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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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2
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Seel W, Reiners S, Kipp K, Simon MC, Dawczynski C. Role of Dietary Fiber and Energy Intake on Gut Microbiome in Vegans, Vegetarians, and Flexitarians in Comparison to Omnivores-Insights from the Nutritional Evaluation (NuEva) Study. Nutrients 2023; 15:nu15081914. [PMID: 37111133 PMCID: PMC10146654 DOI: 10.3390/nu15081914] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/07/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
In recent years, there has been a global trend towards a plant-based lifestyle. In the NuEva study, dietary self-reports of 258 participants following one of four diets (Western diet (WD), flexitarians (Flex), vegetarians (VG), and vegans (VN)) were related to fecal microbiome composition. Reduced consumption of animal products (VN < VG < Flex < WD) was associated with a decreased intake of energy (p < 0.05), and an increased intake of soluble and non-soluble dietary fibers (p < 0.05). We observed the lowest average microbiome diversity in vegans and the highest in WD. Compared to WD, VG (p < 0.05) and VN (p < 0.01) differed significantly in their bacterial composition. These data were related to dietary fiber intake. Furthermore, we identified 14 diet-specific biomarkers at the genus level by using LefSe analysis. Of these, 11 showed minimum or maximum counts in WD or VN. While the VN-specific species were inversely associated with cardiovascular risk factors, a positive association was detected for the WD-specific species. Identifying biomarkers for the diets on extreme ends of the spectrum (WD and VN) and their association with cardiovascular risk factors provides a solid evidence base highlighting the potential and the need for the development of personalized recommendations dependent on dietary patterns. Even so, the mechanisms underlying these diet-specific differences in microbiome composition cannot yet be clearly assessed. The elucidation of these associations will provide the basis for personalized nutritional recommendations based on the microbiome.
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Affiliation(s)
- Waldemar Seel
- Nutrition and Microbiota, Institute of Nutrition and Food Sciences, University of Bonn, 53012 Bonn, Germany
| | - Sarah Reiners
- Junior Research Group Nutritional Concepts, Institute of Nutrition, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Kristin Kipp
- Department of Pediatrics and Adolescent Medicine, Sophien- and Hufeland Hospital, Henry-van-de-Velde-Str. 1, 99425 Weimar, Germany
| | - Marie-Christin Simon
- Nutrition and Microbiota, Institute of Nutrition and Food Sciences, University of Bonn, 53012 Bonn, Germany
| | - Christine Dawczynski
- Junior Research Group Nutritional Concepts, Institute of Nutrition, Friedrich Schiller University Jena, 07743 Jena, Germany
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3
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Rectal swabs as a viable alternative to faecal sampling for the analysis of gut microbiota functionality and composition. Sci Rep 2023; 13:493. [PMID: 36627399 PMCID: PMC9831010 DOI: 10.1038/s41598-022-27131-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 12/26/2022] [Indexed: 01/11/2023] Open
Abstract
Faecal or biopsy samples are frequently used to analyse the gut microbiota, but issues remain with the provision and collection of such samples. Rectal swabs are widely-utilised in clinical practice and previous data demonstrate their potential role in microbiota analyses; however, studies to date have been heterogenous, and there are a particular lack of data concerning the utility of swabs for the analysis of the microbiota's functionality and metabolome. We compared paired stool and rectal swab samples from healthy individuals to investigate whether rectal swabs are a reliable proxy for faecal sampling. There were no significant differences in key alpha and beta diversity measures between swab and faecal samples, and inter-subject variability was preserved. Additionally, no significant differences were demonstrated in abundance of major annotated phyla. Inferred gut functionality using Tax4Fun2 showed excellent correlation between the two sampling techniques (Pearson's coefficient r = 0.9217, P < 0.0001). Proton nuclear magnetic resonance (1H NMR) spectroscopy enabled the detection of 20 metabolites, with overall excellent correlation identified between rectal swab and faecal samples for levels all metabolites collectively, although more variable degrees of association between swab and stool for levels of individual metabolites. These data support the utility of rectal swabs in both compositional and functional analyses of the gut microbiota.
