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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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Rold LS, Guldbæk JM, Lindegaard CS, Kirk S, Nygaard LD, Bundgaard-Nielsen C, Holm-Jacobsen JN, Leutscher P, Viuff ACF, Hagstrøm S, Sørensen S. A comparison of the breast milk microbiota from women diagnosed with gestational diabetes mellitus and women without gestational diabetes mellitus. BMC Pregnancy Childbirth 2024; 24:412. [PMID: 38849751 PMCID: PMC11157733 DOI: 10.1186/s12884-024-06604-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/22/2024] [Indexed: 06/09/2024] Open
Abstract
BACKGROUND Human breast milk (HBM) is a contributing factor in modulating the infant's gut microbiota, as it contains bacteria that are directly transferred to the infant during breastfeeding. It has been shown that children of women diagnosed with gestational diabetes mellitus (GDM) have a different gut microbiota compared to children of women without GDM. Our hypothesis is therefore that women with GDM have a different HBM microbiota, which may influence the metabolic function and capacity of the child later in life. The aim of this study was to investigate whether women with GDM have a different breast milk microbiota 1-3 weeks postpartum compared to women without GDM. METHODS In this case-control study, a total of 45 women were included: 18 women with GDM and 27 women without GDM. A milk sample was collected from each participant 1 to 3 weeks postpartum and the bacterial composition was examined by 16 S rRNA gene sequencing targeting the V4 region. RESULTS High relative abundances of Streptococcus and Staphylococcus were present in samples from both women with and without GDM. No difference could be seen in either alpha diversity, beta diversity, or specific taxa between groups. CONCLUSION Our results did not support the existence of a GDM-associated breast milk microbiota at 1-3 weeks postpartum. Further research is needed to fully understand the development of the gut microbiota of infants born to mothers with GDM.
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Affiliation(s)
- Louise Søndergaard Rold
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Steno Diabetes Center North Denmark, Aalborg, Denmark
| | | | | | - Stine Kirk
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | | | | | - Peter Leutscher
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | - Søren Hagstrøm
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Steno Diabetes Center North Denmark, Aalborg, Denmark
- Department of Pediatrics and Adolescents, Aalborg University Hospital, Aalborg, Denmark
| | - Suzette Sørensen
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
- Steno Diabetes Center North Denmark, Aalborg, Denmark.
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Rostgaard-Hansen AL, Esberg A, Dicksved J, Hansen T, Pelve E, Brunius C, Halkjær J, Tjønneland A, Johansson I, Landberg R. Temporal gut microbiota variability and association with dietary patterns: From the one-year observational Diet, Cancer, and Health - Next Generations MAX study. Am J Clin Nutr 2024; 119:1015-1026. [PMID: 38301827 DOI: 10.1016/j.ajcnut.2024.01.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Knowledge about the variability of gut microbiota within an individual over time is important to allow meaningful investigations of the gut microbiota in relation to diet and health outcomes in observational studies. Plant-based dietary patterns have been associated with a lower risk of morbidity and mortality and may alter gut microbiota in a favorable direction. OBJECTIVES To assess the gut microbiota variability during one year and investigate the association between adherence to diet indexes and the gut microbiota in a Danish population. METHODS Four hundred forty-four participants were included in the Diet, Cancer, and Health - Next Generations MAX study (DCH-NG MAX). Stool samples collected up to three times during a year were analyzed by 16S ribosomal ribonucleic acid gene sequencing. Diet was obtained by 24-hour dietary recalls. Intraclass correlation coefficient (ICC) was calculated to assess temporal microbial variability based on 214 individuals. Diet indexes (Nordic, Mediterranean, and plant-based diets) and food groups thereof were associated with gut microbiota using linear regression analyses. RESULTS We found that 91 out of 234 genera had an ICC >0.5. We identified three subgroups dominated by Bacteroides, Prevotella 9, and Ruminococcaceae and adherence to diet indexes differed between subgroups. Higher adherence to diet indexes was associated with the relative abundance of 22 genera. Across diet indexes, higher intakes of fruit, vegetables, whole grains/cereals, and nuts were most frequently associated with these genera. CONCLUSIONS In the DCH-NG MAX study, 39% of the genera had an ICC >0.5 over one year, suggesting that these genera could be studied with health outcomes in prospective analyses with acceptable precision. Adherence to the Nordic, Mediterranean, and plant-based diets differed between bacterial subgroups and was associated with a higher abundance of genera with fiber-degrading properties. Fruits, vegetables, whole grains/cereals, and nuts were frequently associated with these genera.
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Affiliation(s)
- Agnetha L Rostgaard-Hansen
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden; Department of Diet, Cancer, and Health, Danish Cancer Institute, Copenhagen, Denmark.
