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Long AE, Pitta D, Hennessy M, Indugu N, Vecchiarelli B, Luethy D, Aceto H, Hurcombe S. Assessment of fecal bacterial viability and diversity in fresh and frozen fecal microbiota transplant (FMT) product in horses. BMC Vet Res 2024; 20:306. [PMID: 38987780 PMCID: PMC11234551 DOI: 10.1186/s12917-024-04166-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/01/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Currently, lack of standardization for fecal microbiota transplantation (FMT) in equine practice has resulted in highly variable techniques, and there is no data on the bacterial metabolic activity or viability of the administered product. The objectives of this study were to compare the total and potentially metabolically active bacterial populations in equine FMT, and assess the effect of different frozen storage times, buffers, and temperatures on an equine FMT product. Fresh feces collected from three healthy adult horses was subjected to different storage methods. This included different preservation solutions (saline plus glycerol or saline only), temperature (-20 °C or -80 °C), and time (fresh, 30, 60, or 90 days). Samples underwent DNA extraction to assess total bacterial populations (both live and dead combined) and RNA extraction followed by reverse transcription to cDNA as a proxy to assess viable bacteria, then 16s rRNA gene amplicon sequencing using the V1-V2 region. RESULTS The largest difference in population indices and taxonomic composition at the genus level was seen when evaluating the results of DNA-based (total) and cDNA-based (potentially metabolically active) extraction method. At the community level, alpha diversity (observed species, Shannon diversity) was significantly decreased in frozen samples for DNA-based analysis (P < 0.05), with less difference seen for cDNA-based sequencing. Using DNA-based analysis, length of storage had a significant impact (P < 0.05) on the bacterial community profiles. For potentially metabolically active populations, storage overall had less of an effect on the bacterial community composition, with a significant effect of buffer (P < 0.05). Individual horse had the most significant effect within both DNA and cDNA bacterial communities. CONCLUSIONS Frozen storage of equine FMT material can preserve potentially metabolically active bacteria of the equine fecal microbiome, with saline plus glycerol preservation more effective than saline alone. Larger studies are needed to determine if these findings apply to other individual horses. The ability to freeze FMT material for use in equine patients could allow for easier clinical use of fecal transplant in horses with disturbances in their intestinal microbiome.
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Affiliation(s)
- Alicia E Long
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA.
| | - Dipti Pitta
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Meagan Hennessy
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Nagaraju Indugu
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Bonnie Vecchiarelli
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Daniela Luethy
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Helen Aceto
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
| | - Samuel Hurcombe
- Department of Clinical Studies, New Bolton Center, University of Pennsylvania, Kennett Square, PA, USA
- Veterinary Innovative Partners, New York, NY, USA
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2023:1-19. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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3
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Zhang X, Mao F, Li Y, Wang J, Wu L, Sun J, Cao F. Effects of a maternal mindfulness intervention targeting prenatal psychological distress on infants' meconium microbiota: A randomized controlled trial. Psychoneuroendocrinology 2022; 145:105913. [PMID: 36081227 DOI: 10.1016/j.psyneuen.2022.105913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Maternal psychological distress could affect gut microbiota of the infant; however, previous studies to date have been observational. OBJECTIVE To investigate the effects of mindfulness-based intervention (MBI) during pregnancy on the meconium microbiota of infants by alleviating maternal psychological distress. DESIGN Randomized controlled trial. METHOD Pregnant women with symptoms of depression or anxiety were randomized to either the intervention group (n = 80), comprising usual perinatal care and six digitally guided self-help MBI sessions, or the control group (n = 80) who underwent usual perinatal care. Meconium was collected within 48 h of birth to evaluate the infant's gut microbiota. The Kruskal-Wallis rank sum test, analysis of similarities, and DESeq2 were performed to explore the effects of the MBI on alpha and beta diversity indices and specific genera. RESULTS There were no significant differences between groups regarding the alpha diversity indices, including Chao1 and Simpson (p = 0.83 and p = 0.58). However, there was a significant between-group difference in the beta diversity index (R=0.02, p = 0.03). Bifidobacterium (log2 fold change=-1.90, FDR=0.002) and Blautia (log2 fold change=-1.45, FDR=0.01) were abundant in the intervention group, whereas Staphylococcus (log2 fold change=1.44, FDR=0.01) was abundant in the control group. CONCLUSIONS MBI aimed at alleviating maternal psychological distress can positively alter the meconium microbiota of infants. However, the mechanisms underlying the effects of maternal mindfulness during pregnancy on infant meconium microbiota require further exploration.
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Affiliation(s)
- Xuan Zhang
- School of Nursing and Rehabilitation, Shandong University, Jinan, Shandong, China
| | - Fangxiang Mao
- School of Nursing and Rehabilitation, Shandong University, Jinan, Shandong, China
| | - Yang Li
- School of Nursing, The University of Texas at Austin, Austin, USA
| | - Juan Wang
- School of Nursing and Rehabilitation, Shandong University, Jinan, Shandong, China
| | - Liuliu Wu
- School of Nursing and Rehabilitation, Shandong University, Jinan, Shandong, China
| | - Jiwei Sun
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Fenglin Cao
- School of Nursing and Rehabilitation, Shandong University, Jinan, Shandong, China.
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Zhang N, Zhang Y, Wang Z, Pan F, Ren R, Li Z, Zhao H, Luo X, Li Z, Wang L, Mo R, Sun G, Peng L, Ni M, Yang Y. Regular fecal microbiota transplantation to Senescence Accelerated Mouse-Prone 8 (SAMP8) mice delayed the aging of locomotor and exploration ability by rejuvenating the gut microbiota. Front Aging Neurosci 2022; 14:991157. [PMID: 36262889 PMCID: PMC9574184 DOI: 10.3389/fnagi.2022.991157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/14/2022] [Indexed: 12/04/2022] Open
Abstract
Recent evidence points out the role of the gut microbiota in the aging process. However, the specific changes and relevant interventions remain unclear. In this study, Senescence Accelerated Mouse-Prone 8 (SAMP8) mice were divided into four groups; young-FMT-group transplanted fecal microbiota from young donors (2–3°months old) and old-FMT-group transplanted from old donors (10–11°months old); additionally, other two groups either adult mice injected with saline solution or untreated mice served as the saline and blank control groups, respectively. All mice were intervened from their 7-months-old until 13-months-old. The open field test at 9 and 11°months of age showed that the mice transplanted with gut microbiota from young donors had significantly better locomotor and exploration ability than those of transplanted with old-donors gut microbiota and those of saline control while was comparable with the blank control. 16S rRNA gene sequencing showed that the gut microbiome of recipient mice of young donors was altered at 11°months of age, whereas the alternation of the gut microbiome of old-donor recipient mice was at 9°months. For comparison, the recipient mice in the blank and saline control groups exhibited changes in the gut microbiome at 10°months of age. The hallmark of aging-related gut microbiome change was an increase in the relative abundance of Akkermansia, which was significantly higher in the recipients transplanted with feces from older donors than younger donors at 9°months of age. This study shows that fecal microbiota transplantation from younger donors can delay aging-related declines in locomotor and exploration ability in mice by changing the gut microbiome.
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Affiliation(s)
- Nana Zhang
- Medical School of Chinese PLA, Beijing, China
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yan Zhang
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- Institute of Health Service and Transfusion Medicine, Beijing, China
| | - Zikai Wang
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Fei Pan
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Rongrong Ren
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhengpeng Li
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Huijun Zhao
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xi Luo
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zongwei Li
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Lei Wang
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Rui Mo
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Gang Sun
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Lihua Peng
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Ming Ni
- Institute of Health Service and Transfusion Medicine, Beijing, China
- Ming Ni,
| | - Yunsheng Yang
- Microbiota Division, Department of Gastroenterology and Hepatology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
- National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, China
- *Correspondence: Yunsheng Yang,
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Cryopreservation of stool samples altered the microbial viability quantitively and compositionally. Arch Microbiol 2022; 204:557. [PMID: 35972563 DOI: 10.1007/s00203-022-03169-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 05/24/2022] [Accepted: 08/04/2022] [Indexed: 11/02/2022]
Abstract
Stool is the most commonly used sample for gut microbiota analysis in humans and animals. Cryopreservation of stool at - 80 °C is a feasible and simple method in clinics and researches, especially in large-scale cohort studies. However, the viability of bacteria in stool after freezing has yet well-demonstrated quantitatively and compositionally. This study determined the viable microbiota of samples under cryopreservation at - 80 °C, relative to fresh samples and that stored at ambient. Stool samples were collected from three healthy adults. Propidium monoazide treatment combined with quantitative PCR and 16S rRNA gene sequencing was performed to target viable microbiota. After freezing, the number of viable bacteria decreased, though inter-individual difference existed. Notably, the alpha diversity of viable microbiota after freezing did not change significantly, while its composition changed. Freezing significantly reduced the viable bacteria in Gram-negative genera of Bacteroidetes and Firmicutes, and proportionally increased Gram-positive bacteria in genera of Actinobacteria and Firmicutes, including Bifidobacterium, Collinsella and Blautia, implying that the cell envelope structure associated with the bacterial sensitivity to freezing. On the contrary, the room temperature storage not only decreased the number of viable bacteria, but also decreased the microbial alpha diversity, and remarkably enriched facultative anaerobes of Escherichia-Shigella, Enterococcus and Lactococcus, some of which are opportunistic pathogens. Our findings suggested that changes in viable microbiota in stool samples caused by cryopreservation should be paid enough attention for downstream utilization.
