1
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Gemmell MR, Jayawardana T, Koentgen S, Brooks E, Kennedy N, Berry S, Lees C, Hold GL. Optimised human stool sample collection for multi-omic microbiota analysis. Sci Rep 2024; 14:16816. [PMID: 39039185 PMCID: PMC11263584 DOI: 10.1038/s41598-024-67499-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 07/11/2024] [Indexed: 07/24/2024] Open
Abstract
To accurately define the role of the gut microbiota in health and disease pathogenesis, the preservation of stool sample integrity, in terms of microbial community composition and metabolic function, is critical. This presents a challenge for any studies which rely on participants self-collecting and returning stool samples as this introduces variability and uncertainty of sample storage/handling. Here, we tested the performance of three stool sample collection/preservation buffers when storing human stool samples at different temperatures (room temperature [20 °C], 4 °C and - 80 °C) for up to three days. We compared and quantified differences in 16S rRNA sequencing composition and short-chain fatty acid profiles compared against immediately snap-frozen stool. We found that the choice of preservation buffer had the largest effect on the resulting microbial community and metabolomic profiles. Collectively analysis confirmed that PSP and RNAlater buffered samples most closely recapitulated the microbial diversity profile of the original (immediately - 80 °C frozen) sample and should be prioritised for human stool microbiome studies.
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Affiliation(s)
| | - Thisun Jayawardana
- School of Clinical Medicine, Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Sabrina Koentgen
- School of Clinical Medicine, Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Ella Brooks
- School of Clinical Medicine, Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia
| | - Nicholas Kennedy
- University of Exeter, Exeter, Devon, UK
- Department of Gastroenterology, Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon, UK
| | - Susan Berry
- School of Medicine, Medical Sciences & Dentistry, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Charlie Lees
- Western General Hospital, Edinburgh, UK
- University of Edinburgh Centre for Genomic and Experimental Medicine, Edinburgh, UK
| | - Georgina L Hold
- School of Clinical Medicine, Microbiome Research Centre, University of New South Wales, Sydney, NSW, Australia.
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2
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Khairulmunir M, Gani M, Mohd-Ridwan AR, Karuppannan KV, Abdul-Latiff MAB, Md-Zain BM. Alteration of the gut microbial composition of critically endangered Malayan tigers (Panthera tigris jacksoni) in captivity during enrichment phase. Mol Biol Rep 2024; 51:742. [PMID: 38874703 DOI: 10.1007/s11033-024-09642-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/14/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND Enrichment activities may influence the microbiomes of captive tigers', affecting their health, digestion, and behavior. Currently, there are few studies that address the impact of enrichment activity on tigers' health. This study aimed to determine the diversity of the gut microbiome in captive Malayan tigers at Zoo Melaka and Night Safari during the environmental enrichment phase using a metabarcoding approach. METHODS AND RESULTS This study utilized different enrichment activities which catered for food, sensory, and cognitive enrichment. Eleven fresh fecal samples from captive Malayan tigers at Zoo Melaka and Night Safari were collected under different conditions. All samples were extracted and 16S rRNA V3-V4 region amplicon sequencing was used to characterize the gut microbiome of captive Malayan tigers subjected to various enrichment activities. Firmicutes, Actinobacteriota, and Fusobacteriota were the dominant phyla observed in the gut microbiome of captive Malayan tigers during enrichment activities. This study revealed β-diversity significantly varied between normal and enrichment phase, however no significant differences were observed in α-diversity. This study demonstrates that environmental enrichment improves the gut microbiome of Malayan tigers because gut microbes such as Lachnoclostridium, which has anti-inflammatory effects and helps maintain homeostasis, and Romboutsia, which has a probiotic effect on the gut microbiome. CONCLUSIONS This study provides valuable insights into the effects of enrichment activities on the gut microbiome of captive Malayan tigers, offering guidance for enhancing captive management practices aimed at promoting the health and well-being of Malayan tiger in captivity.
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Affiliation(s)
- Mohamad Khairulmunir
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
| | - Millawati Gani
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN) Peninsular Malaysia, KM 10 Jalan Cheras, Kuala Lumpur, 56100, Malaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, Kota Samarahan, Sarawak, 94300, Malaysia
| | - Kayal Vizi Karuppannan
- National Wildlife Forensic Laboratory (NWFL), Ex-Situ Conservation Division, Department of Wildlife and National Parks (PERHILITAN) Peninsular Malaysia, KM 10 Jalan Cheras, Kuala Lumpur, 56100, Malaysia
| | | | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, 43600, Selangor, Malaysia.
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3
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Isokääntä H, Pinto da Silva L, Karu N, Kallonen T, Aatsinki AK, Hankemeier T, Schimmel L, Diaz E, Hyötyläinen T, Dorrestein PC, Knight R, Orešič M, Kaddurah-Daouk R, Dickens AM, Lamichhane S. Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization. Anal Chem 2024; 96:8893-8904. [PMID: 38782403 PMCID: PMC11154662 DOI: 10.1021/acs.analchem.3c04436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/12/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024]
Abstract
Metabolites from feces provide important insights into the functionality of the gut microbiome. As immediate freezing is not always feasible in gut microbiome studies, there is a need for sampling protocols that provide the stability of the fecal metabolome and microbiome at room temperature (RT). Here, we investigated the stability of various metabolites and the microbiome (16S rRNA) in feces collected in 95% ethanol (EtOH) and commercially available sample collection kits with specific preservatives OMNImet•GUT/OMNIgene•GUT. To simulate field-collection scenarios, the samples were stored at different temperatures at varying durations (24 h + 4 °C, 24 h RT, 36 h RT, 48 h RT, and 7 days RT) and compared to aliquots immediately frozen at -80 °C. We applied several targeted and untargeted metabolomics platforms to measure lipids, polar metabolites, endocannabinoids, short-chain fatty acids (SCFAs), and bile acids (BAs). We found that SCFAs in the nonstabilized samples increased over time, while a stable profile was recorded in sample aliquots stored in 95% EtOH and OMNImet•GUT. When comparing the metabolite levels between aliquots stored at room temperature and at +4 °C, we detected several changes in microbial metabolites, including multiple BAs and SCFAs. Taken together, we found that storing samples at RT and stabilizing them in 95% EtOH yielded metabolomic results comparable to those from flash freezing. We also found that the overall composition of the microbiome did not vary significantly between different storage types. However, notable differences were observed in the α diversity. Altogether, the stability of the metabolome and microbiome in 95% EtOH provided results similar to those of the validated commercial collection kits OMNImet•GUT and OMNIgene•GUT, respectively.