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Verderio P, Ciniselli CM, Gaignaux A, Pastori M, Saracino S, Kofanova O, Betsou F. External Quality Assurance programs for processing methods provide evidence on impact of preanalytical variables. N Biotechnol 2022; 72:29-37. [PMID: 36049650 DOI: 10.1016/j.nbt.2022.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/09/2022] [Accepted: 08/28/2022] [Indexed: 12/14/2022]
Abstract
An annual External Quality Assurance (EQA) program has been provided to processing laboratories over the last ten years, allowing them to assess the performance of their processing methods, such as nucleic acid extractions or peripheral blood mononuclear cell (PBMC) isolation and cryopreservation. The objective of this study was to perform a global analysis on almost 1000 EQA scheme/participant data in order to assess (i) the impact of critical preanalytical factors on quantitative or qualitative attributes of different types of specimens and (ii) laboratory performance pattern over time. Statistical analysis was performed within each EQA scheme based on categorized preanalytical data provided by the participants and on centralized measurements of relevant quality attributes of the produced specimens (z-scores): DNA, cell-free (cf)DNA or RNA extraction from blood, DNA or RNA extraction from formalin fixed tissue, DNA or RNA extraction from frozen tissue, DNA extraction from saliva or stool, viable PBMC isolation and cryopreservation. The most critical preanalytical factors in nucleic acid extraction schemes were the nucleic acid extraction method and kit, the elution buffer, the enzymes used during extraction, the input material quantity and the storage temperature. Several indications of laboratory performance improvement over time could be seen. The conclusions are that EQA for processing methods provides unique evidence-based insights into the impact of preanalytical factors and the comparative performance of different processing methods and kits, while supporting laboratories in validating their processing methods.
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Affiliation(s)
- Paolo Verderio
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy
| | - Chiara Maura Ciniselli
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy
| | - Amélie Gaignaux
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, 1 rue Louis Rech, 3555, Luxembourg
| | - Marta Pastori
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Italy
| | - Sabrina Saracino
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, 1 rue Louis Rech, 3555, Luxembourg
| | - Olga Kofanova
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, 1 rue Louis Rech, 3555, Luxembourg.
| | - Fay Betsou
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, 1 rue Louis Rech, 3555, Luxembourg; Institut Pasteur, Université Paris Cité, CRBIP, F-75015 Paris, France
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5
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Wieser M, Burger S, Ertl R, Kummer S, Stargardt M, Walter I. Example for process validation in biobanking: Fit for purpose testing of a cryopreservation method without isopentane. Front Mol Biosci 2022; 9:876670. [PMID: 36250023 PMCID: PMC9562646 DOI: 10.3389/fmolb.2022.876670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The freezing process of tissue samples is crucial for the preservation of morphological and molecular features. Several biobanking guidelines describe freezing techniques for optimal outcomes. As the Vetbiobank standard freezing protocol does not comply with those recommendations in detail, a process validation was performed to demonstrate that samples are suitable for downstream applications. Here we give a formal example of a process validation in the biobanking setting, as required by the biobanking guideline ISO 20387 (2018).Methods: Three different freezing protocols, freezing in liquid nitrogen, freezing via isopentane precooled on dry ice and freezing via liquid nitrogen vapor, were assessed based on morphological integrity of mouse liver and muscle tissue samples. Samples were either frozen in cryotubes (without Optimal Cutting Temperature compound, OCT) or in cryomolds (with OCT). The protocol providing the best results was validated for reproducibility and robustness in terms of defined acceptance criteria for morphological evaluability, A260/A280 ratio, and RNA integrity number values (RIN). In addition, performance tests were run by gene expression analyzes of selected, tissue specific biomarkers to confirm that processed samples are fit for purpose.Results: From the three applied freezing protocols, freezing in liquid nitrogen generated best results. Reproducibility acceptance criteria were met for both, morphological integrity and RNA quality. The freezing method was robust for the tested tissue types and the application of OCT, with exception of liver tissue, where it led to a significant decrease of the RIN value. Gene expression analyzes showed good comparability of results regardless of the applied freezing method.Conclusion: Freezing of tissue samples in liquid nitrogen provides samples of adequate quality for subsequent RNA investigations. A negative impact of OCT on the RIN value of liver samples was observed, which was independent from the applied freezing protocol and showed no impact on subsequent gene expression analysis.