| | - Anders Esberg
- Department of Odontology, Umeå University, Umeå, Sweden
| | - Johan Dicksved
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Erik Pelve
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Carl Brunius
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Jytte Halkjær
- Department of Diet, Cancer, and Health, Danish Cancer Institute, Copenhagen, Denmark
| | - Anne Tjønneland
- Department of Diet, Cancer, and Health, Danish Cancer Institute, Copenhagen, Denmark; Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | | | - Rikard Landberg
- Division of Food and Nutrition Science, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
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Knudsen JK, Bundgaard-Nielsen C, Leutscher P, Hjerrild S, Nielsen RE, Sørensen S. Differences in bacterial taxa between treatment-naive patients with major depressive disorder and non-affected controls may be related to a proinflammatory profile. BMC Psychiatry 2024; 24:84. [PMID: 38297265 PMCID: PMC10832199 DOI: 10.1186/s12888-024-05547-z] [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: 09/04/2023] [Accepted: 01/21/2024] [Indexed: 02/02/2024] Open
Abstract
BACKGROUND Major depressive disorder (MDD) is characterized by sadness and anhedonia, but also physical symptoms such as changes in appetite and weight. Gut microbiota has been hypothesized to be involved in MDD through gut-brain axis signaling. Moreover, antidepressants display antibacterial properties in the gastrointestinal tract. The aim of this study was to compare the gut microbiota and systemic inflammatory profile of young patients with MDD before and after initiation of antidepressant treatment and/or psychotherapy in comparison with a non-depressed control group (nonMDD). METHODS Fecal and blood samples were collected at baseline and at follow-up after four and twelve weeks, respectively. Patients started treatment immediately after collection of the baseline samples. The gut microbiota was characterized by 16 S rRNA gene sequencing targeting the hypervariable V4 region. Plasma levels of 49 unique immune markers were assessed using Mesoscale. RESULTS In total, 27 MDD patients and 32 nonMDD controls were included in the study. The gut microbiota in the baseline samples of MDD versus nonMDD participants did not differ regarding α- or β-diversity. However, there was a higher relative abundance of the genera Ruminococcus gnavus group, and a lower relative abundance of the genera Desulfovibrio, Tyzzerella, Megamonas, Olsenella, Gordonibacter, Allisonella and Rothia in the MDD group compared to the nonMDD group. In the MDD group, there was an increase in the genera Rothia, Desulfovibrio, Gordinobacteer and Lactobacillus, while genera belonging to the Firmicutes phylum were found depleted at twelve weeks follow-up compared to baseline. In the MDD group, IL-7, IL-8 and IL-17b levels were elevated compared to the nonMDD group at baseline. Furthermore, MDI score in the MDD group was found to correlate with Bray-Curtis dissimilarity at baseline, and several inflammatory markers at both baseline and after initiation of antidepressant treatment. CONCLUSION Several bacterial taxa differed between the MDD group and the nonMDD group at baseline and changed in relative abundance during antidepressant treatment and/or psychotherapy. The MDD group was furthermore found to have a pro-inflammatory profile compared to the nonMDD group at baseline. Further studies are required to investigate the gut microbiota and pro-inflammatory profile of patients with MDD.
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Affiliation(s)
- Julie Kristine Knudsen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, Hjørring, 9800, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Caspar Bundgaard-Nielsen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, Hjørring, 9800, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Peter Leutscher
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, Hjørring, 9800, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Steno Diabetes Center North Denmark, Aalborg, Denmark
| | - Simon Hjerrild
- Psychosis Research Unit, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - René Ernst Nielsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Psychiatry, Aalborg University Hospital, Aalborg, Denmark
| | - Suzette Sørensen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, Hjørring, 9800, Denmark.
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
- Steno Diabetes Center North Denmark, Aalborg, Denmark.
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Klinsawat W, Uthaipaisanwong P, Jenjaroenpun P, Sripiboon S, Wongsurawat T, Kusonmano K. Microbiome variations among age classes and diets of captive Asian elephants (Elephas maximus) in Thailand using full-length 16S rRNA nanopore sequencing. Sci Rep 2023; 13:17685. [PMID: 37848699 PMCID: PMC10582034 DOI: 10.1038/s41598-023-44981-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 10/14/2023] [Indexed: 10/19/2023] Open
Abstract
Asian elephant (Elephas maximus) is the national symbol of Thailand and linked to Thai history and culture for centuries. The elephant welfare improvement is one of the major components to achieve sustainable captive management. Microbiome inhabiting digestive tracts have been shown with symbiotic relations to host health. This work provided high-resolution microbiome profiles of 32 captive elephants at a species level by utilizing full-length 16S rRNA gene nanopore sequencing. Eleven common uncultured bacterial species were found across elephants fed with solid food including uncultured bacterium Rikenellaceae RC9 gut group, Kiritimatiellae WCHB1-41, Phascolarctobacterium, Oscillospiraceae NK4A214 group, Christensenellaceae R-7 group, Oribacterium, Oscillospirales UCG-010, Lachnospiraceae, Bacteroidales F082, uncultured rumen Rikenellaceae RC9 gut group, and Lachnospiraceae AC2044 group. We observed microbiome shifts along the age classes of baby (0-2 years), juvenile (2-10 years), and adult (> 10 years). Interestingly, we found distinct microbiome profiles among adult elephants fed with a local palm, Caryota urens, as a supplement. Potential beneficial microbes have been revealed according to the age classes and feed diets. The retrieved microbiome data could be provided as good baseline microbial profiles for monitoring elephant health, suggesting further studies towards dietary selection suitable for each age class and the use of local supplementary diets.