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Affiliation(s)
- Heidi Isokääntä
- Research
Center for Infections and Immunity, Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Lucas Pinto da Silva
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
| | - Naama Karu
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Teemu Kallonen
- Department
of Clinical Microbiology, Laboratory Division, Turku University Hospital, Kiinamyllynkatu 10 D, 20520 Turku, Finland
- Clinical
Microbiome Bank, Microbe Center, University
Hospital and University of Turku, 20520 Turku, Finland
| | - Anna-Katariina Aatsinki
- Centre
for
Population Health Research, University of
Turku, Kiinamyllynkatu
10A, 20520 Turku, Finland
| | - Thomas Hankemeier
- Metabolomics
and Analytics Centre, Leiden Academic Centre for Drug Research, Leiden University, Leiden 2333 CC, The Netherlands
| | - Leyla Schimmel
- Department
of Psychiatry and Behavioral Sciences, Duke
University, Durham, North Carolina 27708-0187, United States
| | - Edgar Diaz
- Department
of Psychiatry and Behavioral Sciences, Duke
University, Durham, North Carolina 27708-0187, United States
| | - Tuulia Hyötyläinen
- School
of Science and Technology, Örebro
University, 70281 Örebro, Sweden
| | - Pieter C. Dorrestein
- Center
for Microbiome Innovation, University of
California, San Diego, La Jolla, California 92093-6607, United States
- Collaborative
Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and
Pharmaceutical Sciences, University of California,
San Diego, 9500 Gilman, La Jolla, California 92093-0657, United States
| | - Rob Knight
- Center
for Microbiome Innovation, University of
California, San Diego, La Jolla, California 92093-6607, United States
| | - Matej Orešič
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, 702 81 Örebro, Sweden
| | - Rima Kaddurah-Daouk
- Department
of Psychiatry and Behavioral Sciences, Duke
University, Durham, North Carolina 27708-0187, United States
| | - Alex M. Dickens
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
- Department of Chemistry, University of
Turku, Henrikinkatu 2, 20500 Turku, Finland
| | - Santosh Lamichhane
- Turku
Bioscience Centre, University of Turku, Tykistönkatu 6A, 20520 Turku, Finland
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4
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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.
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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.
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5
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Li XM, Shi X, Yao Y, Shen YC, Wu XL, Cai T, Liang LX, Wang F. Effects of Stool Sample Preservation Methods on Gut Microbiota Biodiversity: New Original Data and Systematic Review with Meta-Analysis. Microbiol Spectr 2023; 11:e0429722. [PMID: 37093040 PMCID: PMC10269478 DOI: 10.1128/spectrum.04297-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/16/2023] [Indexed: 04/25/2023] Open
Abstract
Here, we aimed to compare the effects of different preservation methods on outcomes of fecal microbiota. We evaluated the effects of different preservation methods using stool sample preservation experiments for up to 1 year. The stool samples from feces of healthy volunteers were grouped based on whether absolute ethanol was added and whether they were hypothermically preserved. Besides, we performed a systematic review to combine current fecal microbiota preservation evidence. We found that Proteobacteria changed significantly and Veillonellaceae decreased significantly in the 12th month in the room temperature + absolute ethanol group. The four cryopreservation groups have more similarities with fresh sample in the 12 months; however, different cryopreservation methods have different effects on several phyla, families, and genera. A systematic review showed that the Shannon diversity and Simpson index of samples stored in RNAlater for 1 month were not statistically significant compared with those stored immediately at -80°C (P = 0.220 and P = 0.123, respectively). The -80°C refrigerator and liquid nitrogen cryopreservation with 10% glycerine can both maintain stable microbiota of stool samples for long-term preservation. The addition of absolute ethanol to cryopreserved samples had no significant difference in the effect of preserving fecal microbial characteristics. Our study provides empirical insights into preservation details for future studies of the long-term preservation of fecal microbiota. Systematic review and meta-analysis found that the gut microbiota structure, composition, and diversity of samples preserved by storage methods, such as preservation solution, are relatively stable, which were suitable for short-term storage at room temperature. IMPORTANCE The study of gut bacteria has become increasingly popular, and fecal sample preservation methods and times need to be standardized. Here, we detail a 12-month study of fecal sample preservation, and our study provides an empirical reference about experimental details for long-term high-quality storage of fecal samples in the field of gut microbiology research. The results showed that the combination of -80°C/liquid nitrogen deep cryopreservation and 10% glycerol was the most effective method for the preservation of stool samples, which is suitable for long-term storage for at least 12 months. The addition of anhydrous ethanol to the deep cryopreserved samples did not make a significant difference in the preservation of fecal microbiological characteristics. Combined with the results of systematic reviews and meta-analyses, we believe that, when researchers preserve fecal specimens, it is essential to select the proper preservation method and time period in accordance with the goal of the study.
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Affiliation(s)
- Xin-meng Li
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Xiao Shi
- Department of Dermatology, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Yao Yao
- Department of Gastroenterology, Zhangjiajie People’s Hospital, Zhangjiajie, Hunan, China
| | - Yi-cun Shen
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Xiang-ling Wu
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Ting Cai
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Lun-xi Liang
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
- Department of Gastroenterology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Fen Wang
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
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6
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Takagi T, Kunihiro T, Takahashi S, Hisada T, Nagashima K, Mochizuki J, Mizushima K, Naito Y. A newly developed solution for the preservation of short-chain fatty acids, bile acids, and microbiota in fecal specimens. J Clin Biochem Nutr 2023; 72:263-269. [PMID: 37251966 PMCID: PMC10209596 DOI: 10.3164/jcbn.22-107] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/18/2022] [Indexed: 11/29/2023] Open
Abstract
Recent studies have revealed that the gut microbiome affects various health conditions via its metabolites, including short-chain fatty acids (SCFAs) and bile acids (BAs). In the analysis of these, appropriate collection, handling, and storage of fecal specimens are required, and convenient specimen handling processes will facilitate their investigation. Here, we developed a novel preservation solution, "Metabolokeeper®", to stabilize fecal microbiota, organic acids including SCFAs, and BAs at room temperature. In the present study, we collected fecal samples from 20 healthy adult volunteers and stored them at room temperature with Metabolokeeper® and at -80°C without preservatives for up to four weeks to evaluate the usefulness of the novel preservative solution. We found that microbiome profiles and short chain fatty acid contents were stably maintained at room temperature with Metabolokeeper® for 28 days, while the bile acids were stably maintained for 7 days under the same conditions. We conclude that this convenient procedure to obtain a fecal sample for collecting the gut microbiome and gut metabolites can contribute to a better understanding of the health effects of fecal metabolites produced by the gut microbiome.
