1
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Mehra P, Kumar A. Emerging importance of stool preservation methods in OMICS studies with special focus on cancer biology. Cell Biochem Funct 2024; 42:e4063. [PMID: 38961596 DOI: 10.1002/cbf.4063] [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: 12/26/2023] [Revised: 05/12/2024] [Accepted: 05/18/2024] [Indexed: 07/05/2024]
Abstract
The intricate consortium of microorganisms in the human gut plays a crucial role in different physiological functions. The complex known-unknown elements of the gut microbiome are perplexing and the absence of standardized procedures for collecting and preserving samples has hindered continuous research in comprehending it. The technological bias produced because of lack of standard protocols has affected the reproducibility of results. The complex nature of diseases like colorectal cancer, gastric cancer, hepatocellular carcinoma and breast cancer require a thorough understanding of its etiology for an efficient and timely diagnosis. The designated protocols for collection and preservation of stool specimens have great variance, hence generate inconsistencies in OMICS studies. Due to the complications associated to the nature of sample, it is important to preserve the sample to be studied later in a laboratory or to be used in the future research purpose. Stool preservation is gaining importance due to the increased use of treatment options like fecal microbiota transplantation to cure conditions like recurrent Clostridium difficile infections and for OMICS studies including metagenomics, metabolomics and culturomics. This review provides an insight into the importance of omics studies for the identification and development of novel biomarkers for quick and noninvasive diagnosis of various diseases.
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Affiliation(s)
- Parul Mehra
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
| | - Anil Kumar
- Gene Regulation Laboratory, National Institute of Immunology, New Delhi, India
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2
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Roume H, Mondot S, Saliou A, Le Fresne-Languille S, Doré J. Multicenter evaluation of gut microbiome profiling by next-generation sequencing reveals major biases in partial-length metabarcoding approach. Sci Rep 2023; 13:22593. [PMID: 38114587 PMCID: PMC10730622 DOI: 10.1038/s41598-023-46062-7] [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: 02/27/2023] [Accepted: 10/27/2023] [Indexed: 12/21/2023] Open
Abstract
Next-generation sequencing workflows, using either metabarcoding or metagenomic approaches, have massively contributed to expanding knowledge of the human gut microbiota, but methodological bias compromises reproducibility across studies. Where these biases have been quantified within several comparative analyses on their own, none have measured inter-laboratory reproducibility using similar DNA material. Here, we designed a multicenter study involving seven participating laboratories dedicated to partial- (P1 to P5), full-length (P6) metabarcoding, or metagenomic profiling (MGP) using DNA from a mock microbial community or extracted from 10 fecal samples collected at two time points from five donors. Fecal material was collected, and the DNA was extracted according to the IHMS protocols. The mock and isolated DNA were then provided to the participating laboratories for sequencing. Following sequencing analysis according to the laboratories' routine pipelines, relative taxonomic-count tables defined at the genus level were provided and analyzed. Large variations in alpha-diversity between laboratories, uncorrelated with sequencing depth, were detected among the profiles. Half of the genera identified by P1 were unique to this partner and two-thirds of the genera identified by MGP were not detected by P3. Analysis of beta-diversity revealed lower inter-individual variance than inter-laboratory variances. The taxonomic profiles of P5 and P6 were more similar to those of MGP than those obtained by P1, P2, P3, and P4. Reanalysis of the raw sequences obtained by partial-length metabarcoding profiling, using a single bioinformatic pipeline, harmonized the description of the bacterial profiles, which were more similar to each other, except for P3, and closer to the profiles obtained by MGP. This study highlights the major impact of the bioinformatics pipeline, and primarily the database used for taxonomic annotation. Laboratories need to benchmark and optimize their bioinformatic pipelines using standards to monitor their effectiveness in accurately detecting taxa present in gut microbiota.