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Affiliation(s)
- Worata Klinsawat
- Conservation Ecology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Pichahpuk Uthaipaisanwong
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Medical Bioinformatics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Supaphen Sripiboon
- Department of Large Animal and Wildlife Clinical Science, Faculty of Veterinary Medicine, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, Thailand
| | - Thidathip Wongsurawat
- Division of Medical Bioinformatics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
| | - Kanthida Kusonmano
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
- Bioinformatics and Systems Biology Program, Schools of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
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Zhang S, Han Y, Schofield W, Nicosia M, Karell PE, Newhall KP, Zhou JY, Musich RJ, Pan S, Valujskikh A, Sangwan N, Dwidar M, Lu Q, Stappenbeck TS. Select symbionts drive high IgA levels in the mouse intestine. Cell Host Microbe 2023; 31:1620-1638.e7. [PMID: 37776865 DOI: 10.1016/j.chom.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/14/2023] [Accepted: 09/01/2023] [Indexed: 10/02/2023]
Abstract
Immunoglobulin A (IgA) is an important factor in maintaining homeostasis at mucosal surfaces, yet luminal IgA levels vary widely. Total IgA levels are thought to be driven by individual immune responses to specific microbes. Here, we found that the prebiotic, pectin oligosaccharide (pec-oligo), induced high IgA levels in the small intestine in a T cell-dependent manner. Surprisingly, this IgA-high phenotype was retained after cessation of pec-oligo treatment, and microbiome transmission either horizontally or vertically was sufficient to retain high IgA levels in the absence of pec-oligo. Interestingly, the bacterial taxa enriched in the overall pec-oligo bacterial community differed from IgA-coated microbes in this same community. Rather, a group of ethanol-resistant microbes, highly enriched for Lachnospiraceae bacterium A2, drove the IgA-high phenotype. These findings support a model of intestinal adaptive immunity in which a limited number of microbes can promote durable changes in IgA directed to many symbionts.
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Affiliation(s)
- Shanshan Zhang
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Gastroenterology, Qilu Hospital, Shandong University, Jinan 250000, P.R. China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yi Han
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Michael Nicosia
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Paul E Karell
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Kevin P Newhall
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Julie Y Zhou
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ryan J Musich
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Siyi Pan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Anna Valujskikh
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Naseer Sangwan
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Mohammed Dwidar
- Department of Cardiovascular and Metabolic Sciences, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome & Human Health, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Qiuhe Lu
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
| | - Thaddeus S Stappenbeck
- Department of Inflammation and Immunity, Learner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.
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Palmqvist H, Höglund K, Ringmark S, Lundh T, Dicksved J. Effects of whole-grain cereals on fecal microbiota and short-chain fatty acids in dogs: a comparison of rye, oats and wheat. Sci Rep 2023; 13:10920. [PMID: 37407634 DOI: 10.1038/s41598-023-37975-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023] Open
Abstract
Dietary fiber in dog food is reported to promote healthy gut microbiota, but few studies have investigated the effects of whole-grain cereals, which contain a variety of fiber types and other bioactive compounds. The aim of the present study was to compare the effects of diets containing whole-grain rye (RYE), oats (OAT) and wheat (WHE) on fecal microbiota and short-chain fatty acid production. Eighteen dogs were fed three experimental diets, each for four weeks, in a cross-over design. Fecal samples were collected at the end of each diet period. Analysis of 16S rRNA gene amplicons showed that family Lachnospiraceae and genus Bacteroides were the gut microbial groups most affected by diet, with lowest relative abundance following consumption of RYE and a trend for a corresponding increase in genus Prevotella_9. Fecal acetate and propionate concentrations were higher after consumption of RYE compared with OAT. In conclusion, rye had the strongest effect on gut microbiota and short-chain fatty acids, although the implications for dog gut health are not yet elucidated.
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Affiliation(s)
- Hanna Palmqvist
- Department of Animal Nutrition and Management, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Katja Höglund
- Department of Anatomy, Physiology and Biochemistry, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sara Ringmark
- Department of Anatomy, Physiology and Biochemistry, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Torbjörn Lundh
- Department of Animal Nutrition and Management, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Dicksved
- Department of Animal Nutrition and Management, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Li XM, Shi X, Yao Y, Shen YC, Wu XL, Cai T, Liang LX, Wang F. Effects of Stool Sample Preservation Methods on Gut Microbiota Biodiversity: New Original Data and Systematic Review with Meta-Analysis. Microbiol Spectr 2023; 11:e0429722. [PMID: 37093040 PMCID: PMC10269478 DOI: 10.1128/spectrum.04297-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/16/2023] [Indexed: 04/25/2023] Open
Abstract
Here, we aimed to compare the effects of different preservation methods on outcomes of fecal microbiota. We evaluated the effects of different preservation methods using stool sample preservation experiments for up to 1 year. The stool samples from feces of healthy volunteers were grouped based on whether absolute ethanol was added and whether they were hypothermically preserved. Besides, we performed a systematic review to combine current fecal microbiota preservation evidence. We found that Proteobacteria changed significantly and Veillonellaceae decreased significantly in the 12th month in the room temperature + absolute ethanol group. The four cryopreservation groups have more similarities with fresh sample in the 12 months; however, different cryopreservation methods have different effects on several phyla, families, and genera. A systematic review showed that the Shannon diversity and Simpson index of samples stored in RNAlater for 1 month were not statistically significant compared with those stored immediately at -80°C (P = 0.220 and P = 0.123, respectively). The -80°C refrigerator and liquid nitrogen cryopreservation with 10% glycerine can both maintain stable microbiota of stool samples for long-term preservation. The addition of absolute ethanol to cryopreserved samples had no significant difference in the effect of preserving fecal microbial characteristics. Our study provides empirical insights into preservation details for future studies of the long-term preservation of fecal microbiota. Systematic review and meta-analysis found that the gut microbiota structure, composition, and diversity of samples preserved by storage methods, such as preservation solution, are relatively stable, which were suitable for short-term storage at room temperature. IMPORTANCE The study of gut bacteria has become increasingly popular, and fecal sample preservation methods and times need to be standardized. Here, we detail a 12-month study of fecal sample preservation, and our study provides an empirical reference about experimental details for long-term high-quality storage of fecal samples in the field of gut microbiology research. The results showed that the combination of -80°C/liquid nitrogen deep cryopreservation and 10% glycerol was the most effective method for the preservation of stool samples, which is suitable for long-term storage for at least 12 months. The addition of anhydrous ethanol to the deep cryopreserved samples did not make a significant difference in the preservation of fecal microbiological characteristics. Combined with the results of systematic reviews and meta-analyses, we believe that, when researchers preserve fecal specimens, it is essential to select the proper preservation method and time period in accordance with the goal of the study.