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Affiliation(s)
- Tomohisa Takagi
- Molecular Gastroenterology and Hepatology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto 602-8566, Japan
- Department for Medical Innovation and Translational Medical Science, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Tadao Kunihiro
- TechnoSuruga Laboratory Co., Ltd., Shizuoka 424-0065, Japan
| | | | | | - Koji Nagashima
- TechnoSuruga Laboratory Co., Ltd., Shizuoka 424-0065, Japan
| | - Jun Mochizuki
- TechnoSuruga Laboratory Co., Ltd., Shizuoka 424-0065, Japan
| | - Katsura Mizushima
- Department of Human Immunology and Nutrition Science, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto 602-8566, Japan
| | - Yuji Naito
- Department of Human Immunology and Nutrition Science, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto 602-8566, Japan
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7
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Kool J, Tymchenko L, Shetty SA, Fuentes S. Reducing bias in microbiome research: Comparing methods from sample collection to sequencing. Front Microbiol 2023; 14:1094800. [PMID: 37065158 PMCID: PMC10101209 DOI: 10.3389/fmicb.2023.1094800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/22/2023] [Indexed: 04/01/2023] Open
Abstract
BackgroundMicrobiota profiles are strongly influenced by many technical aspects that impact the ability of researchers to compare results. To investigate and identify potential biases introduced by technical variations, we compared several approaches throughout the entire workflow of a microbiome study, from sample collection to sequencing, using commercially available mock communities (from bacterial strains as well as from DNA) and multiple human fecal samples, including a large set of positive controls created as a random mix of several participant samples.MethodsHuman fecal material was sampled, and aliquots were used to test two commercially available stabilization solutions (OMNIgene·GUT and Zymo Research) in comparison to samples frozen immediately upon collection. In addition, the methodology for DNA extraction, input of DNA, or the number of PCR cycles were analyzed. Furthermore, to investigate the potential batch effects in DNA extraction, sequencing, and barcoding, we included 139 positive controls.ResultsSamples preserved in both the stabilization buffers limited the overgrowth of Enterobacteriaceae when compared to unpreserved samples stored at room temperature (RT). These stabilized samples stored at RT were different from immediately frozen samples, where the relative abundance of Bacteroidota was higher and Actinobacteriota and Firmicutes were lower. As reported previously, the method used for cell disruption was a major contributor to variation in microbiota composition. In addition, a high number of cycles during PCR lead to an increase in contaminants detected in the negative controls. The DNA extraction had a significant impact on the microbial composition, also observed with the use of different Illumina barcodes during library preparation and sequencing, while no batch effect was observed in replicate runs.ConclusionOur study reaffirms the importance of the mechanical cell disruption method and immediate frozen storage as critical aspects in fecal microbiota studies. A comparison of storage conditions revealed that the bias was limited in RT samples preserved in stabilization systems, and these may be a suitable compromise when logistics are challenging due to the size or location of a study. Moreover, to reduce the effect of contaminants in fecal microbiota profiling studies, we suggest the use of ~125 pg input DNA and 25 PCR cycles as optimal parameters during library preparation.
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Affiliation(s)
- Jolanda Kool
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Liza Tymchenko
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Sudarshan A. Shetty
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Department of Medical Microbiology and Infection Prevention, Virology and Immunology Research Group, University Medical Center Groningen, Groningen, Netherlands
| | - Susana Fuentes
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- *Correspondence: Susana Fuentes
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8
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Kim JH, Jeon JY, Im YJ, Ha N, Kim JK, Moon SJ, Kim MG. Long-term taxonomic and functional stability of the gut microbiome from human fecal samples. Sci Rep 2023; 13:114. [PMID: 36596832 PMCID: PMC9810722 DOI: 10.1038/s41598-022-27033-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023] Open
Abstract
Appropriate storage of fecal samples is a critical step for unbiased analysis in human microbiome studies. The purpose of this study was to evaluate the stability of the fecal microbial community for up to 18 months. Ten healthy volunteers provided fecal samples at the Jeonbuk National University Hospital. Stool samples were stored under the following six conditions: four different storage temperatures (- 70 °C, - 20 °C, 4 °C, and room temperature [20-25 °C]) and two different collection tubes (OMNIgene-Gut and DNA/RNA shield-fecal collection tubes). The gut microbiome was analyzed with 16S rRNA sequencing. We compared the taxonomic composition, alpha diversity, beta diversity and inferred pathway abundance between the baseline and 18 months after storage. Samples collected in the DNA/RNA Shield-fecal collection tubes showed the best performance in preservation of the taxonomic composition at 18 months. Pairwise differences in alpha diversity metrics showed the least deviation from zero. The PERMANOVA test showed non-significant change of beta diversity metrics (Unweighted Unifrac: q-value 0.268; Weighted Unifrac: q-value 0.848). The functional stability was significantly well preserved in the DNA/RNA Shield-fecal collection tubes (adjusted p value < 0.05). Our results demonstrate the use of the DNA/RNA Shield-fecal collection tube as an alternative storage method for fecal samples to preserve the taxonomic and functional stability of the microbiome over a long term.