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Affiliation(s)
- Hugo Roume
- Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France
- Discovery & Front End Innovation, Lesaffre Institute of Science & Technology, Lesaffre International, 101 rue de Menin, 59700, Marcq-en-Barœul, France
| | - Stanislas Mondot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Adrien Saliou
- BIOASTER, Microbiology Technology Institute, 40 Avenue Tony Garnier, 69007, Lyon, France
| | | | - Joël Doré
- Université Paris-Saclay, INRAE, MetaGenoPolis, 78350, Jouy-en-Josas, France.
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
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3
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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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4
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Multi-omics approach in tea polyphenol research regarding tea plant growth, development and tea processing: current technologies and perspectives. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2021.12.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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5
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Chen M, Huo X, Wang W, Shan H, Jiang P, Liang W, Liu B. Cryopreservation of Infant Gut Microbiota with Natural Cryoprotectants. Biopreserv Biobank 2021; 20:138-148. [PMID: 34714122 DOI: 10.1089/bio.2021.0029] [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
A growing body of evidence has demonstrated the importance of the gut microbiome in human health. In general, fecal microbial samples are used to study the mechanisms of relevant diseases. In this context, it is worth mentioning that an optimized cryopreservation method is urgently needed to successfully perform clinical diagnosis, therapy, and scientific investigations of the gut microbiome without affecting its viability and biological activity. In this study, we aimed to test the relative cryopreservation efficiency of different nontoxic natural cryoprotectants using infant fecal and meconium samples. First, we selected two facultative and two obligate anaerobic bacteria as the experimental gut microbial strain to compare these cryoprotectants' toxicity and concentration-dependent bacteria viabilities after cryopreservation, then the viabilities and bacterial diversity of mixed facultative and obligate anaerobic bacteria. Finally, we explored the effects of optimized cryoprotectants for meconium and infant feces after cryopreservation using 16S rRNA sequencing analyses. In addition, to better understand the effectiveness of these cryoprotectants, we used different freeze-thaw conditions mimicking real-life situations in the process of distribution. We found that the better choice for the infant fecal sample's cryopreservation was 100 mg/mL trehalose, whereas 200 mg/mL trehalose/betaine was the optimum choice for meconium cryopreservation. We hope that our results will shed light on the importance of natural cryoprotectants toward the long-term and stable viability of invaluable human gut microbial specimens.
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Affiliation(s)
- Mu Chen
- Institute of Biothermal Science, University of Shanghai for Science and Technology, Shanghai, China.,Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaoyue Huo
- Lanzhou Institute of Biological Products Co., Ltd, Lanzhou, China
| | - Weiye Wang
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongyun Shan
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Pei Jiang
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wei Liang
- Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Baolin Liu
- Institute of Biothermal Science, University of Shanghai for Science and Technology, Shanghai, China
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6
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Heinzel S, Aho VTE, Suenkel U, von Thaler AK, Schulte C, Deuschle C, Paulin L, Hantunen S, Brockmann K, Eschweiler GW, Maetzler W, Berg D, Auvinen P, Scheperjans F. Gut Microbiome Signatures of Risk and Prodromal Markers of Parkinson Disease. Ann Neurol 2021; 90:E1-E12. [PMID: 34021620 DOI: 10.1002/ana.26128] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/14/2021] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Alterations of the gut microbiome in Parkinson disease (PD) have been repeatedly demonstrated. However, little is known about whether such alterations precede disease onset and how they relate to risk and prodromal markers of PD. We investigated associations of these features with gut microbiome composition. METHODS Established risk and prodromal markers of PD as well as factors related to diet/lifestyle, bowel function, and medication were studied in relation to bacterial α-/β-diversity, enterotypes, and differential abundance in stool samples of 666 elderly TREND (Tübingen Evaluation of Risk Factors for Early Detection of Neurodegeneration) study participants. RESULTS Among risk and prodromal markers, physical inactivity, occupational solvent exposure, and constipation showed associations with α-diversity. Physical inactivity, sex, constipation, possible rapid eye movement sleep behavior disorder (RBD), and smoking were associated with β-diversity. Subthreshold parkinsonism and physical inactivity showed an interaction effect. Among other factors, age and urate-lowering medication were associated with α- and β-diversity. Constipation was highest in individuals with the Firmicutes-enriched enterotype, and physical inactivity was most frequent in the Bacteroides-enriched enterotype. Constipation was lowest and subthreshold parkinsonism least frequent in individuals with the Prevotella-enriched enterotype. Differentially abundant taxa were linked to constipation, physical inactivity, possible RBD, smoking, and subthreshold parkinsonism. Substantia nigra hyperechogenicity, olfactory loss, depression, orthostatic hypotension, urinary/erectile dysfunction, PD family history, and the prodromal PD probability showed no significant microbiome associations. INTERPRETATION Several risk and prodromal markers of PD are associated with gut microbiome composition. However, the impact of the gut microbiome on PD risk and potential microbiome-dependent subtypes in the prodrome of PD need further investigation based on prospective clinical and (multi)omics data in incident PD cases. ANN NEUROL 2021;90:E1-E12.