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6
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Su W, Du Y, Lian F, Wu H, Zhang X, Yang W, Duan Y, Pan Y, Liu W, Wu A, Zhao B, Wu C, Wu S. Standards for Collection, Preservation, and Transportation of Fecal Samples in TCM Clinical Trials. Front Cell Infect Microbiol 2022; 12:783682. [PMID: 35521221 PMCID: PMC9065286 DOI: 10.3389/fcimb.2022.783682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 03/28/2022] [Indexed: 12/21/2022] Open
Abstract
Background Unlike chemical drugs with a single or a few kinds of active compounds, traditional Chinese medicines (TCMs)uses herbal formulas composed of numerous kinds of chemical constituents. Therefore, TCM clinical trials require unique and stricter standards for collecting, preserving, and transporting fecal samples than those used for chemical drugs. Unfortunately, there are no special standards for processing fecal samples in TCM clinical trials. Methods We invited interdisciplinary experts within TCM clinical trials and gut microbiome research to help formulate this standard. After more than a year's in-depth discussion and amendments, we achieved a standard via expert interviews, literature research, questionnaire surveys, and public opinion solicitation. This standard has been reviewed and approved by the Standards Office of China of the Association of Chinese medicine. Results We established a sample information processing method prior to TCM clinical sample collection, which is adapted to the unique features of TCM. The method formulates detailed processing requirements for TCM information in addition to the factors that may disturb the gut microbiome. We also constructed a set of methods for collecting, preserving, and transporting fecal samples that meet the characteristics of TCM. These methods formulate detailed operating specifications on the collection approaches, storage conditions, transportation requirements, and management of fecal samples. Conclusions This standard guides the information processing prior to sample collection and the standard operating procedures for the collection, preservation, and transportation of fecal samples in TCM clinical trials, which also can be used as a reference by clinicians and researchers in modern medicines.
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Affiliation(s)
- Wenquan Su
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yawei Du
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Fengmei Lian
- Department of Endocrinology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hui Wu
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xinrong Zhang
- Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Wenli Yang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yunfeng Duan
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuanming Pan
- The 7th Medical Center, Chinese People’s Liberation Army General Hospital, Beijing, China
| | - Weijng Liu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Aiming Wu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Bowen Zhao
- Beijing QuantiHealth Technology Co, Ltd, Beijing, China
| | - Chongming Wu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Shengxian Wu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
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7
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Hintikka JE, Munukka E, Valtonen M, Luoto R, Ihalainen JK, Kallonen T, Waris M, Heinonen OJ, Ruuskanen O, Pekkala S. Gut Microbiota and Serum Metabolome in Elite Cross-Country Skiers: A Controlled Study. Metabolites 2022; 12:metabo12040335. [PMID: 35448522 PMCID: PMC9028832 DOI: 10.3390/metabo12040335] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 12/11/2022] Open
Abstract
Exercise has been shown to affect gut the microbiome and metabolic health, with athletes typically displaying a higher microbial diversity. However, research on the gut microbiota and systemic metabolism in elite athletes remains scarce. In this study, we compared the gut microbiota profiles and serum metabolome of national team cross-country skiers at the end of an exhausting training and competitive season to those of normally physically-active controls. The gut microbiota were analyzed using 16S rRNA amplicon sequencing. Serum metabolites were analyzed using nuclear magnetic resonance. Phylogenetic diversity and the abundance of several mucin-degrading gut microbial taxa, including Akkermansia, were lower in the athletes. The athletes had a healthier serum lipid profile than the controls, which was only partly explained by body mass index. Butyricicoccus associated positively with HDL cholesterol, HDL2 cholesterol and HDL particle size. The Ruminococcus torques group was less abundant in the athlete group and positively associated with total cholesterol and VLDL and LDL particles. We found the healthier lipid profile of elite athletes to co-occur with known health-beneficial gut microbes. Further studies should elucidate these links and whether athletes are prone to mucin depletion related microbial changes during the competitive season.