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Affiliation(s)
- Jae Hyun Kim
- grid.411545.00000 0004 0470 4320School of Pharmacy and Institute of New Drug Development, Jeonbuk National University, Jeonju, Republic of Korea
| | - Ji-Young Jeon
- grid.411545.00000 0004 0470 4320Center for Clinical Pharmacology and Biomedical Research Institute, Jeonbuk National University Hospital, 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do 54907 Republic of Korea
| | - Yong-Jin Im
- grid.411545.00000 0004 0470 4320Center for Clinical Pharmacology and Biomedical Research Institute, Jeonbuk National University Hospital, 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do 54907 Republic of Korea
| | - Na Ha
- grid.411545.00000 0004 0470 4320Center for Clinical Pharmacology and Biomedical Research Institute, Jeonbuk National University Hospital, 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do 54907 Republic of Korea
| | - Jeon-Kyung Kim
- grid.411545.00000 0004 0470 4320School of Pharmacy and Institute of New Drug Development, Jeonbuk National University, Jeonju, Republic of Korea
| | - Seol Ju Moon
- grid.411545.00000 0004 0470 4320Center for Clinical Pharmacology and Biomedical Research Institute, Jeonbuk National University Hospital, 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do 54907 Republic of Korea ,grid.411545.00000 0004 0470 4320Department of Pharmacology, Medical School, Jeonbuk National University, Jeonju, Republic of Korea
| | - Min-Gul Kim
- grid.411545.00000 0004 0470 4320Center for Clinical Pharmacology and Biomedical Research Institute, Jeonbuk National University Hospital, 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do 54907 Republic of Korea ,grid.411545.00000 0004 0470 4320Department of Pharmacology, Medical School, Jeonbuk National University, Jeonju, Republic of Korea ,grid.411545.00000 0004 0470 4320Research Institute of Clinical Medicine of Jeonbuk National University, Jeonju, Republic of Korea
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9
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Combrink L, Humphreys IR, Washburn Q, Arnold HK, Stagaman K, Kasschau KD, Jolles AE, Beechler BR, Sharpton TJ. Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations. Front Microbiol 2023; 14:1092216. [PMID: 36910202 PMCID: PMC9992432 DOI: 10.3389/fmicb.2023.1092216] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/18/2023] [Indexed: 02/24/2023] Open
Abstract
Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.
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Affiliation(s)
- Leigh Combrink
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
| | - Ian R Humphreys
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Holly K Arnold
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Kristin D Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Anna E Jolles
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Brianna R Beechler
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Statistics, Oregon State University, Corvallis, OR, United States
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10
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Steiner HE, Patterson HK, Giles JB, Karnes JH. Bringing pharmacomicrobiomics to the clinic through well-designed studies. Clin Transl Sci 2022; 15:2303-2315. [PMID: 35899413 PMCID: PMC9579385 DOI: 10.1111/cts.13381] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/05/2022] [Accepted: 07/15/2022] [Indexed: 01/25/2023] Open
Abstract
Pharmacomicrobiomic studies investigate drug-microbiome interactions, such as the effect of microbial variation on drug response and disposition. Studying and understanding the interactions between the gut microbiome and drugs is becoming increasingly relevant to clinical practice due to its potential for avoiding adverse drug reactions or predicting variability in drug response. The highly variable nature of the human microbiome presents significant challenges to assessing microbes' influence. Studies aiming to explore drug-microbiome interactions should be well-designed to account for variation in the microbiome over time and collect data on confounders such as diet, disease, concomitant drugs, and other environmental factors. Here, we assemble a set of important considerations and recommendations for the methodological features required for performing a pharmacomicrobiomic study in humans with a focus on the gut microbiome. Consideration of these factors enable discovery, reproducibility, and more accurate characterization of the relationships between a given drug and the microbiome. Furthermore, appropriate interpretation and dissemination of results from well-designed studies will push the field closer to clinical relevance and implementation.
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Affiliation(s)
- Heidi E. Steiner
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA
| | - Hayley K. Patterson
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA
| | - Jason B. Giles
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA
| | - Jason H. Karnes
- Department of Pharmacy Practice and ScienceUniversity of Arizona R. Ken Coit College of PharmacyTucsonArizonaUSA,Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTennesseeUSA
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11
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Singh A, Mahajan R, Kahlon BK, Dhaliwal AS, Midha V, Mehta V, Bansal N, Singh D, Sood A. Early fecal microbiome transfer after donor defecation determines response in patients with moderate to severe ulcerative colitis. Indian J Gastroenterol 2022; 41:389-396. [PMID: 36121613 DOI: 10.1007/s12664-022-01257-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 03/02/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Fecal microbiome transfer (FMT) targeting gut microbiome dysbiosis is an emerging therapy for ulcerative colitis (UC). There is however no consensus on protocols for performing FMT in UC, especially in relation to time after donor feces defecation. METHODS This is a single-center retrospective analysis of patients with moderate-severe UC (total Mayo Clinic score ≥6 and endoscopic Mayo Clinic subscore of ≥2) treated with FMT between September 2017 and December 2019 at Dayanand Medical College and Hospital, Ludhiana, India. Fresh fecal samples from unrelated healthy voluntary donors were administered through colonoscopy at weeks 0, 2, 6, 10, 14, 18, and 22. Time interval between donor feces defecation and FMT procedure was recorded for each FMT session and the mean time of seven sessions was designated aika. Impact of aika on clinical response and safety of FMT was evaluated. RESULTS During the study period, 123 adult patients (mean age 33.75±11.97 years, 61.8% [n=76] males) with moderate-severe UC (mean total Mayo Clinic and endoscopic Mayo Clinic scores 7.49±1.60 and 2.50±0.50, respectively) were treated with FMT. The mean aika was 2.29±0.75 h. The aika was smaller in patients who responded to FMT as compared to non-responders (2.13±0.75 h vs. 2.71±0.76 h, p=0.0002) as well as in patients achieving clinical remission (2.15±0.76 h vs. 2.42±0.76 h, p=0.05). There was no significant impact of aika on adverse effects except for the incidence of borborygmi after FMT, which was higher in patients with aika ≤2 h. CONCLUSION Early FMT after donor feces defecation favorably impacts the clinical response rates in patients with active UC.