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Affiliation(s)
- Sebastian Heinzel
- Department of Neurology, Christian-Albrechts University, Kiel, Germany
| | - Velma T E Aho
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
- Department of Neurology, Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Helsinki, Finland
| | - Ulrike Suenkel
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Anna-Katharina von Thaler
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Claudia Schulte
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Christian Deuschle
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sari Hantunen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Kathrin Brockmann
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Gerhard W Eschweiler
- Department of Psychiatry and Psychotherapy, Geriatric Center, Tübingen University Hospital, Tübingen, Germany
- Geriatric Center, Tübingen University Hospital, Tübingen, Germany
| | - Walter Maetzler
- Department of Neurology, Christian-Albrechts University, Kiel, Germany
| | - Daniela Berg
- Department of Neurology, Christian-Albrechts University, Kiel, Germany
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Filip Scheperjans
- Department of Neurology, Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Helsinki, Finland
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7
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Phan NN, Chattopadhyay A, Lee TT, Yin HI, Lu TP, Lai LC, Hwa HL, Tsai MH, Chuang EY. High-performance deep learning pipeline predicts individuals in mixtures of DNA using sequencing data. Brief Bioinform 2021; 22:6345217. [PMID: 34368845 DOI: 10.1093/bib/bbab283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/20/2021] [Accepted: 07/03/2021] [Indexed: 11/14/2022] Open
Abstract
In this study, we proposed a deep learning (DL) model for classifying individuals from mixtures of DNA samples using 27 short tandem repeats and 94 single nucleotide polymorphisms obtained through massively parallel sequencing protocol. The model was trained/tested/validated with sequenced data from 6 individuals and then evaluated using mixtures from forensic DNA samples. The model successfully identified both the major and the minor contributors with 100% accuracy for 90 DNA mixtures, that were manually prepared by mixing sequence reads of 3 individuals at different ratios. Furthermore, the model identified 100% of the major contributors and 50-80% of the minor contributors in 20 two-sample external-mixed-samples at ratios of 1:39 and 1:9, respectively. To further demonstrate the versatility and applicability of the pipeline, we tested it on whole exome sequence data to classify subtypes of 20 breast cancer patients and achieved an area under curve of 0.85. Overall, we present, for the first time, a complete pipeline, including sequencing data processing steps and DL steps, that is applicable across different NGS platforms. We also introduced a sliding window approach, to overcome the sequence length variation problem of sequencing data, and demonstrate that it improves the model performance dramatically.