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Affiliation(s)
- Jukka E. Hintikka
- Faculty of Sport and Health Sciences, University of Jyvaskyla, 40014 Jyväskylä, Finland; (J.K.I.); (S.P.)
- Correspondence:
| | - Eveliina Munukka
- Turku Microbiome Biobank, Institute of Biomedicine, University of Turku, 20500 Turku, Finland;
| | - Maarit Valtonen
- Research Institute for Olympic Sports, 40700 Jyväskylä, Finland;
| | - Raakel Luoto
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital, 20521 Turku, Finland; (R.L.); (O.R.)
| | - Johanna K. Ihalainen
- Faculty of Sport and Health Sciences, University of Jyvaskyla, 40014 Jyväskylä, Finland; (J.K.I.); (S.P.)
| | - Teemu Kallonen
- Clinical Microbiology, Turku University Hospital, 20521 Turku, Finland;
| | - Matti Waris
- Institute of Biomedicine, University of Turku, 20500 Turku, Finland;
| | - Olli J. Heinonen
- Paavo Nurmi Centre, Department of Health and Physical Activity, University of Turku, 20540 Turku, Finland;
| | - Olli Ruuskanen
- Department of Pediatrics and Adolescent Medicine, Turku University Hospital, 20521 Turku, Finland; (R.L.); (O.R.)
| | - Satu Pekkala
- Faculty of Sport and Health Sciences, University of Jyvaskyla, 40014 Jyväskylä, Finland; (J.K.I.); (S.P.)
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Rehner J, Schmartz GP, Groeger L, Dastbaz J, Ludwig N, Hannig M, Rupf S, Seitz B, Flockerzi E, Berger T, Reichert MC, Krawczyk M, Meese E, Herr C, Bals R, Becker SL, Keller A, Müller R. Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:405-417. [PMID: 35680095 PMCID: PMC9684153 DOI: 10.1016/j.gpb.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 01/05/2023]
Abstract
High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across datasets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of the specimen type and DNA extraction kit, 20-gigabase (Gb) metagenomic data were generated using short-read sequencing. While profiles of the specimen types showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kits. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution, but DNA-based identification is superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.
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Affiliation(s)
- Jacqueline Rehner
- Institute of Medical Microbiology and Hygiene, Saarland University, D-66421 Homburg, Germany
| | | | - Laura Groeger
- Department of Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Jan Dastbaz
- Helmholtz Institute for Pharmaceutical Research Saarland, D-66123 Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Matthias Hannig
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, D-66421 Homburg, Germany
| | - Stefan Rupf
- Clinic of Operative Dentistry, Periodontology and Preventive Dentistry, Saarland University, D-66421 Homburg, Germany
| | - Berthold Seitz
- Department of Ophthalmology, Saarland University Medical Center, D-66421 Homburg, Germany
| | - Elias Flockerzi
- Department of Ophthalmology, Saarland University Medical Center, D-66421 Homburg, Germany
| | - Tim Berger
- Department of Ophthalmology, Saarland University Medical Center, D-66421 Homburg, Germany
| | | | - Marcin Krawczyk
- Department of Medicine II, Saarland University Medical Center, D-66421 Homburg, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, D-66421 Homburg, Germany
| | - Christian Herr
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, D-66421 Homburg, Germany
| | - Robert Bals
- Department of Internal Medicine V - Pulmonology, Allergology, Intensive Care Medicine, Saarland University, D-66421 Homburg, Germany
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, D-66421 Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, D-66123 Saarbrücken, Germany.