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Affiliation(s)
- Xin-meng Li
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Xiao Shi
- Department of Dermatology, Anhui Provincial Hospital, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, China
| | - Yao Yao
- Department of Gastroenterology, Zhangjiajie People’s Hospital, Zhangjiajie, Hunan, China
| | - Yi-cun Shen
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Xiang-ling Wu
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Ting Cai
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
| | - Lun-xi Liang
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
- Department of Gastroenterology, The Affiliated Changsha Central Hospital, Hengyang Medical School, University of South China, Changsha, China
| | - Fen Wang
- Department of Gastroenterology, the Third Xiangya Hospital, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Non-resolving Inflammation and Cancer, Central South University, Changsha, Hunan, China
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9
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Bolt Botnen A, Bjørnsen MB, Alberdi A, Gilbert MTP, Aizpurua O. A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies. Heliyon 2023; 9:e12861. [PMID: 36699263 PMCID: PMC9868478 DOI: 10.1016/j.heliyon.2023.e12861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences related to the time, storage and chemistry involved. FTA cards have been previously proposed as a simple, reliable and cost-efficient method for the preservation of animal faecal microbiomes. In this study, we report a simplified extraction methodology for recovering microbiome DNA from faeces stored on FTA cards and compare its performance to a common alternative means of characterising such microbiomes; namely, immediate freezing of the faeces followed by DNA extraction using the Qiagen PowerSoil DNA isolation kit. Our results show that overall the application of our simplified DNA extraction methodology yields microbial community results that have higher diversity and an expanded core microbiome than that found using the PowerSoil methodology. This suggests that the FTA card extraction method presented here is a viable alternative for metagenomic studies using faecal material when traditional freeze-based storage methods are not feasible.
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Affiliation(s)
- Amanda Bolt Botnen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - Mads Bjørn Bjørnsen
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark.,University Museum, NTNU, Trondheim, Norway
| | - Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, The GLOBE Institute, University of Copenhagen, Denmark
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10
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Trivedi CB, Keuschnig C, Larose C, Rissi DV, Mourot R, Bradley JA, Winkel M, Benning LG. DNA/RNA Preservation in Glacial Snow and Ice Samples. Front Microbiol 2022; 13:894893. [PMID: 35677909 PMCID: PMC9168539 DOI: 10.3389/fmicb.2022.894893] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
The preservation of nucleic acids for high-throughput sequencing is an ongoing challenge for field scientists. In particular, samples that are low biomass, or that have to be collected and preserved in logistically challenging environments (such as remote sites or during long sampling campaigns) can pose exceptional difficulties. With this work, we compare and assess the effectiveness of three preservation methods for DNA and RNA extracted from microbial communities of glacial snow and ice samples. Snow and ice samples were melted and filtered upon collection in Iceland, and filters were preserved using: (i) liquid nitrogen flash freezing, (ii) storage in RNAlater, or (iii) storage in Zymo DNA/RNA Shield. Comparative statistics covering nucleic acid recovery, sequencing library preparation, genome assembly, and taxonomic diversity were used to determine best practices for the preservation of DNA and RNA samples from these environments. Our results reveal that microbial community composition based on DNA was comparable at the class level across preservation types. Based on extracted RNA, the taxonomic composition of the active community was primarily driven by the filtered sample volume (i.e., biomass content). In low biomass samples (where <200 ml of sample volume was filtered) the taxonomic and functional signatures trend toward the composition of the control samples, while in samples where a larger volume (more biomass) was filtered our data showed comparable results independent of preservation type. Based on all comparisons our data suggests that flash freezing of filters containing low biomass is the preferred method for preserving DNA and RNA (notwithstanding the difficulties of accessing liquid nitrogen in remote glacial field sites). Generally, RNAlater and Zymo DNA/RNA Shield solutions work comparably well, especially for DNA from high biomass samples, but Zymo DNA/RNA Shield is favored due to its higher yield of preserved RNA. Biomass quantity from snow and ice samples appears to be the most important factor in regards to the collection and preservation of samples from glacial environments.