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Hua H, Meydan C, Afshin EE, Lili LN, D’Adamo CR, Rickard N, Dudley JT, Price ND, Zhang B, Mason CE. A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling. Front Immunol 2022; 13:889702. [PMID: 35711426 PMCID: PMC9196042 DOI: 10.3389/fimmu.2022.889702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and a dissolvable wipe used with DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, bacterial metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. These data support that the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.
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Affiliation(s)
- Hui Hua
- Thorne HealthTech, New York, NY, United States
- *Correspondence: Hui Hua, ; Christopher E. Mason,
| | - Cem Meydan
- Thorne HealthTech, New York, NY, United States
| | | | | | - Christopher R. D’Adamo
- Department of Family and Community Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | | | - Nathan D. Price
- Thorne HealthTech, New York, NY, United States
- Institute for Systems Biology, Seattle, WA, United States
| | - Bodi Zhang
- Thorne HealthTech, New York, NY, United States
| | - Christopher E. Mason
- Thorne HealthTech, New York, NY, United States
- The WorldQuant Initiative for Quantitative Prediction, New York, NY, United States
- *Correspondence: Hui Hua, ; Christopher E. Mason,
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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: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [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
- *Correspondence: Shengxian Wu, ; Chongming Wu,
| | - Shengxian Wu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Shengxian Wu, ; Chongming Wu,
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Clinical Metagenomics Is Increasingly Accurate and Affordable to Detect Enteric Bacterial Pathogens in Stool. Microorganisms 2022; 10:microorganisms10020441. [PMID: 35208895 PMCID: PMC8880012 DOI: 10.3390/microorganisms10020441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/29/2022] [Accepted: 02/09/2022] [Indexed: 02/04/2023] Open
Abstract
Stool culture is the gold standard method to diagnose enteric bacterial infections; however, many clinical laboratories are transitioning to syndromic multiplex PCR panels. PCR is rapid, accurate, and affordable, yet does not yield subtyping information critical for foodborne disease surveillance. A metagenomics-based stool testing approach could simultaneously provide diagnostic and public health information. Here, we evaluated shotgun metagenomics to assess the detection of common enteric bacterial pathogens in stool. We sequenced 304 stool specimens from 285 patients alongside routine diagnostic testing for Salmonella spp., Campylobacter spp., Shigella spp., and shiga-toxin producing Escherichia coli. Five analytical approaches were assessed for pathogen detection: microbiome profiling, Kraken2, MetaPhlAn, SRST2, and KAT-SECT. Among analysis tools and databases compared, KAT-SECT analysis provided the best sensitivity and specificity for all pathogens tested compared to culture (91.2% and 96.2%, respectively). Where metagenomics detected a pathogen in culture-negative specimens, standard PCR was positive 85% of the time. The cost of metagenomics is approaching the current combined cost of PCR, reflex culture, and whole genome sequencing for pathogen detection and subtyping. As cost, speed, and analytics for single-approach metagenomics improve, it may be more routinely applied in clinical and public health laboratories.
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Plauzolles A, Toumi E, Bonnet M, Pénaranda G, Bidaut G, Chiche L, Allardet-Servent J, Retornaz F, Goutorbe B, Halfon P. Human Stool Preservation Impacts Taxonomic Profiles in 16S Metagenomics Studies. Front Cell Infect Microbiol 2022; 12:722886. [PMID: 35211421 PMCID: PMC8860989 DOI: 10.3389/fcimb.2022.722886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
Microbiotas play critical roles in human health, yet in most cases scientists lack standardized and reproducible methods from collection and preservation of samples, as well as the choice of omic analysis, up to the data processing. To date, stool sample preservation remains a source of technological bias in metagenomic sequencing, despite newly developed storage solutions. Here, we conducted a comparative study of 10 storage methods for human stool over a 14-day period of storage at fluctuating temperatures. We first compared the performance of each stabilizer with observed bacterial composition variation within the same specimen. Then, we identified the nature of the observed variations to determine which bacterial populations were more impacted by the stabilizer. We found that DNA stabilizers display various stabilizing efficacies and affect the recovered bacterial profiles thus highlighting that some solutions are more performant in preserving the true gut microbial community. Furthermore, our results showed that the bias associated with the stabilizers can be linked to the phenotypical traits of the bacterial populations present in the studied samples. Although newly developed storage solutions have improved our capacity to stabilize stool microbial content over time, they are nevertheless not devoid of biases hence requiring the implantation of standard operating procedures. Acknowledging the biases and limitations of the implemented method is key to better interpret and support true associated microbiome patterns that will then lead us towards personalized medicine, in which the microbiota profile could constitute a reliable tool for clinical practice.
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Affiliation(s)
- Anne Plauzolles
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
- *Correspondence: Anne Plauzolles,
| | - Eya Toumi
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
- MEPHI, IHU Méditerranée Infection, Aix Marseille Université, Marseille, France
| | - Marion Bonnet
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
| | - Guillaume Pénaranda
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
| | - Ghislain Bidaut
- CRCM, Aix‐Marseille Univ U105, Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Marseille, France
| | - Laurent Chiche
- Infectious and Internal Medicine Department, Hôpital Européen Marseille, Marseille, France
| | | | - Frédérique Retornaz
- Infectious and Internal Medicine Department, Hôpital Européen Marseille, Marseille, France
| | - Benoit Goutorbe
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
- CRCM, Aix‐Marseille Univ U105, Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Marseille, France
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Philippe Halfon
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
- Infectious and Internal Medicine Department, Hôpital Européen Marseille, Marseille, France
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Jurek L, Sevil M, Jay A, Schröder C, Baghdadli A, Héry-Arnaud G, Geoffray MM. Is there a dysbiosis in individuals with a neurodevelopmental disorder compared to controls over the course of development? A systematic review. Eur Child Adolesc Psychiatry 2021; 30:1671-1694. [PMID: 32385698 DOI: 10.1007/s00787-020-01544-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/24/2020] [Indexed: 12/16/2022]
Abstract
Many scientific papers reported that an unbalanced gut microbiota could lead to or worsen neurodevelopmental disorders (NDD). A dysbiosis may then be observed in the course of development and mark a dysfunction within what is called the gut-brain axis. The aim of this systematic review is to investigate potential evidence of dysbiosis in children and young adults with NDD compared to controls. Using the PRISMA guidelines we systematically reviewed studies that compared the gut microbiota in NDD participants (with an age inferior to thirty) to the gut microbiota of controls, regardless of the data analysis methods used. The MEDLINE, Scopus and PsycINFO databases were searched up to September 2018. 31 studies with a total sample size of 3002 ASD (Autism Spectrum Disorder) and 84 ADHD (Attention Deficit Hyperactivity Disorder) participants were included in this systematic review. Independent data extraction and quality assessment were conducted. The quality of the studies was rated from low to high. Population characterization and experimental methods were highly heterogeneous in terms of the data available, selection of criteria, and dysbiosis measurement. A dysbiosis was reported in 28 studies in terms of either diversity, bacterial composition or metabolome dysfunction. Due to heterogeneity, a quantitative synthesis was not applicable. In this paper, we discuss the different biases to understand the complexity of microbiota and neurodevelopmental disorders to provide leads for future cohort studies looking to answer the questions raised by the trillions of microorganisms that inhabit key body niches.