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, D-66123 Saarbrücken, Germany
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Mommaerts K, Bellora C, Lambert P, Türkmen S, Schwamborn JC, Betsou F. Method Optimization of Skin Biopsy-Derived Fibroblast Culture for Reprogramming Into Induced Pluripotent Stem Cells. Biopreserv Biobank 2021; 20:12-23. [PMID: 34407379 DOI: 10.1089/bio.2020.0159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Fibroblasts can be isolated from skin biopsies using a chemical dissociation, a physical dissociation, or a combination of both techniques. They can be reprogrammed into induced pluripotent stem cells (iPSCs) through the introduction of defined sets of key transcription factors. This study aimed to identify the optimal protocol for skin biopsy dissociation, fibroblast culture, and fibroblast cryopreservation in the scope of reprogramming into iPSCs and in the context of biobank accreditation. Methods: First, four dissociation techniques typically used in the laboratory (explant based, enzymatic, and/or mechanical) and two cryopreservation media containing 10% dimethyl sulfoxide, either commercial or homemade, were evaluated in terms of post-thaw recovery, viability, growth curves, and karyotyping analyses of the fibroblasts. Next, the clones reprogrammed from the fibroblasts isolated with the two optimal dissociation methods and cryopreservation media were further assessed by reprogramming quality before cryopreservation and post-thaw pluripotency comparison. Results: Fibroblasts isolated from skin biopsies using an explant-based or enzymatic dissociation method showed higher viability, higher proliferative potential, and higher genome stability post-thaw compared to the other dissociation techniques. Fibroblasts obtained by the explant-based dissociation technique showed a slightly higher reprogramming quality. The iPSC reprogrammed from explant-based dissociated fibroblasts showed successful recovery of iPSC clones. No difference between the two cryopreservation media was detected for the tested endpoints, with the exception of a higher visual count of colonies at the end of the reprogramming for the explant-based dissociation method. Conclusions: This article presents a formal method optimization for biospecimen processing in the context of accreditation in laboratories and biobanks. We validated skin biopsy-derived fibroblast isolation, culture, and cryopreservation for downstream mRNA reprogramming into iPSCs. The explant-based dissociation technique and homemade medium are selected as optimal to isolate and cryopreserve fibroblasts from skin biopsies in the scope of reprogramming into iPSCs.
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Affiliation(s)
- Kathleen Mommaerts
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, Dudelange, Luxembourg.,Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Camille Bellora
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, Dudelange, Luxembourg
| | - Pauline Lambert
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, Dudelange, Luxembourg
| | - Seval Türkmen
- Hematooncogenetics, National Center of Genetics (NCG), Laboratoire National de Santé (LNS), Dudelange, Luxembourg
| | - Jens C Schwamborn
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Fay Betsou
- Integrated Biobank of Luxembourg (IBBL), Luxembourg Institute of Health, Dudelange, Luxembourg
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10
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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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11
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Haro C, Anguita-Maeso M, Metsis M, Navas-Cortés JA, Landa BB. Evaluation of Established Methods for DNA Extraction and Primer Pairs Targeting 16S rRNA Gene for Bacterial Microbiota Profiling of Olive Xylem Sap. FRONTIERS IN PLANT SCIENCE 2021; 12:640829. [PMID: 33777075 PMCID: PMC7994608 DOI: 10.3389/fpls.2021.640829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 02/08/2021] [Indexed: 06/12/2023]
Abstract
