38000, Grenoble, France
| | | | - Frédéric Reynier
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France
| | - Gaspard Gervasi
- bioMérieux, 376 Chemin de l'Orme, 69280, Marcy-l'Étoile, France
| | - Adrien Saliou
- BIOASTER, Microbiology Research Institute, 40 avenue Tony Garnier, 69007, Lyon, France.
| |
Collapse
|
2
|
Porath‐Krause A, Strauss AT, Henning JA, Seabloom EW, Borer ET. Pitfalls and pointers: An accessible guide to marker gene amplicon sequencing in ecological applications. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Anita Porath‐Krause
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Alexander T. Strauss
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Jeremiah A. Henning
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Eric W. Seabloom
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| | - Elizabeth T. Borer
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
| |
Collapse
|
3
|
Sidiropoulos DN, Al-Ghalith GA, Shields-Cutler RR, Ward TL, Johnson AJ, Vangay P, Knights D, Kashyap PC, Xian Y, Ramer-Tait AE, Clayton JB. Wild primate microbiomes prevent weight gain in germ-free mice. Anim Microbiome 2020; 2:16. [PMID: 33499991 PMCID: PMC7807445 DOI: 10.1186/s42523-020-00033-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/14/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The gut microbiome harbors trillions of bacteria that play a major role in dietary nutrient extraction and host metabolism. Metabolic diseases such as obesity and diabetes are associated with shifts in microbiome composition and have been on the rise in Westernized or highly industrialized countries. At the same time, Westernized diets low in dietary fiber have been shown to cause loss of gut microbial diversity. However, the link between microbiome composition, loss of dietary fiber, and obesity has not been well defined. RESULTS To study the interactions between gut microbiota, dietary fiber, and weight gain, we transplanted captive and wild douc gut microbiota into germ-free mice and then exposed them to either a high- or low-fiber diet. The group receiving captive douc microbiota gained significantly more weight, regardless of diet, while mice receiving a high-fiber diet and wild douc microbiota remained lean. In the presence of a low-fiber diet, the wild douc microbiota partially prevented weight gain. Using 16S rRNA gene amplicon sequencing we identified key bacterial taxa in each group, specifically a high relative abundance of Bacteroides and Akkermansia in captive douc FMT mice and a higher relative abundance of Lactobacillus and Clostridium in the wild douc FMT mice. CONCLUSIONS In the context of our germ-free mouse experiment, wild douc microbiota could serve as a reservoir for microbes for cross-species transplants. Our results suggest that wild douc microbiota are tailored to diverse fiber diets and can prevent weight gain when exposed to a native diet.
Collapse
Affiliation(s)
- Dimitrios N Sidiropoulos
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
- Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Gabriel A Al-Ghalith
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Robin R Shields-Cutler
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
- Department of Biology, Macalester College, Saint Paul, MN, 55105, USA
| | - Tonya L Ward
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Abigail J Johnson
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
| | - Pajau Vangay
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Dan Knights
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, 55455, USA
- Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
- Department of Computer Science and Engineering, University of Minnesota, 4-192 Keller Hall, 200 Union St SE, Minneapolis, MN, 55455, USA
| | - Purna C Kashyap
- Enteric Neuroscience Program, Division of Gastroenterology & Hepatology, Departments of Medicine and Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, 55902, USA
| | - Yibo Xian
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Amanda E Ramer-Tait
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA
| | - Jonathan B Clayton
- Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN, 55108, USA.
- Primate Microbiome Project, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
- Department of Computer Science and Engineering, University of Minnesota, 4-192 Keller Hall, 200 Union St SE, Minneapolis, MN, 55455, USA.
- Present address: Department of Biology, University of Nebraska at Omaha, Omaha, NE, 68182, USA.
| |
Collapse
|
4
|
Martínez N, Hidalgo-Cantabrana C, Delgado S, Margolles A, Sánchez B. Filling the gap between collection, transport and storage of the human gut microbiota. Sci Rep 2019; 9:8327. [PMID: 31171823 PMCID: PMC6554407 DOI: 10.1038/s41598-019-44888-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 05/20/2019] [Indexed: 12/11/2022] Open
Abstract
Stool collection devices minimizing the exposure of gut bacteria to oxygen are critical for the standardization of further microbiota-based studies, analysis and developments. The aim of this work was to evidence that keeping anaerobiosis has a deep impact on the viability and diversity of the fecal microbiota that is recovered in the laboratory. Recovering certain microbial populations, such as obligate anaerobic bacteria, is particularly critical if the purpose of the study is to envisage personalized therapeutic purposes, such as autologous Fecal Microbiota Transplant. In this study the same fecal specimens were sampled in conventional stool containers and GutAlive, a disposable device that minimizes exposure of the gut microbiota to oxygen. Samples from five healthy donors were analysed and 150 differential colonies were recovered and identified by 16S rRNA gene sequencing. Globally, GutAlive maintained extremely oxygen sensitive (EOS) populations that were lost in conventional stool containers, and thus viability of species such as as Akkermansia muciniphila, Faecalibacterium prausnitzii and a novel member of the Clostridiales order was kept. These obligate anaerobes were not recovered using the conventional stool collection device. In conclusion, the use of GutAlive for stool collection and transport optimized the viability and recovery of EOS bacteria in the lab by diminishing oxygen toxicity.
Collapse
Affiliation(s)
- Noelia Martínez
- Microviable Therapeutics SL. Edificio Severo Ochoa, Campus de El Cristo. C/Fernando Bonguera s/n, 33006, Oviedo, Spain
| | - Claudio Hidalgo-Cantabrana
- Department of Food, Processing and Nutrition Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Susana Delgado
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas, Asturias, CSIC, Spain
| | - Abelardo Margolles
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas, Asturias, CSIC, Spain
| | - Borja Sánchez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas, Asturias, CSIC, Spain.
| |
Collapse
|