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Affiliation(s)
- Lucie Jurek
- Child and Adolescent Psychiatry Departement, Center for Assessment and Diagnostic of Autism, Le Vinatier Hospital, Bron, France.
- Health Services and Performance Research EA7425, Claude Bernard Lyon 1 University (CBL1), Lyon, France.
| | - Marine Sevil
- Child and Adolescent Psychiatry Departement, Center for Assessment and Diagnostic of Autism, Le Vinatier Hospital, Bron, France
| | - Agathe Jay
- Child and Adolescent Psychiatry Departement, Center for Assessment and Diagnostic of Autism, Le Vinatier Hospital, Bron, France
| | - Carmen Schröder
- Department of Child and Adolescent Psychiatry, Strasbourg University Hospital, Strasbourg, France
- CNRS UPR 3212, Team 9 Institute of Cellular and Integrative Neurosciences (INCI), Strasbourg, France
| | - Amaria Baghdadli
- Child and Adolescent Psychiatry Departement, Montpellier University Hospital, Montpellier, France
- INSERM U1178 Centre de Recherche en Epidémiologie Et Santé Des Populations (CESP), Paris Sud University (UPS) Et Versailles Saint Quentin University (UVSQ), Versailles, France
| | - Geneviève Héry-Arnaud
- UMR1078, Génétique, Génomique Fonctionnelle Et Biotechnologies, INSERM, Université de Brest, EFS, IBSAM, Brest, France
- Unité de Bactériologie, Pôle de Biologie-Pathologie, Hôpital La Cavale Blanche, CHRU de Brest, Brest, France
| | - Marie-Maude Geoffray
- Child and Adolescent Psychiatry Departement, Center for Assessment and Diagnostic of Autism, Le Vinatier Hospital, Bron, France
- Health Services and Performance Research EA7425, Claude Bernard Lyon 1 University (CBL1), Lyon, France
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Yu Z, Pei Y, Zhao S, Kakade A, Khan A, Sharma M, Zain H, Feng P, Ji J, Zhou T, Wang H, Wu J, Li X. Metatranscriptomic analysis reveals active microbes and genes responded to short-term Cr(VI) stress. ECOTOXICOLOGY (LONDON, ENGLAND) 2021; 30:1527-1537. [PMID: 33123966 DOI: 10.1007/s10646-020-02290-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/10/2020] [Indexed: 06/11/2023]
Abstract
Heavy metals have been severely polluting the environment. However, the response mechanism of microbial communities to short-term heavy metals stress remains unclear. In this study, metagenomics (MG) and metatranscriptomics (MT) was performed to observe the microbial response to short-term Cr(VI) stress. MG data showed that 99.1% of species were similar in the control and Cr(VI) treated groups. However, MT data demonstrated that 83% of the microbes were active in which 58.7% increased, while the relative abundance of 41.3% decreased after short-term Cr(VI) incubation. The MT results also revealed 9% of microbes were dormant in samples. Genes associated with oxidative stress, Cr(VI) transport, resistance, and reduction, as well as genes with unknown functions were 2-10 times upregulated after Cr(VI) treatment. To further confirm the function of unknown genes, two genes (314 and 494) were selected to detect the Cr(VI) resistance and reduction ability. The results showed that these genes significantly increased the Cr(VI) remediation ability of Escherichia coli. MT results also revealed an increase in the expression of some rare genera (at least two times) after Cr(VI) treatment, indicating these rare species played a crucial role in microbial response to short-term Cr(VI) stress. In summary, MT is an efficient way to understand the role of active and dormant microbes in specific environmental conditions.
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Affiliation(s)
- Zhengsheng Yu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Yaxin Pei
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Shuai Zhao
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Apurva Kakade
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Aman Khan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Monika Sharma
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Hajira Zain
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Pengya Feng
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Jing Ji
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Tuoyu Zhou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Haoyang Wang
- McMaster University, 1280 Main Street West, Hamilton, ON, Canada
| | - Jingyuan Wu
- The First Clinical Medical College, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China.
- Gansu Key Laboratory of Biomonitoring and Bioremediation for Environment Pollution, School of Life Science, Lanzhou University, Tianshuinanlu #222, Lanzhou, 730000, Gansu, PR China.
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12
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Baunwall SMD, Dahlerup JF, Engberg JH, Erikstrup C, Helms M, Juel MA, Kjeldsen J, Nielsen HL, Nilsson AC, Rode AA, Vinter-Jensen L, Hvas CL. Danish national guideline for the treatment of Clostridioides difficile infection and use of faecal microbiota transplantation (FMT). Scand J Gastroenterol 2021; 56:1056-1077. [PMID: 34261379 DOI: 10.1080/00365521.2021.1922749] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Aim: This Danish national guideline describes the treatment of adult patients with Clostridioides (formerly Clostridium) difficile (CD) infection and the use of faecal microbiota transplantation (FMT). It suggests minimum standard for implementing an FMT service.Method: Four scientific societies appointed members for a working group which conducted a systematic literature review and agreed on the text and recommendations. All clinical recommendations were evalluated for evidence level and grade of recommendation.Results: In CD infection, the use of marketed and experimental antibiotics as well as microbiota-based therapies including FMT are described. An algorithm for evaluating treatment effect is suggested. The organisation of FMT, donor recruitment and screening, laboratory preparation, clinical application and follow-up are described.Conclusion: Updated evidence for the treatment of CD infection and the use of FMT is provided.
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Affiliation(s)
| | - Jens Frederik Dahlerup
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | | | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Morten Helms
- Department of Infectious Diseases, Hvidovre Hospital, Hvidovre, Denmark
| | | | - Jens Kjeldsen
- Department of Gastroenterology, Odense University Hospital, Odense, Denmark
| | - Hans Linde Nielsen
- Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Anne Abildtrup Rode
- Department of Internal Medicine, Zealand University Hospital, Roskilde, Denmark
| | - Lars Vinter-Jensen
- Department of Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
| | - Christian Lodberg Hvas
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
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13
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Shivakumar N, Sivadas A, Devi S, Jahoor F, McLaughlin J, Smith CP, Kurpad AV, Mukhopadhyay A. Gut microbiota profiles of young South Indian children: Child sex-specific relations with growth. PLoS One 2021; 16:e0251803. [PMID: 33989353 PMCID: PMC8121364 DOI: 10.1371/journal.pone.0251803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/04/2021] [Indexed: 12/21/2022] Open
Abstract
Gut microbiota has been implicated as a modifier of childhood growth. Here, 16S rRNA sequencing-based fecal microbiota profiles of 18–24 month old Indian children were evaluated (n = 41), in relation to their anthropometric parameters, intestinal permeability, body composition and total energy expenditure. Pathway analyses were conducted to assess microbial functions related to stunting, underweight and wasting. The fecal microbiota was enriched in Prevotella 9, Bifidobacterium and Escherichia-Shigella. Weight, weight-for-age Z-scores (WAZ) and weight-for-length Z-scores (WLZ), along with age, acted as covariates of microbiota variation specifically in boys (n = 23). Bifidobacterium longum subsp longum abundance was positively associated with WAZ while Bifidobacterium bifidum and Bifidobacterium breve abundances were negatively associated with age. The lipopolysaccharide biosynthesis pathway was upregulated in stunted (n = 16) and wasted (n = 8) children. Findings from this study indicate that child sex may be a critical modifier of the role of gut microbiota on childhood growth.