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Affiliation(s)
- Christopher B Trivedi
- Interface Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | | | - Catherine Larose
- Environmental Microbial Genomics, Université de Lyon, Ecully Cedex, France
| | | | - Rey Mourot
- Interface Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany.,Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
| | - James A Bradley
- Interface Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany.,School of Geography, Queen Mary University of London, London, United Kingdom
| | - Matthias Winkel
- Interface Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany
| | - Liane G Benning
- Interface Geochemistry, GFZ German Research Centre for Geosciences, Potsdam, Germany.,Department of Earth Sciences, Freie Universität Berlin, Berlin, Germany
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11
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Melgaard D, Sørensen J, Riis J, Ovesen TS, Leutscher P, Sørensen S, Knudsen JK, Bundgaard-Nielsen C, Ejstrup J, Jensen AM, Borre M, Krarup AL. Efficacy of FODMAP Elimination and Subsequent Blinded Placebo-Controlled Provocations in a Randomised Controlled Study in Patients with Ulcerative Colitis in Remission and Symptoms of Irritable Bowel Syndrome: A Feasibility Study. Nutrients 2022; 14:nu14061296. [PMID: 35334953 PMCID: PMC8955641 DOI: 10.3390/nu14061296] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/01/2022] [Accepted: 03/15/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Patients with inflammatory bowel disease (IBD) and symptoms of irritable bowel syndrome (IBS) may be intolerant to fermentable carbohydrates (FODMAPs). The aim of this study was to test the feasibility of eliminating and subsequently reintroducing FODMAPs in patients with IBS symptoms as part of the IBD manifestation and to compare the severity of IBS symptoms and pain, bloating and quality of life (QoL). Methods: An eight-week randomised open-label FODMAP elimination with double-blinded, crossover provocations of FODMAP and placebo. Diet patients were on a low-FODMAP diet for eight weeks with blinded two-week provocations after two and six weeks. Questionnaires, blood and stool samples were collected. Results: Patient enrolment was challenging. Nineteen participants were included in the study. Eliminating low FODMAP for two weeks resulted in significant decreases in pain and bloating scores (p < 0.003), whereas there were no statistical differences in pain scores between diet patients and controls. Pain and bloating scores increased, returning to baseline levels after two weeks of double-blinded provocations with placebo, (p > 0.05). Conclusions: The results document the possibility of performing a randomised controlled study following the gold standard for testing food intolerance with blinding of the Low FODMAP diet. Recruitment of participants was challenging.
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Affiliation(s)
- Dorte Melgaard
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (J.R.); (P.L.); (S.S.); (J.K.K.); (C.B.-N.); (A.-M.J.)
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark;
- Correspondence: ; Tel.: +45-26281086
| | - Jeanette Sørensen
- Department of Medicine, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (J.S.); (T.S.O.); (J.E.)
| | - Johannes Riis
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (J.R.); (P.L.); (S.S.); (J.K.K.); (C.B.-N.); (A.-M.J.)
| | - Tine S. Ovesen
- Department of Medicine, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (J.S.); (T.S.O.); (J.E.)
- Department of Clinical Nutrition, North Denmark Regional Hospital, 9800 Hjoerring, Denmark
| | - Peter Leutscher
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (J.R.); (P.L.); (S.S.); (J.K.K.); (C.B.-N.); (A.-M.J.)
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark;
| | - Suzette Sørensen
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (J.R.); (P.L.); (S.S.); (J.K.K.); (C.B.-N.); (A.-M.J.)
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark;
| | - Julie K. Knudsen
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (J.R.); (P.L.); (S.S.); (J.K.K.); (C.B.-N.); (A.-M.J.)
| | - Caspar Bundgaard-Nielsen
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (J.R.); (P.L.); (S.S.); (J.K.K.); (C.B.-N.); (A.-M.J.)
| | - Jeanette Ejstrup
- Department of Medicine, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (J.S.); (T.S.O.); (J.E.)
| | - Ann-Maria Jensen
- Centre for Clinical Research, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (J.R.); (P.L.); (S.S.); (J.K.K.); (C.B.-N.); (A.-M.J.)
| | - Mette Borre
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, 8210 Aarhus, Denmark;
| | - Anne L. Krarup
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark;
- Department of Medicine, North Denmark Regional Hospital, 9800 Hjoerring, Denmark; (J.S.); (T.S.O.); (J.E.)
- Department of Acute Medicine and Trauma Care, Aalborg University Hospital, 9000 Aalborg, Denmark
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12
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Rold LS, Bundgaard-Nielsen C, Niemann Holm-Jacobsen J, Glud Ovesen P, Leutscher P, Hagstrøm S, Sørensen S. Characteristics of the gut microbiome in women with gestational diabetes mellitus: A systematic review. PLoS One 2022; 17:e0262618. [PMID: 35025980 PMCID: PMC8757951 DOI: 10.1371/journal.pone.0262618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022] Open
Abstract
Background The incidence of women developing gestational diabetes mellitus (GDM) is increasing, which is associated with an increased risk of type 2 diabetes mellitus (T2DM) for both mother and child. Gut microbiota dysbiosis may contribute to the pathogenesis of both GDM and the accompanying risk of T2DM. Thus, a better understanding of the microbial communities associated with GDM could offer a potential target for intervention and treatment in the future. Therefore, we performed a systematic review to investigate if the GDM women have a distinct gut microbiota composition compared to non-GDM women. Methods We identified 21 studies in a systematic literature search of Embase and PubMed up to February 24, 2021. Data on demographics, methodology and identified microbial metrics were extracted. The quality of each study was assessed according to the Newcastle-Ottawa Scale. Results Sixteen of the studies did find a GDM-associated gut microbiota, although no consistency could be seen. Only Collinsella and Blautia showed a tendency to be increased in GDM women, whereas the remaining genera were significantly different in opposing directions. Conclusion Although most of the studies found an association between GDM and gut microbiota dysbiosis, no overall GDM-specific gut microbiota could be identified. All studies in the second trimester found a difference between GDM and non-GDM women, indicating that dysbiosis is present at the time of diagnosis. Nevertheless, it is still unclear when the dysbiosis develops, as no consensus could be seen between the studies investigating the gut microbiota in the first trimester of pregnancy. However, studies varied widely concerning methodology and study design, which might explain the highly heterogeneous gut microbiota compositions between studies. Therefore, future studies need to include multiple time points and consider possible confounding factors such as ethnicity, pre-pregnancy body mass index, and GDM treatment.