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Affiliation(s)
- Arshdeep Singh
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, 141 001, India
| | - Ramit Mahajan
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, 141 001, India
| | | | | | - Vandana Midha
- Department of Internal Medicine, Dayanand Medical College, Ludhiana, 141 001, India
| | - Varun Mehta
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, 141 001, India
| | - Namita Bansal
- Research and Development Centre, Dayanand Medical College, Ludhiana, 141 001, India
| | - Dharmatma Singh
- Research and Development Centre, Dayanand Medical College, Ludhiana, 141 001, India
| | - Ajit Sood
- Department of Gastroenterology, Dayanand Medical College and Hospital, Ludhiana, 141 001, India.
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12
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Natarajan A, Zlitni S, Brooks EF, Vance SE, Dahlen A, Hedlin H, Park RM, Han A, Schmidtke DT, Verma R, Jacobson KB, Parsonnet J, Bonilla HF, Singh U, Pinsky BA, Andrews JR, Jagannathan P, Bhatt AS. Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infection. MED (NEW YORK, N.Y.) 2022; 3:371-387.e9. [PMID: 35434682 PMCID: PMC9005383 DOI: 10.1016/j.medj.2022.04.001] [Citation(s) in RCA: 168] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/01/2022] [Accepted: 04/05/2022] [Indexed: 02/01/2023]
Abstract
Background COVID-19 manifests with respiratory, systemic, and gastrointestinal (GI) symptoms.1, SARS-CoV-2 RNA is detected in respiratory and fecal samples, and recent reports demonstrate viral replication in both the lung and intestinal tissue.2, 3, 4 Although much is known about early fecal RNA shedding, little is known about long-term shedding, especially in those with mild COVID-19. Furthermore, most reports of fecal RNA shedding do not correlate these findings with GI symptoms.5. Methods We analyzed the dynamics of fecal RNA shedding up to 10 months after COVID-19 diagnosis in 113 individuals with mild to moderate disease. We also correlated shedding with disease symptoms. Findings Fecal SARS-CoV-2 RNA is detected in 49.2% [95% confidence interval, 38.2%-60.3%] of participants within the first week after diagnosis. Whereas there was no ongoing oropharyngeal SARS-CoV-2 RNA shedding in subjects at 4 months, 12.7% [8.5%-18.4%] of participants continued to shed SARS-CoV-2 RNA in the feces at 4 months after diagnosis and 3.8% [2.0%-7.3%] shed at 7 months. Finally, we found that GI symptoms (abdominal pain, nausea, vomiting) are associated with fecal shedding of SARS-CoV-2 RNA. Conclusions The extended presence of viral RNA in feces, but not in respiratory samples, along with the association of fecal viral RNA shedding with GI symptoms suggest that SARS-CoV-2 infects the GI tract and that this infection can be prolonged in a subset of individuals with COVID-19. Funding This research was supported by a Stanford ChemH-IMA grant; fellowships from the AACR and NSF; and NIH R01-AI148623, R01-AI143757, and UL1TR003142.
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Affiliation(s)
- Aravind Natarajan
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, CA, USA,Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Soumaya Zlitni
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, CA, USA,Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Erin F. Brooks
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Summer E. Vance
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Alex Dahlen
- Quantitative Science Unit, Stanford University, Stanford, CA, USA
| | - Haley Hedlin
- Quantitative Science Unit, Stanford University, Stanford, CA, USA
| | - Ryan M. Park
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, CA, USA,Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Alvin Han
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Danica T. Schmidtke
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Renu Verma
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Karen B. Jacobson
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Julie Parsonnet
- Department of Medicine (Infectious Diseases), Stanford University, Stanford, CA, USA,Department of Medicine (Epidemiology and Population Health), Stanford University, Stanford, CA, USA
| | - Hector F. Bonilla
- Department of Medicine (Infectious Diseases), Stanford University, Stanford, CA, USA
| | - Upinder Singh
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Benjamin A. Pinsky
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jason R. Andrews
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Prasanna Jagannathan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA,Department of Medicine (Infectious Diseases), Stanford University, Stanford, CA, USA
| | - Ami S. Bhatt
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, CA, USA,Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA,Corresponding author
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13
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Bhattacharjee A, Dubey S, Sharma S. Storage of soil microbiome for application in sustainable agriculture: prospects and challenges. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3171-3183. [PMID: 34718953 DOI: 10.1007/s11356-021-17164-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Soil microbiome is a dynamic micro-ecosystem driving and fine-tuning several biological processes in the global macro-ecosystems. Its tremendous potential towards mediating sustainability in the ecosystem necessitates the urgent need to store it optimally and efficiently as "next-generation biologicals" for future applications via soil transplantation. The challenge, therefore, is to devise a strategy for the storage of soil microbiome such that its "functionality" is preserved for later application. This review discusses the current endeavours made towards storage of the soil microbiome. The methods for assessing the integrity of soil microbiome by targeting the structural diversity and functional potential of the preserved microbiomes have also been discussed. Further, the success stories related to the storage of fecal microbiome for application in transplants have also been highlighted. This is done primarily with the objective of learning lessons, and parallel application of the knowledge gained, in bringing about improvement in the research domain of soil microbiome storage. Subsequently, the limitations of current techniques of preservation have also been delineated. Further, the open questions in the area have been critically discussed. In conclusion, possible alternatives for storage, comprehensive analyses of the composition of the stored microbiome and their potential have been presented.