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Affiliation(s)
- Nirupama Shivakumar
- Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Bangalore, India
| | - Ambily Sivadas
- Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Bangalore, India
| | - Sarita Devi
- Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Bangalore, India
| | - Farook Jahoor
- Department of Pediatrics, USDA/Agricultural Research Service Children’s Nutrition Research Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - John McLaughlin
- Faculty of Biology, Division of Diabetes, Endocrinology and Gastroenterology, School of Medical Sciences, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Clinical Sciences Building, Salford Royal Hospital, Salford, United Kingdom
| | - Craig P. Smith
- Faculty of Biology, Division of Diabetes, Endocrinology and Gastroenterology, School of Medical Sciences, Medicine & Health, Manchester Academic Health Sciences Centre, University of Manchester, Clinical Sciences Building, Salford Royal Hospital, Salford, United Kingdom
| | - Anura V. Kurpad
- Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Bangalore, India
- Department of Physiology, St. John’s Medical College, St. John’s National Academy of Health Sciences, Bangalore, India
| | - Arpita Mukhopadhyay
- Division of Nutrition, St. John’s Research Institute, St. John’s National Academy of Health Sciences, Bangalore, India
- * E-mail:
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14
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Keller JJ, Ooijevaar RE, Hvas CL, Terveer EM, Lieberknecht SC, Högenauer C, Arkkila P, Sokol H, Gridnyev O, Mégraud F, Kump PK, Nakov R, Goldenberg SD, Satokari R, Tkatch S, Sanguinetti M, Cammarota G, Dorofeev A, Gubska O, Laniro G, Mattila E, Arasaradnam RP, Sarin SK, Sood A, Putignani L, Alric L, Baunwall SMD, Kupcinskas J, Link A, Goorhuis AG, Verspaget HW, Ponsioen C, Hold GL, Tilg H, Kassam Z, Kuijper EJ, Gasbarrini A, Mulder CJJ, Williams HRT, Vehreschild MJGT. A standardised model for stool banking for faecal microbiota transplantation: a consensus report from a multidisciplinary UEG working group. United European Gastroenterol J 2021; 9:229-247. [PMID: 33151137 PMCID: PMC8259288 DOI: 10.1177/2050640620967898] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 09/27/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Faecal microbiota transplantation is an emerging therapeutic option, particularly for the treatment of recurrent Clostridioides difficile infection. Stool banks that organise recruitment and screening of faeces donors are being embedded within the regulatory frameworks described in the European Union Tissue and Cells Directive and the technical guide to the quality and safety of tissue and cells for human application, published by the European Council. OBJECTIVE Several European and international consensus statements concerning faecal microbiota transplantation have been issued. While these documents provide overall guidance, we aim to provide a detailed description of all processes that relate to the collection, handling and clinical application of human donor stool in this document. METHODS Collaborative subgroups of experts on stool banking drafted concepts for all domains pertaining to stool banking. During a working group meeting in the United European Gastroenterology Week 2019 in Barcelona, these concepts were discussed and finalised to be included in our overall guidance document about faecal microbiota transplantation. RESULTS A guidance document for all domains pertaining to stool banking was created. This document includes standard operating manuals for several processes involved with stool banking, such as handling of donor material, storage and donor screening. CONCLUSION The implementation of faecal microbiota transplantation by stool banks in concordance with our guidance document will enable quality assurance and guarantee the availability of donor faeces preparations for patients.
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15
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The Multiomics Analyses of Fecal Matrix and Its Significance to Coeliac Disease Gut Profiling. Int J Mol Sci 2021; 22:ijms22041965. [PMID: 33671197 PMCID: PMC7922330 DOI: 10.3390/ijms22041965] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 12/15/2022] Open
Abstract
Gastrointestinal (GIT) diseases have risen globally in recent years, and early detection of the host’s gut microbiota, typically through fecal material, has become a crucial component for rapid diagnosis of such diseases. Human fecal material is a complex substance composed of undigested macromolecules and particles, and the processing of such matter is a challenge due to the unstable nature of its products and the complexity of the matrix. The identification of these products can be used as an indication for present and future diseases; however, many researchers focus on one variable or marker looking for specific biomarkers of disease. Therefore, the combination of genomics, transcriptomics, proteomics and metabonomics can give a detailed and complete insight into the gut environment. The proper sample collection, sample preparation and accurate analytical methods play a crucial role in generating precise microbial data and hypotheses in gut microbiome research, as well as multivariate data analysis in determining the gut microbiome functionality in regard to diseases. This review summarizes fecal sample protocols involved in profiling coeliac disease.
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16
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Gut microbiota composition is associated with newborn functional brain connectivity and behavioral temperament. Brain Behav Immun 2021; 91:472-486. [PMID: 33157257 DOI: 10.1016/j.bbi.2020.11.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/27/2020] [Accepted: 11/01/2020] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome appears to play an important role in human health and disease. However, only little is known about how variability in the gut microbiome contributes to individual differences during early and sensitive stages of brain and behavioral development. The current study examined the link between gut microbiome, brain, and behavior in newborn infants (N = 63; M [age] = 25 days). Infant gut microbiome diversity was measured from stool samples using metagenomic sequencing, infant functional brain network connectivity was assessed using a resting state functional near infrared spectroscopy (rs-fNIRS) procedure, and infant behavioral temperament was assessed using parental report. Our results show that gut microbiota composition is linked to individual variability in brain network connectivity, which in turn mediated individual differences in behavioral temperament, specifically negative emotionality, among infants. Furthermore, virulence factors, possibly indexing pathogenic activity, were associated with differences in brain network connectivity linked to negative emotionality. These findings provide novel insights into the early developmental origins of the gut microbiome-brain axis and its association with variability in important behavioral traits. This suggests that the gut microbiome is an important biological factor to consider when studying human development and health.
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17
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An ambient temperature collection and stabilization strategy for canine microbiota studies. Sci Rep 2020; 10:13383. [PMID: 32770113 PMCID: PMC7414149 DOI: 10.1038/s41598-020-70232-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 07/27/2020] [Indexed: 12/14/2022] Open
Abstract
Similar to humans, the fecal microbiome of dogs may be useful in diagnosing diseases or assessing dietary interventions. The accuracy and reproducibility of microbiome data depend on sample integrity, which can be affected by storage methods. Here, we evaluated the ability of a stabilization device to preserve canine fecal samples under various storage conditions simulating shipping in hot or cold climates. Microbiota data from unstabilized samples stored at room temperature (RT) and samples placed in PERFORMAbiome·GUT collection devices (PB-200) (DNA Genotek, Inc. Ottawa, Canada) and stored at RT, 37 °C, 50 °C, or undergoing repeated freeze-thaw cycles, were compared with freshly extracted samples. Alpha- and beta diversity indices were not affected in stabilized samples, regardless of storage temperature. Unstabilized samples stored at RT, however, had higher alpha diversity. Moreover, the relative abundance of dominant bacterial phyla (Firmicutes, Fusobacteria, Bacteriodetes, and Actinobacteria) and 24 genera were altered in unstabilized samples stored at RT, while microbiota abundance was not significantly changed in stabilized samples stored at RT. Our results suggest that storage method is important in microbiota studies and that the stabilization device may be useful in maintaining microbial profile integrity, especially for samples collected off-site and/or those undergoing temperature changes during shipment or storage.
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18
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Ma J, Sheng L, Hong Y, Xi C, Gu Y, Zheng N, Li M, Chen L, Wu G, Li Y, Yan J, Han R, Li B, Qiu H, Zhong J, Jia W, Li H. Variations of Gut Microbiome Profile Under Different Storage Conditions and Preservation Periods: A Multi-Dimensional Evaluation. Front Microbiol 2020; 11:972. [PMID: 32536906 PMCID: PMC7267014 DOI: 10.3389/fmicb.2020.00972] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 04/22/2020] [Indexed: 12/11/2022] Open
Abstract
Gut dysbiosis is heavily involved in the development of various human diseases. There are thousands of publications per year for investigating the role of gut microbiota in diseases. However, emerging evidence has indicated the frequent data inconsistency between different studies, which is largely overlooked. There are many factors that can cause data variation and inconsistency during the process of microbiota study, in particular, sample storage conditions and sequencing process. Here, we systemically evaluated the impacts of six fecal sample storage conditions (three non-commercial storage protocols, −80°C, −80°C with 70% ethanol (ET_−80°C), 4°C with 70% ethanol (ET_4°C), and three commercial storage reagents, OMNIgeneGUT OMR-200 (GT) and MGIEasy (MGIE) at room temperature, and Longsee at 4°C (LS) on gut microbiome profile based on 16S rRNA gene sequencing. In addition, we also investigated the impacts of storage periods (1 and 2 weeks, or 6 months) and sequencing platform on microbiome profile. The efficacy of storage conditions was evaluated by DNA yield and quality, α and β diversity, relative abundance of the dominant and functional bacteria associated with short-chain fatty acid (SCFA) production, and BAs metabolism. Our current study suggested that −80°C was acceptable for fecal sample storage, and the addition of 70% ethanol had some benefits in maintaining the microbial community structure. Meanwhile, we found that samples in ET_4°C and GT reagents were comparable, both of them introduced some biases in α or β diversity, and the relative abundance of functional bacteria. Samples stored in MGIE reagent resulted in the least variation, whereas the most obvious variations were introduced by LS reagents. In addition, our results indicated that variations caused by storage condition were larger than that of storage time and sequencing platform. Collectively, our study provided a multi-dimensional evaluation on the impacts of storage conditions, storage time periods, and sequencing platform on gut microbial profile.