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Affiliation(s)
- Nam Nhut Phan
- Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Biomedical Electronics and Bioinformatics, Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan.,Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Amrita Chattopadhyay
- Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Tsui-Ting Lee
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsiang-I Yin
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Tzu-Pin Lu
- Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan.,Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Liang-Chuan Lai
- Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan.,Graduate Institute of Physiology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
| | - Hsiao-Lin Hwa
- Department and Graduate Institute of Forensic Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Mong-Hsun Tsai
- Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan.,Institute of Biotechnology, National Taiwan University, Taipei 10672, Taiwan.,Center of Biotechnology, National Taiwan University, Taipei 10672, Taiwan
| | - Eric Y Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, Department of Electrical Engineering, National Taiwan University, Taipei, Taiwan.,Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei 10055, Taiwan.,Master Program for Biomedical Engineering, China Medical University, Taichung 110122, Taiwan
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8
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Pribyl AL, Parks DH, Angel NZ, Boyd JA, Hasson AG, Fang L, MacDonald SL, Wills BA, Wood DLA, Krause L, Tyson GW, Hugenholtz P. Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME COMMUNICATIONS 2021; 1:14. [PMID: 37938632 PMCID: PMC9645250 DOI: 10.1038/s43705-021-00014-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/14/2021] [Accepted: 04/06/2021] [Indexed: 05/04/2023]
Abstract
The ability to preserve microbial communities in faecal samples is essential as increasing numbers of studies seek to use the gut microbiome to identify biomarkers of disease. Here we use shotgun metagenomics to rigorously evaluate the technical and compositional reproducibility of five room temperature (RT) microbial stabilisation methods compared to the best practice of flash-freezing. These methods included RNALater, OMNIGene-GUT, a dry BBL swab, LifeGuard, and a novel method for preserving faecal samples, a Copan FLOQSwab in an active drying tube (FLOQSwab-ADT). Each method was assessed using six replicate faecal samples from five participants, totalling 180 samples. The FLOQSwab-ADT performed best for both technical and compositional reproducibility, followed by RNAlater and OMNIgene-GUT. LifeGuard and the BBL swab had unpredictable outgrowth of Escherichia species in at least one replicate from each participant. We further evaluated the FLOQSwab-ADT in an additional 239 samples across 10 individuals after storage at -20 °C, RT, and 50 °C for four weeks compared to fresh controls. The FLOQSwab-ADT maintained its performance across all temperatures, indicating this method is an excellent alternative to existing RT stabilisation methods.
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Affiliation(s)
| | | | | | - Joel A Boyd
- Microba Life Sciences, Brisbane, QLD, Australia
| | | | - Liang Fang
- Microba Life Sciences, Brisbane, QLD, Australia
| | | | | | | | - Lutz Krause
- Microba Life Sciences, Brisbane, QLD, Australia
| | - Gene W Tyson
- Microba Life Sciences, Brisbane, QLD, Australia
- Centre for Microbiome Research, School of Biomedical Science, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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9
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Abstract
Expanding our knowledge of microbial communities across diverse environments includes collecting samples in places far from the laboratory. Identifying cost-effective preservatives that will enable room temperature storage of microbial communities for sequencing analysis is crucial to enabling microbiome analyses across diverse populations. As the number of human microbiome studies expand, it is increasingly important to identify cost-effective, practical preservatives that allow for room temperature sample storage. Here, we reanalyzed 16S rRNA gene amplicon sequencing data from a large sample storage study published in 2016 and performed shotgun metagenomic sequencing on remnant DNA from this experiment. Both results support the initial findings that 95% ethanol, a nontoxic, cost-effective preservative, is effective at preserving samples at room temperature for weeks. We expanded on this analysis by collecting a new set of fecal, saliva, and skin samples to determine the optimal ratio of 95% ethanol to sample. We identified optimal collection protocols for fecal samples (storing a fecal swab in 95% ethanol) and saliva samples (storing unstimulated saliva in 95% ethanol at a ratio of 1:2). Storing skin swabs in 95% ethanol reduced microbial biomass and disrupted community composition, highlighting the difficulties of low biomass sample preservation. The results from this study identify practical solutions for large-scale analyses of fecal and oral microbial communities. IMPORTANCE Expanding our knowledge of microbial communities across diverse environments includes collecting samples in places far from the laboratory. Identifying cost-effective preservatives that will enable room temperature storage of microbial communities for sequencing analysis is crucial to enabling microbiome analyses across diverse populations. Here, we validate findings that 95% ethanol efficiently preserves microbial composition at room temperature for weeks. We also identified the optimal ratio of 95% ethanol to sample for stool and saliva to preserve both microbial load and composition. These results provide rationale for an accessible, nontoxic, cost-effective solution that will enable crowdsourcing microbiome studies, such as The Microsetta Initiative, and lower the barrier for collecting diverse samples.