Next-generation sequencing has revolutionized our ability to investigate the microbiota composition of diverse and complex environments. However, a number of factors can affect the accuracy of microbial community assessment, such as the DNA extraction method, the hypervariable region of 16S rRNA gene targeted, or the PCR primers used for amplification. The aim of this study was to assess the influence of commercially available DNA extraction kits and different primer pairs to provide a non-biased vision of the composition of bacterial communities present in olive xylem sap. For that purpose, branches from "Picual" and "Arbequina" olive cultivars were used for xylem sap extraction using a Scholander chamber device. The DNA extraction protocol significantly affected xylem sap bacterial community assessment. That resulted in significant differences in alpha (Richness) and beta diversity (UniFrac distances) metrics among DNA extraction protocols, with the 12 DNA extraction kits evaluated being clustered in four groups behaving differently. Although the core number of taxa detected by all DNA extraction kits included four phyla, seven classes, 12 orders, 16 or 21 families, and 12 or 14 genera when using the Greengenes or Silva database for taxonomic assignment, respectively, some taxa, particularly those identified at low frequency, were detected by some DNA extraction kits only. The most accurate depiction of a bacterial mock community artificially inoculated on sap samples was generated when using the PowerPlant DNA extraction kit, the combination of 799F/1193R primers amplifying the hypervariable V5-V7 region, and the Silva 132 database for taxonomic assignment. The DESeq2 analysis displayed significant differences among genera abundance between the different PCR primer pairs tested. Thus, Enterobacter, Granulicatella, Prevotella, and Brevibacterium presented a significant higher abundance in all PCR protocols when compared with primer pair 799F/1193R, while the opposite was true for Pseudomonas and Pectobacterium. The methodological approach followed in this study can be useful to optimize plant-associated microbiome analysis, especially when exploring new plant niches. Some of the DNA extraction kits and PCR primers selected in this study will contribute to better characterize bacterial communities inhabiting the xylem sap of olives or other woody crop species.
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Affiliation(s)
- Carmen Haro
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | - Manuel Anguita-Maeso
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | | | - Juan A. Navas-Cortés
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
| | - Blanca B. Landa
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Córdoba, Spain
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12
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Spichak S, Bastiaanssen TFS, Berding K, Vlckova K, Clarke G, Dinan TG, Cryan JF. Mining microbes for mental health: Determining the role of microbial metabolic pathways in human brain health and disease. Neurosci Biobehav Rev 2021; 125:698-761. [PMID: 33675857 DOI: 10.1016/j.neubiorev.2021.02.044] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/12/2022]
Abstract
There is increasing knowledge regarding the role of the microbiome in modulating the brain and behaviour. Indeed, the actions of microbial metabolites are key for appropriate gut-brain communication in humans. Among these metabolites, short-chain fatty acids, tryptophan, and bile acid metabolites/pathways show strong preclinical evidence for involvement in various aspects of brain function and behaviour. With the identification of neuroactive gut-brain modules, new predictive tools can be applied to existing datasets. We identified 278 studies relating to the human microbiota-gut-brain axis which included sequencing data. This spanned across psychiatric and neurological disorders with a small number also focused on normal behavioural development. With a consistent bioinformatics pipeline, thirty-five of these datasets were reanalysed from publicly available raw sequencing files and the remainder summarised and collated. Among the reanalysed studies, we uncovered evidence of disease-related alterations in microbial metabolic pathways in Alzheimer's Disease, schizophrenia, anxiety and depression. Amongst studies that could not be reanalysed, many sequencing and technical limitations hindered the discovery of specific biomarkers of microbes or metabolites conserved across studies. Future studies are warranted to confirm our findings. We also propose guidelines for future human microbiome analysis to increase reproducibility and consistency within the field.
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Affiliation(s)
- Simon Spichak
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Thomaz F S Bastiaanssen
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Kirsten Berding
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Klara Vlckova
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland
| | - Gerard Clarke
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - Timothy G Dinan
- APC Microbiome Institute, University College Cork, Cork, Ireland; Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - John F Cryan
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland; APC Microbiome Institute, University College Cork, Cork, Ireland.