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Affiliation(s)
- Louise Søndergaard Rold
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark
- Steno Diabetes Centre North Denmark, Aalborg, Denmark
| | - Caspar Bundgaard-Nielsen
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | - Per Glud Ovesen
- Department of Obstetrics and Gynecology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
- Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Peter Leutscher
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark
- Steno Diabetes Centre North Denmark, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Søren Hagstrøm
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark
- Steno Diabetes Centre North Denmark, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Pediatrics, Aalborg University Hospital, Aalborg, Denmark
| | - Suzette Sørensen
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark
- Steno Diabetes Centre North Denmark, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- * E-mail:
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13
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Knudsen JK, Michaelsen TY, Bundgaard-Nielsen C, Nielsen RE, Hjerrild S, Leutscher P, Wegener G, Sørensen S. Faecal microbiota transplantation from patients with depression or healthy individuals into rats modulates mood-related behaviour. Sci Rep 2021; 11:21869. [PMID: 34750433 PMCID: PMC8575883 DOI: 10.1038/s41598-021-01248-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/26/2021] [Indexed: 02/02/2023] Open
Abstract
Differences in gut microbiota composition have been observed in patients with major depressive disorder (MDD) compared to healthy individuals. Here, we investigated if faecal microbiota transplantation (FMT) from patients with MDD into rats could induce a depressive-like phenotype. We performed FMT from patients with MDD (FMT-MDD) and healthy individuals (FMT-Healthy) into male Flinders Sensitive Line (FSL) and Flinders Resistant Line (FRL) rats and assessed depressive-like behaviour. No behavioural differences were observed in the FSL rats. In FRL rats, the FMT-Healthy group displayed significantly less depressive-like behaviour than the FMT-MDD group. However, there was no difference in behaviour between FMT-MDD FRL rats and negative controls, indicating that FMT-Healthy FRL rats received beneficial bacteria. We additionally found different taxa between the FMT-MDD and the FMT-Healthy FRL rats, which could be traced to the donors. Four taxa, three belonging to the family Ruminococcaceae and the genus Lachnospira, were significantly elevated in relative abundance in FMT-MDD rats, while the genus Coprococcus was depleted. In this study, the FMT-MDD group was different from the FMT-Healthy group based on behaviour and intestinal taxa.
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Affiliation(s)
- Julie Kristine Knudsen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | | | - Caspar Bundgaard-Nielsen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - René Ernst Nielsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Psychiatry, Aalborg University Hospital, Aalborg, Denmark
| | - Simon Hjerrild
- Psychosis Research Unit, Aarhus University Hospital, Aarhus, Denmark.,Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
| | - Peter Leutscher
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Gregers Wegener
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
| | - Suzette Sørensen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjørring, Denmark. .,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
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14
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Gut microbial changes of patients with psychotic and affective disorders: A systematic review. Schizophr Res 2021; 234:1-10. [PMID: 31952911 DOI: 10.1016/j.schres.2019.12.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/16/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Many diverse inflammatory pathophysiologic mechanisms have been linked to mental disorders, and through the past decade an increasing interest in the gut microbiota and its relation to mental health has been arising. We aimed to systematically review studies of alterations in gut microbiota of patients suffering from psychotic disorders, bipolar disorder or depression compared to healthy controls. METHODS We systematically searched the databases CENTRAL, PubMed, EMBASE, PsycINFO and LILACS. Primary outcome was to compare the gut microbiota of patients suffering from psychotic disorders, bipolar disorder or depression with healthy controls. RESULTS We identified 17 studies, covering 744 patients and 620 healthy controls. The most consistent microbiota changes were a tendency towards higher abundance of Actinobacteria and lower abundance of Firmicutes at the phylum level, lower abundance of Lachnospiraceae at family level and lower abundance of Faecalibacterium at genus level for the mental disorders overall. However, we found that all studies had risk of bias and that the included studies displayed great variability in methods of storage, analysis of the fecal samples, reporting of results and statistics used. CONCLUSION Due to the many limitations of the included studies the findings should be interpreted with caution. Larger studies (especially of schizophrenia and major depressive disorder) are needed, but it is also of great importance to gather information of and control for factors that influence the result of a microbiota analysis including body mass index (BMI), smoking, alcohol consumption, diet habits, antibiotics, sample handling, wet laboratory methods and statistics.