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Affiliation(s)
- Junli Ma
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lili Sheng
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ying Hong
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Chuchu Xi
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yu Gu
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ningning Zheng
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mengci Li
- Shanghai Key Laboratory of Diabetes Mellitus, Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Linlin Chen
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Gaosong Wu
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yue Li
- Department of Endocrinology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Juan Yan
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ruiting Han
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bingbing Li
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Huihui Qiu
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Jing Zhong
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China.,Huzhou Key Laboratory of Molecular Medicine, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, China
| | - Wei Jia
- Shanghai Key Laboratory of Diabetes Mellitus, Center for Translational Medicine, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China.,University of Hawaii Cancer Center, University of Hawai'i at Manoa, Honolulu, HI, United States
| | - Houkai Li
- Functional Metabolomic and Gut Microbiome Laboratory, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai, China
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Carruthers LV, Moses A, Adriko M, Faust CL, Tukahebwa EM, Hall LJ, Ranford-Cartwright LC, Lamberton PHL. The impact of storage conditions on human stool 16S rRNA microbiome composition and diversity. PeerJ 2019; 7:e8133. [PMID: 31824766 PMCID: PMC6894433 DOI: 10.7717/peerj.8133] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/01/2019] [Indexed: 12/14/2022] Open
Abstract
Background Multiple factors can influence stool sample integrity upon sample collection. Preservation of faecal samples for microbiome studies is therefore an important step, particularly in tropical regions where resources are limited and high temperatures may significantly influence microbiota profiles. Freezing is the accepted standard to preserve faecal samples however, cold chain methods are often unfeasible in fieldwork scenarios particularly in low and middle-income countries and alternatives are required. This study therefore aimed to address the impact of different preservative methods, time-to-freezing at ambient tropical temperatures, and stool heterogeneity on stool microbiome diversity and composition under real-life physical environments found in resource-limited fieldwork conditions. Methods Inner and outer stool samples collected from one specimen obtained from three children were stored using different storage preservation methods (raw, ethanol and RNAlater) in a Ugandan field setting. Mixed stool was also stored using these techniques and frozen at different time-to-freezing intervals post-collection from 0-32 h. Metataxonomic profiling was used to profile samples, targeting the V1-V2 regions of 16S rRNA with samples run on a MiSeq platform. Reads were trimmed, combined and aligned to the Greengenes database. Microbial diversity and composition data were generated and analysed using Quantitative Insights Into Microbial Ecology and R software. Results Child donor was the greatest predictor of microbiome variation between the stool samples, with all samples remaining identifiable to their child of origin despite the stool being stored under a variety of conditions. However, significant differences were observed in composition and diversity between preservation techniques, but intra-preservation technique variation was minimal for all preservation methods, and across the time-to-freezing range (0-32 h) used. Stool heterogeneity yielded no apparent microbiome differences. Conclusions Stool collected in a fieldwork setting for comparative microbiome analyses should ideally be stored as consistently as possible using the same preservation method throughout.
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Affiliation(s)
- Lauren V Carruthers
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.,Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Arinaitwe Moses
- Vector Control Divison, Ugandan Ministry of Health, Kampala, Uganda
| | - Moses Adriko
- Vector Control Divison, Ugandan Ministry of Health, Kampala, Uganda
| | - Christina L Faust
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.,Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | | | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich, UK
| | - Lisa C Ranford-Cartwright
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | - Poppy H L Lamberton
- Institute of Biodiversity Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK.,Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
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20
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Hickl O, Heintz-Buschart A, Trautwein-Schult A, Hercog R, Bork P, Wilmes P, Becher D. Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome. Microorganisms 2019; 7:microorganisms7090367. [PMID: 31546776 PMCID: PMC6780314 DOI: 10.3390/microorganisms7090367] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/13/2019] [Accepted: 09/17/2019] [Indexed: 12/27/2022] Open
Abstract
With the technological advances of the last decade, it is now feasible to analyze microbiome samples, such as human stool specimens, using multi-omic techniques. Given the inherent sample complexity, there exists a need for sample methods which preserve as much information as possible about the biological system at the time of sampling. Here, we analyzed human stool samples preserved and stored using different methods, applying metagenomics as well as metaproteomics. Our results demonstrate that sample preservation and storage have a significant effect on the taxonomic composition of identified proteins. The overall identification rates, as well as the proportion of proteins from Actinobacteria were much higher when samples were flash frozen. Preservation in RNAlater overall led to fewer protein identifications and a considerable increase in the share of Bacteroidetes, as well as Proteobacteria. Additionally, a decrease in the share of metabolism-related proteins and an increase of the relative amount of proteins involved in the processing of genetic information was observed for RNAlater-stored samples. This suggests that great care should be taken in choosing methods for the preservation and storage of microbiome samples, as well as in comparing the results of analyses using different sampling and storage methods. Flash freezing and subsequent storage at −80 °C should be chosen wherever possible.
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Affiliation(s)
- Oskar Hickl
- Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany.
| | - Anna Heintz-Buschart
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, D-04103 Leipzig, Germany.
- Helmholtz Centre for Environmental Research GmbH - UFZ, D-06120 Halle, Germany.
- Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg.
| | | | - Rajna Hercog
- European Molecular Biology Laboratory Heidelberg, D-69117 Heidelberg, Germany.
| | - Peer Bork
- European Molecular Biology Laboratory Heidelberg, D-69117 Heidelberg, Germany.
- Max Delbrück Centre for Molecular Medicine, D-13125 Berlin, Germany.
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory and University Hospital Heidelberg, D-69120 Heidelberg, Germany.
- Faculty of Biology, University of Würzburg, D-97074 Würzburg, Germany.
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, Université du Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg.
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany.
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21
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Sun X, Wang M, Guo L, Shu C, Zhang J, Geng L. Guanidine thiocyanate solution facilitates sample collection for plant rhizosphere microbiome analysis. PeerJ 2019; 7:e6440. [PMID: 30809445 PMCID: PMC6385689 DOI: 10.7717/peerj.6440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 01/13/2019] [Indexed: 11/30/2022] Open
Abstract
The interactions between rhizosphere microorganisms and plants are important for the health and development of crops. Analysis of plant rhizosphere bacterial compositions, particularly of those with resistance to biotic/abiotic stresses, may improve their applications in sustainable agriculture. Large-scale rhizosphere samplings in the field are usually required; however, such samples, cannot be immediately frozen. We found that the storage of samples at room temperature for 2 days leads to a considerable reduction in the operational taxonomic unit (OTU) number and the indices of bacterial alpha-diversity of rhizosphere communities. In this study, in order to overcome these problems, we established a method using guanidine thiocyanate (GTC) solution for the preservation of rhizosphere samples after their collection. This method allowed the maintenance of the samples for at least 1 day at room temperature prior to their cryopreservation and was shown to be compatible with conventional DNA isolation protocols. Illumina sequencing of V3 and V4 hypervariable regions of the 16S rRNA gene was used to assess the feasibility and reliability of this method, and no significant differences were observed in the number of OTUs and in the Chao and Shannon indices between samples stored at −70 °C and those stored in GTC solution. Moreover, the representation of Pseudomonas spp. in samples stored in GTC solution was not significantly different from that in samples stored at −70 °C, as determined by real-time quantitative polymerase chain reaction (p > 0.05). Both types of samples were shown to cluster together according to principal coordinate analysis. Furthermore, GTC solution did not affect the bacterial taxon profiles at different storage periods compared with those observed when storing the samples below −70 °C. Even incubation of thawed samples (frozen at −70 °C) for 15 min at room temperature induced minor changes in the bacterial composition. Taken together, our results demonstrated that GTC solution may provide a reliable alternative for the preservation of rhizosphere samples in the field.