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10
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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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11
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Reitmeier S, Kiessling S, Neuhaus K, Haller D. Comparing Circadian Rhythmicity in the Human Gut Microbiome. STAR Protoc 2020; 1:100148. [PMID: 33377042 PMCID: PMC7757335 DOI: 10.1016/j.xpro.2020.100148] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Targeted sequencing of 16S rRNA genes enables the analysis of microbiomes. Here, we describe a protocol for the collection, storage, and preparation of fecal samples. We describe how we cluster similar sequences and assign bacterial taxonomies. Using diversity analysis and machine learning, we can extract disease-associated features. We also describe a circadian analysis to identify the presence or absence of rhythms in taxonomies. Differences in rhythmicity between cohorts can contribute to determining disease-associated bacterial signatures. For complete details on the use and execution of this protocol, please refer to Reitmeier et al. (2020). Walkthrough of sample preparation for 16S rRNA gene sequencing for human stool samples Determine disease-associated microbial features based on machine learning Circadian analysis to identify presence of rhythms in a population-based cohort study Define bacterial signatures by differences in rhythmicity within/between cohorts
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Affiliation(s)
- Sandra Reitmeier
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.,Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Silke Kiessling
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.,Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
| | - Klaus Neuhaus
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany
| | - Dirk Haller
- ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.,Chair of Nutrition and Immunology, Technical University of Munich, Gregor-Mendel-Str. 2, 85354 Freising, Germany
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12
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Heinzel S, Aho VTE, Suenkel U, von Thaler AK, Schulte C, Deuschle C, Paulin L, Hantunen S, Brockmann K, Eschweiler GW, Maetzler W, Berg D, Auvinen P, Scheperjans F. Gut Microbiome Signatures of Risk and Prodromal Markers of Parkinson Disease. Ann Neurol 2020; 88:320-331. [PMID: 32441370 DOI: 10.1002/ana.25788] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Alterations of the gut microbiome in Parkinson disease (PD) have been repeatedly demonstrated. However, little is known about whether such alterations precede disease onset and how they relate to risk and prodromal markers of PD. We investigated associations of these features with gut microbiome composition. METHODS Established risk and prodromal markers of PD as well as factors related to diet/lifestyle, bowel function, and medication were studied in relation to bacterial α-/β-diversity, enterotypes, and differential abundance in stool samples of 666 elderly TREND (Tübingen Evaluation of Risk Factors for Early Detection of Neurodegeneration) study participants. RESULTS Among risk and prodromal markers, physical activity, occupational solvent exposure, and constipation showed associations with α-diversity. Physical activity, sex, constipation, possible rapid eye movement sleep behavior disorder (RBD), and smoking were associated with β-diversity. Subthreshold parkinsonism and physical activity showed an interaction effect. Among other factors, age and urate-lowering medication were associated with α- and β-diversity. Physical inactivity and constipation were highest in individuals with the Firmicutes-enriched enterotype. Constipation was lowest and subthreshold parkinsonism least frequent in individuals with the Prevotella-enriched enterotype. Differentially abundant taxa were linked to constipation, physical activity, possible RBD, smoking, and subthreshold parkinsonism. Substantia nigra hyperechogenicity, olfactory loss, depression, orthostatic hypotension, urinary/erectile dysfunction, PD family history, and the prodromal PD probability showed no significant microbiome associations. INTERPRETATION Several risk and prodromal markers of PD are associated with gut microbiome composition. However, the impact of the gut microbiome on PD risk and potential microbiome-dependent subtypes in the prodrome of PD need further investigation based on prospective clinical and (multi)omics data in incident PD cases. ANN NEUROL 2020;88:320-331.