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Affiliation(s)
- Annapurna Bhattacharjee
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shubham Dubey
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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14
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Abstract
Integrative analysis of high-quality metagenomics and metabolomics data from fecal samples provides novel clues for the mechanism underpinning gut microbe-human interactions. However, data regarding the influence of fecal collection methods on both metagenomics and metabolomics are sparse. Six fecal collection methods (the gold standard [GS] [i.e., immediate freezing at −80°C with no solution], 95% ethanol, RNAlater, OMNIgene Gut, fecal occult blood test [FOBT] cards, and Microlution) were used to collect 88 fecal samples from eight healthy volunteers for whole-genome shotgun sequencing (WGSS) and untargeted metabolomic profiling. Metrics assessed included the abundances of predominant phyla and α- and β-diversity at the species, gene, and pathway levels. Intraclass correlation coefficients (ICCs) were calculated for microbes and metabolites to estimate (i) stability (day 4 versus day 0 within each method), (ii) concordance (day 0 for each method versus the GS), and (iii) reliability (day 4 for each method versus the GS). For the top 4 phyla and microbial diversity metrics at the species, gene, and pathway levels, generally high stability and reliability were observed for most methods except for 95% ethanol; similar concordances were seen for different methods. For metabolomics data, 95% ethanol showed the highest stability, concordance, and reliability (median ICCs = 0.71, 0.71, and 0.65, respectively). Taken together, OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles. We recommend using separate collecting methods for gut metagenomic sequencing and fecal metabolomic profiling in large population studies. IMPORTANCE The choice of fecal collection method is essential for studying gut microbe-human interactions in large-scale population-based research. In this study, we examined the effects of fecal collection methods and storage time at ambient temperature on variations in the gut microbiome community composition; microbial diversity metrics at the species, gene, and pathway levels; antibiotic resistance genes; and metabolome profiling. Our findings suggest using different fecal sample collection methods for different data generation purposes. OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles.
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15
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Natarajan A, Han A, Zlitni S, Brooks EF, Vance SE, Wolfe M, Singh U, Jagannathan P, Pinsky BA, Boehm A, Bhatt AS. Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. Nat Commun 2021; 12:5753. [PMID: 34599164 PMCID: PMC8486790 DOI: 10.1038/s41467-021-25576-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022] Open
Abstract
Patients with COVID-19 shed SARS-CoV-2 RNA in stool, sometimes well after their respiratory infection has cleared. This may be significant for patient health, epidemiology, and diagnosis. However, methods to preserve stool, and to extract and quantify viral RNA are not standardized. We test the performance of three preservative approaches at yielding detectable SARS-CoV-2 RNA: the OMNIgene-GUT kit, Zymo DNA/RNA shield kit, and the most commonly applied, storage without preservative. We test these in combination with three extraction kits: QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. We also test the utility of ddPCR and RT-qPCR for the reliable quantification of SARS-CoV-2 RNA from stool. We identify that the Zymo DNA/RNA preservative and the QiaAMP extraction kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR. Taken together, we recommend a comprehensive methodology for preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.
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Affiliation(s)
- Aravind Natarajan
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Alvin Han
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Soumaya Zlitni
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Erin F Brooks
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Summer E Vance
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Marlene Wolfe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Upinder Singh
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Prasanna Jagannathan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Alexandria Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
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16
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The maintenance of microbial community in human fecal samples by a cost effective preservation buffer. Sci Rep 2021; 11:13453. [PMID: 34188136 PMCID: PMC8242035 DOI: 10.1038/s41598-021-92869-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 06/16/2021] [Indexed: 12/25/2022] Open
Abstract
In the burgeoning microbiome field, powerful sequencing approaches and accompanied bioanalytical methods have made tremendous contributions to the discoveries of breakthroughs, which favor to unravel the intimate interplay between gut microbiota and human health. The proper preservation of samples before being processed is essential to guarantee the authenticity and reliability of microbiome studies. Hence, the development of preservation methods is extremely important to hold samples eligible for the consequent analysis, especially population cohort-based investigations or those spanning species or geography, which frequently facing difficulties in suppling freezing conditions. Although there are several commercial products available, the exploration of cost-efficient and ready-to-use preservation methods are still in a large demand. Here, we performed shotgun metagenomic sequencing and demonstrated that microbial consortia in human fecal samples were substantially preserved within a temporary storage of 4 h, independent of the storage temperature. We also verified a previous reported self-made preservation buffer (PB buffer) could not only preserve fecal microbiota at room temperature up to 4 weeks but also enable samples to endure a high temperature condition which mimics temperature variations in summer logistics. Moreover, PB buffer exhibited suitability for human saliva as well. Collectively, PB buffer may be a valuable choice to stabilize samples if neither freezing facilities nor liquid nitrogen is available.
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17
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Natarajan A, Han A, Zlitni S, Brooks EF, Vance SE, Wolfe M, Singh U, Jagannathan P, Pinsky BA, Boehm A, Bhatt AS. Standardized and optimized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.04.10.21255250. [PMID: 33880485 PMCID: PMC8057253 DOI: 10.1101/2021.04.10.21255250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
COVID-19 patients shed SARS-CoV-2 viral RNA in their stool, sometimes well after they have cleared their respiratory infection. This feature of the disease may be significant for patient health, epidemiology, and diagnosis. However, to date, methods to preserve stool samples from COVID patients, and to extract and quantify viral RNA concentration have yet to be optimized. We sought to meet this urgent need by developing and benchmarking a standardized protocol for the fecal detection of SARS-CoV-2 RNA. We test three preservative conditions for their ability to yield detectable SARS-CoV-2 RNA: OMNIgene-GUT, Zymo DNA/RNA shield kit, and the most common condition, storage without any preservative. We test these in combination with three extraction kits: the QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. Finally, we also test the utility of two detection methods, ddPCR and RT-qPCR, for the robust quantification of SARS-CoV-2 viral RNA from stool. We identify that the Zymo DNA/RNA shield collection kit and the QiaAMP viral RNA mini kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR assays. We also demonstrate key features of experimental design including the incorporation of appropriate controls and data analysis, and apply these techniques to effectively extract viral RNA from fecal samples acquired from COVID-19 outpatients enrolled in a clinical trial. Finally, we recommend a comprehensive methodology for future preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.