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Affiliation(s)
- Xiaoxiao Sun
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meiling Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lin Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.,Department of Agronomy, Jinlin Agriculture University, Changchun, Jilin, China
| | - Changlong Shu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lili Geng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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22
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Tap J, Cools-Portier S, Pavan S, Druesne A, Öhman L, Törnblom H, Simren M, Derrien M. Effects of the long-term storage of human fecal microbiota samples collected in RNAlater. Sci Rep 2019; 9:601. [PMID: 30679604 PMCID: PMC6345939 DOI: 10.1038/s41598-018-36953-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/23/2018] [Indexed: 12/14/2022] Open
Abstract
The adequate storage of fecal samples from clinical trials is crucial if analyses are to be performed later and in long-term studies. However, it is unknown whether the composition of the microbiota is preserved during long-term stool storage (>1 year). We therefore evaluated the influence of long-term storage on the microbiota composition of human stool samples collected in RNAlater and stored for approximately five years at −80 °C. We compared storage effects on stool samples from 24 subjects with the effects of technical variation due to different sequencing runs and biological variation (intra- and inter-subject), in another 101 subjects, based on alpha-diversity, beta-diversity and taxonomic composition. We also evaluated the impact of initial alpha-diversity and fecal microbiota composition on beta-diversity instability upon storage. Overall, long-term stool storage at −80 °C had only limited effects on the microbiota composition of human feces. The magnitude of changes in alpha- and beta- diversity and taxonomic composition after long-term storage was similar to inter-sequencing variation and smaller than biological variation (both intra- and inter-subject). The likelihood of fecal samples being affected by long-term storage correlated with the initial relative abundance of some genera and tend to be affected by initial taxonomic richness.
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Affiliation(s)
- Julien Tap
- Danone Nutricia Research, Innovation, Science and Nutrition Department, RD 128 - Avenue de la Vauve, 91767, Palaiseau, France
| | - Stéphanie Cools-Portier
- Danone Nutricia Research, Innovation, Science and Nutrition Department, RD 128 - Avenue de la Vauve, 91767, Palaiseau, France
| | | | - Anne Druesne
- Danone Nutricia Research, Innovation, Science and Nutrition Department, RD 128 - Avenue de la Vauve, 91767, Palaiseau, France
| | - Lena Öhman
- Department of Immunology and Microbiology, Inst. of Biomedicine, University of Gothenburg, Gothenburg, Sweden.,Department of Internal Medicine and Clinical Nutrition, Inst. Of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Hans Törnblom
- Department of Internal Medicine and Clinical Nutrition, Inst. Of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simren
- Department of Internal Medicine and Clinical Nutrition, Inst. Of Medicine, University of Gothenburg, Gothenburg, Sweden.,Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Muriel Derrien
- Danone Nutricia Research, Innovation, Science and Nutrition Department, RD 128 - Avenue de la Vauve, 91767, Palaiseau, France.
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23
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Yeoh YK, Chen Z, Hui M, Wong MCS, Ho WCS, Chin ML, Ng SC, Chan FKL, Chan PKS. Impact of inter- and intra-individual variation, sample storage and sampling fraction on human stool microbial community profiles. PeerJ 2019; 7:e6172. [PMID: 30648014 PMCID: PMC6330951 DOI: 10.7717/peerj.6172] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/28/2018] [Indexed: 12/14/2022] Open
Abstract
Stools are commonly used as proxies for studying human gut microbial communities as sample collection is straightforward, cheap and non-invasive. In large-scale human population surveys, however, sample integrity becomes an issue as it is not logistically feasible for researchers to personally collect stools from every participant. Instead, participants are usually given guidelines on sample packaging and storage, and asked to deliver their stools to a centralised facility. Here, we tested a number of delivery conditions (temperature, duration and addition of preservative medium) and assessed their effects on stool microbial community composition using 16S rRNA gene amplicon sequencing. The largest source of variability in stool community composition was attributable to inter-individual differences regardless of delivery condition. Although the relative effect of delivery condition on community composition was small compared to inter-individual variability (1.6% vs. 60.5%, permutational multivariate analysis of variance [PERMANOVA]) and temporal variation within subjects over 10 weeks (5.2%), shifts in microbial taxa associated with delivery conditions were non-systematic and subject-specific. These findings indicated that it is not possible to model or accurately predict shifts in stool community composition associated with sampling logistics. Based on our findings, we recommend delivery of fresh, preservative-free stool samples to laboratories within 2 hr either at ambient or chilled temperatures to minimise perturbations to microbial community composition. In addition, subsamples from different fractions of the same stool displayed a small (3.3% vs. 72.6% inter-individual variation, PERMANOVA) but significant effect on community composition. Collection of larger sample volumes for homogenisation is recommended.
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Affiliation(s)
- Yun Kit Yeoh
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Mamie Hui
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Martin C S Wong
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Jockey Club School of Public Health and Primary Care, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wendy C S Ho
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Miu Ling Chin
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Siew C Ng
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Francis K L Chan
- Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Paul K S Chan
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.,Centre for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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24
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Ribeiro RM, Souza-Basqueira MD, Oliveira LCD, Salles FC, Pereira NB, Sabino EC. An alternative storage method for characterization of the intestinal microbiota through next generation sequencing. Rev Inst Med Trop Sao Paulo 2018; 60:e77. [PMID: 30517247 PMCID: PMC6282504 DOI: 10.1590/s1678-9946201860077] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 11/07/2018] [Indexed: 12/20/2022] Open
Abstract
Gut microbiota has been the subject of various molecular studies mainly due to its importance and wide-ranging relationships with human hosts. However, the storage of fecal samples prior to DNA extraction is critical when characterizing the composition of intestinal microbiota. Therefore, we aimed to understand the effects of different fecal storage methods to characterize intestinal microbiota using Next Generation Sequencing (NGS) as well as to establish an alternative conservation method of bacterial genetic material in these samples using guanidine. Stool samples from 10 healthy volunteers were collected. Each sample was divided into five aliquots: one aliquot was extracted immediately after collection (fresh) and two aliquots were subjected to freezing at -20 °C or -80 °C and extracted after 48 h. The other two aliquots were stored in guanidine at room temperature or 4 °C and extracted after 48 h. The V4 hypervariable regions of the bacterial and archeal 16S rRNA gene were amplified by PCR and sequenced using an Ion Torrent PGM platform for NGS. The data were analyzed using QIIME software. Statistical significance was determined using a non-parametric Kruskal-Wallis test. A total of 11,494,688 reads with acceptable quality were obtained. Unweighted principal coordinate analysis (PCoA) revealed that the samples were clustered based on the host rather than by the storage group. At the phylum and genus levels, we observed statistically significant differences between two genera, Proteobacteria (p=0.013) and Suterella (p=0.004), comparing frozen samples with guanidine-stored samples. Our data suggest that the use of guanidine can preserve bacterial genetic materials as well as freezing, providing additional conveniences.
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Affiliation(s)
- Roberto Marques Ribeiro
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Parasitologia (LIM 46), São Paulo, São Paulo, Brazil
| | - Marcela de Souza-Basqueira
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Parasitologia (LIM 46), São Paulo, São Paulo, Brazil
| | - Léa Campos de Oliveira
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Medicina Laboratorial (LIM 03), São Paulo, São Paulo, Brazil
| | - Flavia Cristina Salles
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Parasitologia (LIM 46), São Paulo, São Paulo, Brazil
| | - Natalia Bueno Pereira
- Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Parasitologia (LIM 46), São Paulo, São Paulo, Brazil
| | - Ester Cerdeira Sabino
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Moléstias Infecciosas, São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Faculdade de Medicina, Hospital das Clínicas, Laboratório de Parasitologia (LIM 46), São Paulo, São Paulo, Brazil.,Universidade de São Paulo, Instituto de Medicina Tropical de São Paulo, São Paulo, São Paulo, Brazil
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25
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Stewart HL, Pitta D, Indugu N, Vecchiarelli B, Engiles JB, Southwood LL. Characterization of the fecal microbiota of healthy horses. Am J Vet Res 2018; 79:811-819. [DOI: 10.2460/ajvr.79.8.811] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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27
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Golob JL, Pergam SA, Srinivasan S, Fiedler TL, Liu C, Garcia K, Mielcarek M, Ko D, Aker S, Marquis S, Loeffelholz T, Plantinga A, Wu MC, Celustka K, Morrison A, Woodfield M, Fredricks DN. Stool Microbiota at Neutrophil Recovery Is Predictive for Severe Acute Graft vs Host Disease After Hematopoietic Cell Transplantation. Clin Infect Dis 2018; 65:1984-1991. [PMID: 29020185 PMCID: PMC5850019 DOI: 10.1093/cid/cix699] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/03/2017] [Indexed: 12/13/2022] Open
Abstract
Background Graft-versus-host disease (GVHD) is common after allogeneic hematopoietic cell transplantation (HCT). Risk for death from GVHD has been associated with low bacterial diversity in the stool microbiota early after transplant; however, the specific species associated with GVHD risk remain poorly defined. Methods We prospectively collected serial weekly stool samples from 66 patients who underwent HCT, starting pre-transplantation and continuing weekly until 100 days post-transplant, a total of 694 observations in HCT recipients. We used 16S rRNA gene polymerase chain reaction with degenerate primers, followed by high-throughput sequencing to assess the relative abundance of sequence reads from bacterial taxa in stool samples over time. Results The gut microbiota was highly dynamic in HCT recipients, with loss and appearance of taxa common on short time scales. As in prior studies, GVHD was associated with lower alpha diversity of the stool microbiota. At neutrophil recovery post-HCT, the presence of oral Actinobacteria and oral Firmicutes in stool was positively correlated with subsequent GVHD; Lachnospiraceae were negatively correlated. A gradient of bacterial species (difference of the sum of the relative abundance of positive correlates minus the sum of the relative abundance of negative correlates) was most predictive (receiver operator characteristic area under the curve of 0.83) of subsequent severe acute GVHD. Conclusions The stool microbiota around the time of neutrophil recovery post-HCT is predictive of subsequent development of severe acute GVHD in this study.