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Hardy T, Wonders K, Younes R, Aithal GP, Aller R, Allison M, Bedossa P, Betsou F, Boursier J, Brosnan MJ, Burt A, Cobbold J, Cortez-Pinto H, Day CP, Dufour JF, Ekstedt M, Francque S, Harrison S, Miele L, Nasr P, Papatheodoridis G, Petta S, Tiniakos D, Torstenson R, Valenti L, Holleboom AG, Yki-Jarvinen H, Geier A, Romero-Gomez M, Ratziu V, Bugianesi E, Schattenberg JM, Anstee QM. The European NAFLD Registry: A real-world longitudinal cohort study of nonalcoholic fatty liver disease. Contemp Clin Trials 2020; 98:106175. [PMID: 33045403 DOI: 10.1016/j.cct.2020.106175] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 10/03/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023]
Abstract
Non-Alcoholic Fatty Liver Disease (NAFLD), a progressive liver disease that is closely associated with obesity, type 2 diabetes, hypertension and dyslipidaemia, represents an increasing global public health challenge. There is significant variability in the disease course: the majority exhibit only fat accumulation in the liver but a significant minority develop a necroinflammatory form of the disease (non-alcoholic steatohepatitis, NASH) that may progress to cirrhosis and hepatocellular carcinoma. At present our understanding of pathogenesis, disease natural history and long-term outcomes remain incomplete. There is a need for large, well characterised patient cohorts that may be used to address these knowledge gaps and to support the development of better biomarkers and novel therapies. The European NAFLD Registry is an international, prospectively recruited observational cohort study that aims to establish a large, highly-phenotyped patient cohort and linked bioresource. Here we describe the infrastructure, data management and monitoring plans, and the standard operating procedures implemented to ensure the timely and systematic collection of high-quality data and samples. Already recruiting subjects at secondary/tertiary care centres across Europe, the Registry is supporting the European Union IMI2-funded LITMUS 'Liver Investigation: Testing Marker Utility in Steatohepatitis' consortium, which is a major international effort to robustly validate biomarkers that diagnose, risk stratify and/or monitor NAFLD progression and liver fibrosis stage. The European NAFLD Registry has the demonstrable capacity to support research and biomarker development at scale and pace.
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Affiliation(s)
- Timothy Hardy
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Kristy Wonders
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Ramy Younes
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Division of Gastroenterology, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Guruprasad P Aithal
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Rocio Aller
- Department of Gastroenterology, Clinic University Hospital, Medical School, University of Valladolid, Valladolid, Spain
| | - Michael Allison
- Liver Unit, Department of Medicine, Cambridge NIHR Biomedical Research Centre, Cambridge University NHS Foundation Trust, United Kingdom
| | - Pierre Bedossa
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Fay Betsou
- Integrated BioBank of Luxembourg (IBBL), 1, rue Louis Rech, L-3555, 3531 Dudelange, Luxembourg
| | - Jerome Boursier
- Service d'Hépato-Gastroentérologie, Centre Hospitalier Universitaire d'Angers, Angers, France; & Laboratoire HIFIH UPRES EA3859, Université d'Angers, Angers, France
| | | | - Alastair Burt
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Jeremy Cobbold
- Department of Gastroenterology and Hepatology, Oxford NIHR Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Helena Cortez-Pinto
- Clínica Universitária de Gastrenterologia, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Chris P Day
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Jean-Francois Dufour
- Department of Hepatology and Clinical Research, University of Bern, Bern, Switzerland
| | - Mattias Ekstedt
- Department of Gastroenterology and Hepatology, Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - Sven Francque
- Department of Gastroenterology Hepatology, Antwerp University Hospital, Belgium; Translational Sciences in Inflammation and Immunology, Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Stephen Harrison
- Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Luca Miele
- Department of Translational Medicine and Surgery, Medical School, Università Cattolica del S. Cuore and Fondazione Pol. Gemelli IRCCS Hospital, Rome, Italy
| | - Patrik Nasr
- Department of Gastroenterology and Hepatology, Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - George Papatheodoridis
- Department of Gastroenterology, Medical School of National and Kapodistrian University of Athens, General Hospital of Athens "Laiko", Athens, Greece