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15
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Fredsgaard L, Thorsteinsson K, Bundgaard-Nielsen C, Ammitzbøll N, Leutscher P, Chai Q, Jensen AM, Sørensen S, Pedersen LM, Hagstrøm S, Arenholt LTS. Description of the voided urinary microbiota in asymptomatic prepubertal children - A pilot study. J Pediatr Urol 2021; 17:545.e1-545.e8. [PMID: 34053859 DOI: 10.1016/j.jpurol.2021.03.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/12/2021] [Accepted: 03/21/2021] [Indexed: 01/04/2023]
Abstract
BACKGROUND Recently, it has been established that the urine of a healthy adult bladder contains a microbiota and that urinary dysbiosis may be involved in the development of urinary tract diseases. The urinary microbiota and its relation to bladder health and disease in children is yet to be established. The objective of the present study was to investigate the voided urinary microbiota in asymptomatic prepubertal children. STUDY DESIGN Thirty asymptomatic children (15 boys and 15 girls) participated in the study. Bacterial DNA in "clean-catch" midstream urine (CC MSU) samples was analysed using Illumina MiSeq sequencing of the V4 region of the bacterial 16 S rRNA gene. All children had normal bladder function as ensured by uroflowmetry, ultrasonic post-void residual, and frequency-volume charts. Bladder-related parameters and gender comparisons were analysed statistically by parametric and non-parametric tests. Alpha diversity, beta diversity, and a Venn diagram were used to analyse sequencing data. RESULTS All CC MSU samples contained bacterial DNA. The voided urinary microbiota differed significantly between girls and boys in terms of operational taxonomic unit (OTU) richness, Shannon diversity index, and relative abundances of bacterial genera, but not for evenness. The urine of girls was dominated by Prevotella (18.2%), Porphyromonas (12.9%), Ezakiella (8.1%), Prevotella 6 (7.4%), and Dialister (7.0%). Porphyromonas (22.4%) was the most abundant genus in boys, followed by Ezakiella (12.0%), Campylobacter (11.6%), Prevotella (8.6%), and Dialister (3.7%). Girls had 10 unique core OTUs, whereas boys had no unique core OTUs. Porphyromonas appeared as a shared core OTU between genders. DISCUSSION Contrary to previous findings, this study found significant differences in the voided urinary bacterial composition among asymptomatic prepubertal children. Moreover, the bacterial composition diverged from that found among healthy adults by other research groups. Among adults, the gender specific urinary microbiota has been hypothesised to be caused by anatomical differences in the reproductive organs and differences in sex hormone levels. This could also be evident for asymptomatic prepubertal children as sex hormone levels are different even at the prepubertal stage. The limitations of the study encompass small sample size and urine collection by CC MSU with risk of contamination from surrounding areas. CONCLUSIONS This study documents that CC MSU samples of asymptomatic prepubertal children are not sterile. The composition of the voided urinary microbiota seems gender specific and unequal to that of healthy adults. The role of the urinary microbiota in paediatric urological disorders should be considered in future studies.
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Affiliation(s)
- Lea Fredsgaard
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjoerring, Denmark
| | - Kristina Thorsteinsson
- Department of Paediatrics, Aalborg University Hospital, Reberbansgade 15, 9000, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Sdr. Skovvej 15, 9000, Aalborg, Denmark.
| | - Caspar Bundgaard-Nielsen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjoerring, Denmark; Department of Clinical Medicine, Aalborg University, Sdr. Skovvej 15, 9000, Aalborg, Denmark
| | - Nadia Ammitzbøll
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjoerring, Denmark
| | - Peter Leutscher
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjoerring, Denmark; Department of Clinical Medicine, Aalborg University, Sdr. Skovvej 15, 9000, Aalborg, Denmark; Steno Diabetes Center North Jutland, Sdr. Skovvej 3E, 9000, Aalborg, Denmark
| | - Qing Chai
- Department of Paediatrics, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjoerring, Denmark
| | - Ann-Maria Jensen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjoerring, Denmark
| | - Suzette Sørensen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjoerring, Denmark; Department of Clinical Medicine, Aalborg University, Sdr. Skovvej 15, 9000, Aalborg, Denmark; Steno Diabetes Center North Jutland, Sdr. Skovvej 3E, 9000, Aalborg, Denmark
| | - Lia M Pedersen
- Department of Paediatrics, Aalborg University Hospital, Reberbansgade 15, 9000, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Sdr. Skovvej 15, 9000, Aalborg, Denmark
| | - Søren Hagstrøm
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjoerring, Denmark; Department of Paediatrics, Aalborg University Hospital, Reberbansgade 15, 9000, Aalborg, Denmark; Department of Clinical Medicine, Aalborg University, Sdr. Skovvej 15, 9000, Aalborg, Denmark; Steno Diabetes Center North Jutland, Sdr. Skovvej 3E, 9000, Aalborg, Denmark
| | - Louise T S Arenholt
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjoerring, Denmark; Department of Clinical Medicine, Aalborg University, Sdr. Skovvej 15, 9000, Aalborg, Denmark; Department of Obstetrics and Gynaecology, North Denmark Regional Hospital, Bispensgade 37, 9800, Hjoerring, Denmark
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16
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Espinosa-Gongora C, Jessen LR, Kieler IN, Damborg P, Bjørnvad CR, Gudeta DD, Pires Dos Santos T, Sablier-Gallis F, Sayah-Jeanne S, Corbel T, Nevière A, Hugon P, Saint-Lu N, de Gunzburg J, Guardabassi L. Impact of oral amoxicillin and amoxicillin/clavulanic acid treatment on bacterial diversity and β-lactam resistance in the canine faecal microbiota. J Antimicrob Chemother 2021; 75:351-361. [PMID: 31778166 DOI: 10.1093/jac/dkz458] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/03/2019] [Accepted: 10/10/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Aminopenicillins with or without a β-lactamase inhibitor are widely used in both human and veterinary medicine. However, little is known about their differential impact on the gut microbiota and development of antimicrobial resistance. OBJECTIVES To investigate changes in the faecal microbiota of dogs treated with amoxicillin or amoxicillin/clavulanic acid. METHODS Faeces collected from 42 dogs (21 per treatment group) immediately before, during and 1 week after termination of oral treatment with amoxicillin or amoxicillin/clavulanic acid were analysed by culture and 16S rRNA gene sequence analysis. RESULTS In both groups, bacterial counts on ampicillin selective agar revealed an increase in the proportion of ampicillin-resistant Escherichia coli during treatment, and an increased occurrence and proportion of ampicillin-resistant enterococci during and after treatment. 16S rRNA gene analysis showed reductions in microbial richness and diversity during treatment followed by a return to pre-treatment conditions approximately 1 week after cessation of amoxicillin or amoxicillin/clavulanic acid treatment. While no significant differences were observed between the effects of amoxicillin and amoxicillin/clavulanic acid on microbial richness and diversity, treatment with amoxicillin/clavulanic acid reduced the abundance of taxa that are considered part of the beneficial microbiota (such as Roseburia, Dialister and Lachnospiraceae) and enriched Escherichia, although the latter result was not corroborated by phenotypic counts. CONCLUSIONS Our results suggest a limited effect of clavulanic acid on selection of antimicrobial resistance and microbial richness when administered orally in combination with amoxicillin. However, combination with this β-lactamase inhibitor appears to broaden the spectrum of amoxicillin, with potential negative consequences on gut health.