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Affiliation(s)
- Jonathan L Golob
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute.,Division of Allergy and Infectious Diseases, University of Washington
| | - Steven A Pergam
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute.,Division of Allergy and Infectious Diseases, University of Washington
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Congzhou Liu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Kristina Garcia
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Marco Mielcarek
- Clinical Research Division, Fred Hutchinson Cancer Institute.,Medicine
| | - Daisy Ko
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Sarah Aker
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Sara Marquis
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Tillie Loeffelholz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | | | - Michael C Wu
- Public Health Sciences Division, Fred Hutchinson Cancer Institute
| | - Kevin Celustka
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Alex Morrison
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Maresa Woodfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute.,Division of Allergy and Infectious Diseases, University of Washington.,Department of Microbiology, University of Washington, Seattle
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28
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Fazlollahi M, Chun Y, Grishin A, Wood RA, Burks AW, Dawson P, Jones SM, Leung DY, Sampson HA, Sicherer SH, Bunyavanich S. Early-life gut microbiome and egg allergy. Allergy 2018; 73:1515-1524. [PMID: 29318631 PMCID: PMC6436531 DOI: 10.1111/all.13389] [Citation(s) in RCA: 127] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/23/2017] [Indexed: 12/12/2022]
Abstract
BACKGROUND Gut microbiota may play a role in egg allergy. We sought to examine the association between early-life gut microbiota and egg allergy. METHODS We studied 141 children with egg allergy and controls from the multicenter Consortium of Food Allergy Research study. At enrollment (age 3 to 16 months), fecal samples were collected, and clinical evaluation, egg-specific IgE measurement, and egg skin prick test were performed. Gut microbiome was profiled by 16S rRNA sequencing. Analyses for the primary outcome of egg allergy at enrollment, and the secondary outcomes of egg sensitization at enrollment and resolution of egg allergy by age 8 years, were performed using Quantitative Insights into Microbial Ecology, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, and Statistical Analysis of Metagenomic Profiles. RESULTS Compared to controls, increased alpha diversity and distinct taxa (PERMANOVA P = 5.0 × 10-4 ) characterized the early-life gut microbiome of children with egg allergy. Genera from the Lachnospiraceae, Streptococcaceae, and Leuconostocaceae families were differentially abundant in children with egg allergy. Predicted metagenome functional analyses showed differential purine metabolism by the gut microbiota of egg-allergic subjects (Kruskal-Wallis Padj = 0.021). Greater gut microbiome diversity and genera from Lachnospiraceae and Ruminococcaceae were associated with egg sensitization (PERMANOVA P = 5.0 × 10-4 ). Among those with egg allergy, there was no association between early-life gut microbiota and egg allergy resolution by age 8 years. CONCLUSION The distinct early-life gut microbiota in egg-allergic and egg-sensitized children identified by our study may point to targets for preventive or therapeutic intervention.
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Affiliation(s)
- Mina Fazlollahi
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yoojin Chun
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alexander Grishin
- Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robert A. Wood
- Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA
| | - A. Wesley Burks
- Department of Pediatrics, University of North Carolina, Chapel Hill, NC
| | | | - Stacie M. Jones
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children’s Hospital, Little Rock, AR, USA
| | | | - Hugh A. Sampson
- Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Scott H. Sicherer
- Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Supinda Bunyavanich
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Division of Pediatric Allergy and Immunology, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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29
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Methodology challenges in studying human gut microbiota - effects of collection, storage, DNA extraction and next generation sequencing technologies. Sci Rep 2018; 8:5143. [PMID: 29572539 PMCID: PMC5865204 DOI: 10.1038/s41598-018-23296-4] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/09/2018] [Indexed: 12/25/2022] Open
Abstract
The information on microbiota composition in the human gastrointestinal tract predominantly originates from the analyses of human faeces by application of next generation sequencing (NGS). However, the detected composition of the faecal bacterial community can be affected by various factors including experimental design and procedures. This study evaluated the performance of different protocols for collection and storage of faecal samples (native and OMNIgene.GUT system) and bacterial DNA extraction (MP Biomedicals, QIAGEN and MO BIO kits), using two NGS platforms for 16S rRNA gene sequencing (Ilumina MiSeq and Ion Torrent PGM). OMNIgene.GUT proved as a reliable and convenient system for collection and storage of faecal samples although favouring Sutterella genus. MP provided superior DNA yield and quality, MO BIO depleted Gram positive organisms while using QIAGEN with OMNIgene.GUT resulted in greatest variability compared to other two kits. MiSeq and IT platforms in their supplier recommended setups provided comparable reproducibility of donor faecal microbiota. The differences included higher diversity observed with MiSeq and increased capacity of MiSeq to detect Akkermansia muciniphila, [Odoribacteraceae], Erysipelotrichaceae and Ruminococcaceae (primarily Faecalibacterium prausnitzii). The results of our study could assist the investigators using NGS technologies to make informed decisions on appropriate tools for their experimental pipelines.
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30
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Han M, Hao L, Lin Y, Li F, Wang J, Yang H, Xiao L, Kristiansen K, Jia H, Li J. A novel affordable reagent for room temperature storage and transport of fecal samples for metagenomic analyses. MICROBIOME 2018; 6:43. [PMID: 29482661 PMCID: PMC5828344 DOI: 10.1186/s40168-018-0429-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 02/20/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND The number of large-scale studies on the gut microbiota in human cohorts is rapidly increasing. However, the few and expensive options for storage of fecal samples at room temperature have been an obstacle for large-scale metagenomic studies and the development of clinical/commercial personal metagenomic sequencing. RESULTS In this study, we systematically tested a novel N-octylpyridinium bromide-based fecal sample preservation method and compared it with other currently used storage methods. We found that the N-octylpyridinium bromide-based method enabled preservation of the bacterial composition in fecal samples transported and stored at room temperature for up to at least 14 days. CONCLUSIONS We describe a novel chemical stabilizer that allows cost-effective transportation and storage at room temperature for several days with preservation of bacterial composition. This method will facilitate sample collection even in remote area and also enable transport via normal commercial transportation routes.
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Affiliation(s)
- Mo Han
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Lilan Hao
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yuxiang Lin
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Fang Li
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Liang Xiao
- BGI-Shenzhen, Shenzhen, 518083, China
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, Shenzhen, 518083, China
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biology, Laboratory of Genomics and Molecular Biomedicine, University of Copenhagen, Universitetsparken 13, 2100, Copenhagen, Denmark
| | - Huijue Jia
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China.
- Shenzhen Key Laboratory of Human commensal microorganisms and Health Research, BGI-Shenzhen, Shenzhen, 518083, China.
| | - Junhua Li
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National Genebank, BGI-Shenzhen, Shenzhen, 518120, China.
- School of Bioscience and Biotechnology, South China University of Technology, Guangzhou, 510006, China.
- Shenzhen Key Laboratory of Human commensal microorganisms and Health Research, BGI-Shenzhen, Shenzhen, 518083, China.