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Affiliation(s)
- Sebastian Heinzel
- Department of Neurology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Velma T E Aho
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Department of Neurology, Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Helsinki, Finland
| | - Ulrike Suenkel
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Anna-Katharina von Thaler
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Claudia Schulte
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Christian Deuschle
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Sari Hantunen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Kathrin Brockmann
- Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany.,German Center for Neurodegenerative Diseases, University of Tübingen, Tübingen, Germany
| | - Gerhard W Eschweiler
- Department of Psychiatry and Psychotherapy, University of Tübingen, Tübingen, Germany.,Geriatric Center at the University Hospital Tübingen, Tübingen, Germany
| | - Walter Maetzler
- Department of Neurology, Christian-Albrechts University of Kiel, Kiel, Germany
| | - Daniela Berg
- Department of Neurology, Christian-Albrechts University of Kiel, Kiel, Germany.,Department of Neurodegeneration, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Filip Scheperjans
- Department of Neurology, Helsinki University Hospital and Department of Clinical Neurosciences (Neurology), University of Helsinki, Helsinki, Finland
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13
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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: 106] [Impact Index Per Article: 26.5] [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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14
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Neuberger-Castillo L, Hamot G, Marchese M, Sanchez I, Ammerlaan W, Betsou F. Method Validation for Extraction of DNA from Human Stool Samples for Downstream Microbiome Analysis. Biopreserv Biobank 2020; 18:102-116. [PMID: 31999474 DOI: 10.1089/bio.2019.0112] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background: A formal method validation for biospecimen processing in the context of accreditation in laboratories and biobanks is lacking. A previously optimized stool processing protocol was validated for fitness-for-purpose for downstream microbiome analysis. Materials and Methods: DNA extraction from human stool was validated with various collection tubes, stabilizing solutions and storage conditions in terms of fitness-for-purpose for downstream microbiome analysis, robustness, and sample stability. Acceptance criteria were based on accurate identification of a reference material, homogeneity of extracted samples, and sample stability in a 2-year period. Results: The automated DNA extraction using the chemagic™ Magnetic Separation Module I (MSM I) extracted 8 out of 8 bacteria in the ZymoBIOMICS® Microbial Community Standard. Seven tested stabilizing solutions (OMNIgene®•GUT, RNAlater®, AquaStool™, RNAssist, PerkinElmer SEB lysis buffer, and DNA Genotek's CP-150) were all compatible with the chemagic MSM I and showed no significant difference in microbiome alpha diversity and no significant difference in the overall microbiome composition compared to the baseline snap-frozen stool sample. None of the stabilizing solutions showed intensive polymerase chain reaction (PCR) inhibition in the SPUD assay. However, when we take into account more stringent criteria which include a higher double-stranded DNA yield, higher DNA purity, and absence of PCR inhibition, we recommend the use of OMNIgene•GUT, RNAlater, or AquaStool as alternatives to rapid freezing of samples. The highest sample homogeneity was achieved with RNAlater- and OMNIgene•GUT -stabilized samples. Sample stability after a 2-year storage in -80°C was seen with OMNIgene•GUT -stabilized samples. Conclusions: We validated a combination of a stool processing method with various collection methods, suitable for downstream microbiome applications. Sample collection, storage conditions and DNA extraction methods can influence the microbiome profile results. Laboratories and biobanks should ensure that these conditions are systematically recorded in the scope of accreditation.
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Affiliation(s)
| | - Gaël Hamot
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Monica Marchese
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Ignacio Sanchez
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Wim Ammerlaan
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
| | - Fay Betsou
- Integrated BioBank of Luxembourg (IBBL), Dudelange, Luxembourg
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