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Affiliation(s)
- Aravind Natarajan
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Alvin Han
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Soumaya Zlitni
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Erin F. Brooks
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Summer E. Vance
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Marlene Wolfe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Upinder Singh
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Prasanna Jagannathan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Department of Medicine (Infectious Diseases), Stanford University, Stanford, CA, USA
| | - Benjamin A. Pinsky
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Alexandria Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Ami S. Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
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18
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Fitness for purpose of stabilized stool samples for bile acid metabolite analyses. Sci Rep 2021; 11:7904. [PMID: 33846363 PMCID: PMC8042040 DOI: 10.1038/s41598-021-86784-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/18/2021] [Indexed: 01/01/2023] Open
Abstract
Biobanks and cohort studies are increasingly utilizing chemical stabilizers to collect and store stool samples for downstream DNA-based microbiome analyses. While stabilizers permit ambient-temperature collection and storage of samples for gut microbiome studies, the use of the same sample type for downstream metabolomics assays has not been explored. Microbiome-metabolomics analysis of fecal samples is increasingly getting attention to further elucidate the mechanisms by which the gut microbiota influences the host. In this study, we evaluated fitness-for-purpose of OMNIgene-GUT-collected stool samples for downstream metabolomics assays in the scope of fecal bile acids (BA) quantification. Biocrates Bile Acids Kit was used for the quantification of BA from eight healthy donors' samples collected in (1) OMNIgene-GUT kit and (2) snap frozen in -80 °C in duplicates. A highly selective reversed phase LC-MS/MS analysis method in negative ion multiple reaction monitoring (MRM) detection mode was applied to determine the BA concentrations in each sample.Total fecal BA levels were detectable in OMNIgene-GUT-collected samples (range: 29.9-903.7 pmol/mg). Paired t-test confirmed that there was a significant difference in the total BAs between the OMNIgene-GUT and snap frozen samples (p < 0.05). Extractions from snap frozen samples resulted in higher concentrations of total BAs (range: 243.7-1136.2 pmol/mg). Qualitative differences between individual donors' BA profiles were detectable using the two sample collection methods. No significant difference was found in the relative concentrations of primary (CA, CDCA) or secondary (DCA, LCA, UDCA) unconjugated BAs to the total BA concentrations in OMNIgene-GUT-collected samples as compared with the snap frozen samples (Wilcoxon-Mann-Whitney test, p > 0.05). Passing-Bablok method comparison and correlation analyis showed a high degree of correlation in the relative concentrations of CA, CDCA, DCA and LCA between OMNIgene-GUT and snap frozen samples. For these four bile acids, the two methods are comparable at an acceptability bias of 30%. We conclude that the OMNIgene-GUT-collected stool samples are fit-for-purpose for downstream fecal bile acids analysis.
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19
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Deng P, Valentino T, Flythe MD, Moseley HNB, Leachman JR, Morris AJ, Hennig B. Untargeted Stable Isotope Probing of the Gut Microbiota Metabolome Using 13C-Labeled Dietary Fibers. J Proteome Res 2021; 20:2904-2913. [PMID: 33830777 DOI: 10.1021/acs.jproteome.1c00124] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The gut microbiome generates numerous metabolites that exert local effects and enter the circulation to affect the functions of many organs. Despite extensive sequencing-based characterization of the gut microbiome, there remains a lack of understanding of microbial metabolism. Here, we developed an untargeted stable isotope-resolved metabolomics (SIRM) approach for the holistic study of gut microbial metabolites. Viable microbial cells were extracted from fresh mice feces and incubated anaerobically with 13C-labeled dietary fibers including inulin or cellulose. High-resolution mass spectrometry was used to monitor 13C enrichment in metabolites associated with glycolysis, the Krebs cycle, the pentose phosphate pathway, nucleotide synthesis, and pyruvate catabolism in both microbial cells and the culture medium. We observed the differential use of inulin and cellulose as substrates for biosynthesis of essential and non-essential amino acids, neurotransmitters, vitamin B5, and other coenzymes. Specifically, the use of inulin for these biosynthetic pathways was markedly more efficient than the use of cellulose, reflecting distinct metabolic pathways of dietary fibers in the gut microbiome, which could be related with host effects. This technology facilitates deeper and holistic insights into the metabolic function of the gut microbiome (Metabolomic Workbench Study ID: ST001651).
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Affiliation(s)
- Pan Deng
- Superfund Research Center, University of Kentucky, Lexington 40536, Kentucky, United States.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington 40536, Kentucky, United States
| | - Taylor Valentino
- Department of Physiology, University of Kentucky, Lexington 40536, Kentucky, United States
| | - Michael D Flythe
- Department of Animal and Food Sciences, University of Kentucky, Lexington 40536, Kentucky, United States.,United States Department of Agriculture, Agriculture Research Service, Forage Animal Production Research Unit, Lexington 40536, Kentucky, United States
| | - Hunter N B Moseley
- Superfund Research Center, University of Kentucky, Lexington 40536, Kentucky, United States.,Institute for Biomedical Informatics, University of Kentucky, Lexington 40536, Kentucky, United States.,Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington 40536, Kentucky, United States
| | - Jacqueline R Leachman
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington 40536, Kentucky, United States
| | - Andrew J Morris
- Superfund Research Center, University of Kentucky, Lexington 40536, Kentucky, United States.,Division of Cardiovascular Medicine, University of Kentucky, Lexington 40536, Kentucky, United States
| | - Bernhard Hennig
- Superfund Research Center, University of Kentucky, Lexington 40536, Kentucky, United States.,Department of Animal and Food Sciences, University of Kentucky, Lexington 40536, Kentucky, United States
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20
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Wegl G, Grabner N, Köstelbauer A, Klose V, Ghanbari M. Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies. Front Microbiol 2021; 12:627539. [PMID: 33708184 PMCID: PMC7940207 DOI: 10.3389/fmicb.2021.627539] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 02/01/2021] [Indexed: 11/24/2022] Open
Abstract
Understanding the roles of microorganisms in the animal gastrointestinal microenvironment is highly important for the development of effective strategies to manage and manipulate these microbial communities. In order to guide future animal gut microbiota research projects and standardization efforts, we have conducted a systematic comparison of 10 currently used sample preservation and DNA extraction approaches for pig and chicken microbiota samples and quantified their effects on bacterial DNA yield, quality, integrity, and on the resulting sequence-based bacterial composition estimates. The results showed how key stages of conducting a microbiota study, including the sample storage and DNA extraction, can substantially affect DNA recovery from the microbial community, and therefore, biological interpretation in a matrix-dependent manner. Our results highlight the fact that the influence of storage and extraction methods on the resulting microbial community structure differed by sample type, even within the same species. As the effects of these technical steps are potentially large compared with the real biological variability to be explained, standardization is crucial for accelerating progress in the area of livestock microbiota research. This study provided a framework to assist future animal gut microbiota research projects and standardization efforts.