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31
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Wong WS, Clemency N, Klein E, Provenzano M, Iyer R, Niederhuber JE, Hourigan SK. Collection of non-meconium stool on fecal occult blood cards is an effective method for fecal microbiota studies in infants. MICROBIOME 2017; 5:114. [PMID: 28870234 PMCID: PMC5583988 DOI: 10.1186/s40168-017-0333-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 08/25/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND Effective methods are needed to collect fecal samples from children for large-scale microbiota studies. Stool collected on fecal occult blood test (FOBT) cards that can be mailed provides an effective solution; however, the quality of sequencing resulting from this method is unknown. The aim of this study is to compare microbiota metrics of 16S ribosomal RNA (rRNA) gene sequencing from stool and meconium collected on FOBT cards with stool collected in an Eppendorf tube (ET) under different conditions. METHODS Eight stool samples from children in diapers aged 0 month-2 years and three meconium samples were collected and stored as follows: (1) ≤ 2 days at room temperature (RT) in an ET, (2) 7 days at - 80 °C in an ET, (3) 3-5 days at RT on a FOBT card, (4) 7 days at RT on a FOBT card, and (5) 7 days at - 80 °C on a FOBT card. Samples stored at - 80 °C were frozen immediately. Each specimen/condition underwent 16S rRNA gene sequencing with replicates on the Illumina MiSeq. Alpha and beta diversity measures and relative abundance of major phyla were compared between storage conditions and container (ET vs. FOBT card), with pairwise comparison between different storage conditions and the "standard" of 7 days at - 80 °C in an ET and fresh stool in an ET. RESULTS Stool samples clustered mainly by individual diaper (P < 10-5, Adonis), rather than by storage condition (P = 0.42) or container (P = 0.16). However, meconium samples clustered more by container (P = 0.002) than by individual diaper (P = 0.009) and storage condition (P = 0.02). Additionally, there were no differences in alpha diversity measures and relative abundance of major phyla after Bonferroni correction between stool stored on a FOBT card at RT for 7 days with stool stored in an ET tube at - 80 °C; differences in alpha diversity were seen however when compared to fresh stool in an ET. Overall, based on the intraclass correlation coefficient (ICC), the different storage containers/conditions are reliable in preserving the microbial memberships and slightly less reliable in preserving the alpha diversity and relative microbial composition of infant stool. CONCLUSIONS Acknowledging certain limitations, FOBT cards may be a useful tool in large-scale stool microbiota studies in children requiring outpatient follow-up where only small amounts of stool can be obtained, but should not be used when studying meconium.
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Affiliation(s)
- Wendy S.W. Wong
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
| | - Nicole Clemency
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
| | - Elisabeth Klein
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
| | - Marina Provenzano
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
| | - Ramaswamy Iyer
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
| | - John E. Niederhuber
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
- Johns Hopkins School of Medicine, 733 N Broadway, Baltimore, MD 21205 USA
| | - Suchitra K. Hourigan
- Inova Translational Medicine Institute (ITMI), 3300 Gallows Road, Claude Moore Bldg, 2nd Floor, Falls Church, VA 22042 USA
- Inova Children’s Hospital, 3300 Gallows Road, Falls Church, VA 22042 USA
- Pediatric Specialists of Virginia, 3023 Hamaker Court, Suite 600, Fairfax, VA 22031 USA
- Johns Hopkins School of Medicine, 733 N Broadway, Baltimore, MD 21205 USA
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Vandeputte D, Tito RY, Vanleeuwen R, Falony G, Raes J. Practical considerations for large-scale gut microbiome studies. FEMS Microbiol Rev 2017; 41:S154-S167. [PMID: 28830090 PMCID: PMC7207147 DOI: 10.1093/femsre/fux027] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 06/19/2017] [Indexed: 12/14/2022] Open
Abstract
First insights on the human gut microbiome have been gained from medium-sized, cross-sectional studies. However, given the modest portion of explained variance of currently identified covariates and the small effect size of gut microbiota modulation strategies, upscaling seems essential for further discovery and characterisation of the multiple influencing factors and their relative contribution. In order to guide future research projects and standardisation efforts, we here review currently applied collection and preservation methods for gut microbiome research. We discuss aspects such as sample quality, applicable omics techniques, user experience and time and cost efficiency. In addition, we evaluate the protocols of a large-scale microbiome cohort initiative, the Flemish Gut Flora Project, to give an idea of perspectives, and pitfalls of large-scale faecal sampling studies. Although cryopreservation can be regarded as the gold standard, freezing protocols generally require more resources due to cold chain management. However, here we show that much can be gained from an optimised transport chain and sample aliquoting before freezing. Other protocols can be useful as long as they preserve the microbial signature of a sample such that relevant conclusions can be drawn regarding the research question, and the obtained data are stable and reproducible over time.
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Affiliation(s)
- Doris Vandeputte
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
- Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Raul Y. Tito
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
- Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Rianne Vanleeuwen
- Universiteit Antwerpen, Productontwikkeling, Ambtmanstraat 1, B-2000 Antwerpen, Belgium
| | - Gwen Falony
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology and Immunology, Rega Institute, Herestraat 49, B-3000 Leuven, Belgium
- VIB, Center for Microbiology, Herestraat 49, B-3000 Leuven, Belgium
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Hao L, Xia Z, Yang H, Wang J, Han M. Ionic liquid-based reagents improve the stability of midterm fecal sample storage. J Microbiol Methods 2017; 139:68-73. [PMID: 28506638 DOI: 10.1016/j.mimet.2017.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 11/17/2022]
Abstract
Fecal samples are widely used in metagenomic research, which aims to elucidate the relationship between human health and the intestinal microbiota. However, the best conditions for stable and reliable storage and transport of these samples at room temperature are still unknown, and whether samples stored at room temperature for several days will maintain their microbiota composition is still unknown. Here, we established and tested a preservation method using reagents containing imidazolium- or pyridinium-based ionic liquids. We stored human fecal samples in these reagents for up to 7 days at different temperatures. Subsequently, all samples were sequenced and compared with fresh samples and/or samples treated under other conditions. The 16S rRNA sequencing results suggested that ionic liquid-based reagents could stabilize the composition of the microbiota in fecal samples during a 7-day storage period, particularly when stored at room temperature. Thus, this method may have implications in the storage of fecal samples for metagenomic research.
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Affiliation(s)
- Lilan Hao
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China; BGI Research, BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Zhongkui Xia
- BGI Research, BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- BGI Research, BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China; James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI Research, BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China; James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Mo Han
- BGI Research, BGI-Shenzhen, Shenzhen, China; China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, China.
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Menke S, Gillingham MAF, Wilhelm K, Sommer S. Home-Made Cost Effective Preservation Buffer Is a Better Alternative to Commercial Preservation Methods for Microbiome Research. Front Microbiol 2017; 8:102. [PMID: 28197142 PMCID: PMC5281576 DOI: 10.3389/fmicb.2017.00102] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/13/2017] [Indexed: 02/01/2023] Open
Abstract
The investigation of wildlife gastrointestinal microbiomes by next-generation sequencing approaches is a growing field in microbial ecology and conservation. Such studies often face difficulties in sample preservation if neither freezing facilities nor liquid nitrogen (LQN) are readily available. Thus, in order to prevent microbial community changes because of bacterial growth after sampling, preservation buffers need to be applied to samples. However, the amount of microbial community variation attributable to the different preservation treatments and potentially affecting biological interpretation is hardly known. Here, we sampled feces of 11 sheep (Ovis aries sp.) by using swabs and analyzed the effect of air-drying, an inexpensive self-made nucleic acid preservation buffer (NAP), DNA/RNA Shield™, and RNAlater®, each together with freezing (for 10 days) or storing at room temperature (for 10 days) prior to 16S rRNA gene high-throughput sequencing to determine bacterial communities. Results revealed that the proportions of operational taxonomic units (OTUs) belonging to a bacterial phylum were affected by the preservation treatments, and that alpha diversities [observed OTUs, Shannon index, and phylogenetic diversity (PD)] were lower in all preservation treatments than in samples taken by forensic swabs and immediately frozen which is considered as the favored preservation treatment in the absence of any logistic constraints. Overall, NAP had better preservation qualities than RNAlater® and DNA/RNA Shield™ making this self-made buffer a valuable solution in wildlife microbiome studies.
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Affiliation(s)
- Sebastian Menke
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm Ulm, Germany
| | - Mark A F Gillingham
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm Ulm, Germany
| | - Kerstin Wilhelm
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm Ulm, Germany
| | - Simone Sommer
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm Ulm, Germany
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