| | - Salvatore Petta
- Sezione di Gastroenterologia, Dipartimento Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Dina Tiniakos
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Department of Pathology, Aretaieion Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | | | - Luca Valenti
- Department of Pathophysiology and Transplantation, University of Milan, Translational Medicine - Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Adriaan G Holleboom
- Department of Vascular Medicine, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - Hannele Yki-Jarvinen
- University of Helsinki, Helsinki University Hospital, and Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Andreas Geier
- Department of Hepatology, University of Würzburg, Würzburg, Germany
| | - Manuel Romero-Gomez
- UCM Digestive Diseases, ciberehd and IBIS, Virgen del Rocío University Hospital, University of Seville, Seville, Spain
| | - Vlad Ratziu
- Sorbonne Université, Institute of Cardiometabolism and Nutrition, Pitié-Salpêtrière Hospital, Paris, France
| | - Elisabetta Bugianesi
- Division of Gastroenterology, Department of Medical Sciences, University of Torino, Torino, Italy
| | - Jörn M Schattenberg
- Metabolic Liver Research Program, I. Department of Medicine, University Medical Centre, Mainz, Germany
| | - Quentin M Anstee
- Translational & Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Newcastle NIHR Biomedical Research Centre, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.
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14
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Baldini F, Hertel J, Sandt E, Thinnes CC, Neuberger-Castillo L, Pavelka L, Betsou F, Krüger R, Thiele I. Parkinson's disease-associated alterations of the gut microbiome predict disease-relevant changes in metabolic functions. BMC Biol 2020; 18:62. [PMID: 32517799 PMCID: PMC7285525 DOI: 10.1186/s12915-020-00775-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 03/27/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is a systemic disease clinically defined by the degeneration of dopaminergic neurons in the brain. While alterations in the gut microbiome composition have been reported in PD, their functional consequences remain unclear. Herein, we addressed this question by an analysis of stool samples from the Luxembourg Parkinson's Study (n = 147 typical PD cases, n = 162 controls). RESULTS All individuals underwent detailed clinical assessment, including neurological examinations and neuropsychological tests followed by self-reporting questionnaires. Stool samples from these individuals were first analysed by 16S rRNA gene sequencing. Second, we predicted the potential secretion for 129 microbial metabolites through personalised metabolic modelling using the microbiome data and genome-scale metabolic reconstructions of human gut microbes. Our key results include the following. Eight genera and seven species changed significantly in their relative abundances between PD patients and healthy controls. PD-associated microbial patterns statistically depended on sex, age, BMI, and constipation. Particularly, the relative abundances of Bilophila and Paraprevotella were significantly associated with the Hoehn and Yahr staging after controlling for the disease duration. Furthermore, personalised metabolic modelling of the gut microbiomes revealed PD-associated metabolic patterns in the predicted secretion potential of nine microbial metabolites in PD, including increased methionine and cysteinylglycine. The predicted microbial pantothenic acid production potential was linked to the presence of specific non-motor symptoms. CONCLUSION Our results suggest that PD-associated alterations of the gut microbiome can translate into substantial functional differences affecting host metabolism and disease phenotype.
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Affiliation(s)
- Federico Baldini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
| | - Johannes Hertel
- School of Medicine, National University of Ireland, Galway, Ireland
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Estelle Sandt
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | | | | | - Lukas Pavelka
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg City, Luxembourg
| | - Fay Betsou
- Integrated BioBank of Luxembourg, Dudelange, Luxembourg
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg City, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Ines Thiele
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, Esch-sur-Alzette, Luxembourg.
- School of Medicine, National University of Ireland, Galway, Ireland.
- Discipline of Microbiology, School of Natural Sciences, National University of Ireland, Galway, Ireland.
- APC Microbiome, Cork, Ireland.
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