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21
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Ramamoorthy S, Levy S, Mohamed M, Abdelghani A, Evans AM, Miller LAD, Mehta L, Moore S, Freinkman E, Hourigan SK. An ambient-temperature storage and stabilization device performs comparably to flash-frozen collection for stool metabolomics in infants. BMC Microbiol 2021; 21:59. [PMID: 33618670 PMCID: PMC7901118 DOI: 10.1186/s12866-021-02104-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/02/2021] [Indexed: 02/08/2023] Open
Abstract
Background Stool metabolites provide essential insights into the function of the gut microbiome. The current gold standard for storage of stool samples for metabolomics is flash-freezing at − 80 °C which can be inconvenient and expensive. Ambient temperature storage of stool is more practical, however no available methodologies adequately preserve the metabolomic profile of stool. A novel sampling kit (OMNImet.GUT; DNA Genotek, Inc.) was introduced for ambient temperature storage and stabilization of feces for metabolomics; we aimed to test the performance of this kit vs. flash-freezing. To do this stool was collected from an infant’s diaper was divided into two aliquots: 1) flash-frozen and 2) stored in an OMNImet.GUT tube at ambient temperature for 3–4 days. Samples from the same infant were collected at 2 different time points to assess metabolite changes over time. Subsequently, all samples underwent metabolomic analysis by liquid chromatography – tandem mass spectrometry (LC-MS/MS). Results Paired fecal samples (flash-frozen and ambient temperature) from 16 infants were collected at 2 time points (32 individual samples, 64 aliquots). Similar numbers of metabolites were detected in both the frozen and ambient temperature samples (1126 in frozen, 1107 in ambient temperature, 1064 shared between sample types). Metabolite abundances were strongly correlated between storage methods (median Spearman correlation Rs = 0.785 across metabolites). Hierarchical clustering analysis and principal component analysis showed that samples from the same individuals at a given time point clustered closely, regardless of the storage method. Repeat samples from the same individual were compared by paired t-test, separately for the frozen and OMNImet.GUT. The number of metabolites in each biochemical class that significantly changed (p < 0.05) at timepoint 2 relative to timepoint 1 was similar in flash-frozen versus ambient temperature storage. Changes in microbiota modified metabolites over time were also consistent across both methodologies. Conclusion Ambient temperature storage and stabilization of stool in the OMNImet.GUT device yielded comparable metabolomic results to flash freezing in terms of 1) the identity and abundance of detected biochemicals 2) the distinct metabolomic profiles of subjects and 3) changes in metabolites over time that are plausibly microbiota-induced. This method potentially provides a more convenient, less expensive home collection and storage option for stool metabolomic analysis. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02104-6.
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Affiliation(s)
| | - Shira Levy
- Inova Children's Hospital, 3300 Gallows Rd, Falls Church, VA, 22042, USA
| | - Masouma Mohamed
- Inova Children's Hospital, 3300 Gallows Rd, Falls Church, VA, 22042, USA
| | - Alaa Abdelghani
- Inova Children's Hospital, 3300 Gallows Rd, Falls Church, VA, 22042, USA
| | - Anne M Evans
- Metabolon, 617 Davis Dr UNIT 100, Morrisville, NC, 27560, USA
| | - Luke A D Miller
- Metabolon, 617 Davis Dr UNIT 100, Morrisville, NC, 27560, USA
| | - Lopa Mehta
- Inova Health System, 3300 Gallows Rd, Falls Church, VA, 22042, USA
| | - Sean Moore
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, University of Virginia, 200 Jeanette Lancaster Way, Charlottesville, VA, 22903, USA
| | | | - Suchitra K Hourigan
- Inova Children's Hospital, 3300 Gallows Rd, Falls Church, VA, 22042, USA. .,Pediatric Specialists of Virginia, 3023 Hamaker Ct, Fairfax, VA, 22031, USA.
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22
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Lim MY, Park YS, Kim JH, Nam YD. Evaluation of fecal DNA extraction protocols for human gut microbiome studies. BMC Microbiol 2020; 20:212. [PMID: 32680572 PMCID: PMC7367376 DOI: 10.1186/s12866-020-01894-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 07/08/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND DNA extraction is an important factor influencing the microbiome profile in fecal samples. Considering that the QIAamp DNA Stool Mini Kit, one of the most commonly used DNA extraction kits, is no longer manufactured, this study aimed to investigate whether a new commercially available kit, the QIAamp PowerFecal Pro DNA Kit, yields comparable microbiome profiles with those previously obtained using the QIAamp DNA Stool Mini Kit. RESULTS We extracted DNA from fecal samples of 10 individuals using three protocols (protocol P of the QIAamp PowerFecal Pro DNA Kit, and protocols SB and S of the QIAamp DNA Stool Mini Kit with and without an additional bead-beating step, respectively) in triplicate. Ninety extracted DNA samples were subjected to 16S rRNA gene sequencing. DNA quality measured by 260/280 absorbance ratios was found to be optimal in protocol P. Additionally, the DNA quantity and microbiome diversity obtained using protocol P were significantly higher than those of protocol S, however, did not differ significantly from those of protocol SB. Based on the overall microbiome profiles, variations between protocol P and protocol SB or S were significantly less than between-individual variations. Furthermore, most genera were not differentially abundant in protocol P compared to the other protocols, and the number of differentially abundant genera, as well as the degree of fold-changes were smaller between protocols P and SB than between protocols P and S. CONCLUSIONS The QIAamp PowerFecal Pro DNA Kit exhibited microbiome analysis results that were comparable with those of the QIAamp DNA Stool Mini Kit with a bead-beating step. These results will prove useful for researchers investigating the gut microbiome in selecting an alternative protocol to the widely used but discontinued kit.
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Affiliation(s)
- Mi Young Lim
- Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do, 55365, Republic of Korea
| | - Yong-Soo Park
- Food Processing Support Team, Korea Food Research Institute, Jeollabuk-do, 55365, Republic of Korea
| | - Jung-Ha Kim
- Department of Family Medicine, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, 06973, Republic of Korea
| | - Young-Do Nam
- Research Group of Healthcare, Korea Food Research Institute, Jeollabuk-do, 55365, Republic of Korea. .,Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
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