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Affiliation(s)
- Carmen Espinosa-Gongora
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK 1870, Frederiksberg C, Denmark
| | - Lisbeth Rem Jessen
- Department of Veterinary Clinical Sciences, University of Copenhagen, Dyrlægevej 16, DK 1870, Frederiksberg C, Denmark
| | - Ida Nordang Kieler
- Department of Veterinary Clinical Sciences, University of Copenhagen, Dyrlægevej 16, DK 1870, Frederiksberg C, Denmark
| | - Peter Damborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK 1870, Frederiksberg C, Denmark
| | - Charlotte Reinhard Bjørnvad
- Department of Veterinary Clinical Sciences, University of Copenhagen, Dyrlægevej 16, DK 1870, Frederiksberg C, Denmark
| | - Dereje Dadi Gudeta
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK 1870, Frederiksberg C, Denmark
| | - Teresa Pires Dos Santos
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK 1870, Frederiksberg C, Denmark
| | | | | | - Tanguy Corbel
- Da Volterra, 172 rue de Charonne, 75011 Paris, France
| | | | - Perrine Hugon
- Da Volterra, 172 rue de Charonne, 75011 Paris, France
| | | | | | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK 1870, Frederiksberg C, Denmark.,Department of Pathobiology & Population Sciences, Royal Veterinary College, Hawkhead Lane, North Mymms, Hatfield, Herts AL9 7TA, UK
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17
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Towards Standards for Human Fecal Sample Preparation in Targeted and Untargeted LC-HRMS Studies. Metabolites 2021; 11:metabo11060364. [PMID: 34200487 PMCID: PMC8230323 DOI: 10.3390/metabo11060364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 12/22/2022] Open
Abstract
Gut microbiota and their metabolic products are increasingly being recognized as important modulators of human health. The fecal metabolome provides a functional readout of the interactions between human metabolism and the gut microbiota in health and disease. Due to the high complexity of the fecal matrix, sample preparation often introduces technical variation, which must be minimized to accurately detect and quantify gut bacterial metabolites. Here, we tested six different representative extraction methods (single-phase and liquid–liquid extractions) and compared differences due to fecal amount, extraction solvent type and solvent pH. Our results indicate that a minimum fecal (wet) amount of 0.50 g is needed to accurately represent the complex texture of feces. The MTBE method (MTBE/methanol/water, 3.6/2.8/3.5, v/v/v) outperformed the other extraction methods, reflected by the highest extraction efficiency for 11 different classes of compounds, the highest number of extracted features (97% of the total identified features in different extracts), repeatability (CV < 35%) and extraction recovery (≥70%). Importantly, optimization of the solvent volume of each step to the initial dried fecal material (µL/mg feces) offers a major step towards standardization, which enables confident assessment of the contributions of gut bacterial metabolites to human health.
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18
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Kazantseva J, Malv E, Kaleda A, Kallastu A, Meikas A. Optimisation of sample storage and DNA extraction for human gut microbiota studies. BMC Microbiol 2021; 21:158. [PMID: 34051731 PMCID: PMC8164492 DOI: 10.1186/s12866-021-02233-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023] Open
Abstract
Background New developments in next-generation sequencing technologies and massive data received from this approach open wide prospects for personalised medicine and nutrition studies. Metagenomic analysis of the gut microbiota is paramount for the characterization of human health and wellbeing. Despite the intensive research, there is a huge gap and inconsistency between different studies due to the non-standardised and biased pipeline. Methodical and systemic understanding of every stage in the process is necessary to overcome all bottlenecks and grey zones of gut microbiota studies, where all details and interactions between processes are important. Results Here we show that an inexpensive, but reliable iSeq 100 platform is an excellent tool to perform the analysis of the human gut microbiota by amplicon sequencing of the 16 S rRNA gene. Two commercial DNA extraction kits and different starting materials performed similarly regarding the taxonomic distribution of identified bacteria. DNA/RNA Shield reagent proved to be a reliable solution for stool samples collection, preservation, and storage, as the storage of faecal material in DNA/RNA Shield for three weeks at different temperatures and thawing cycles had a low impact on the bacterial distribution. Conclusions Altogether, a thoroughly elaborated pipeline with close attention to details ensures high reproducibility with significant biological but not technical variations. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02233-y.
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Affiliation(s)
- Jekaterina Kazantseva
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia.
| | - Esther Malv
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
| | - Aleksei Kaleda
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
| | - Aili Kallastu
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
| | - Anne Meikas
- Center of Food and Fermentation Technologies, Akadeemia tee 15a, 12618, Tallinn, Estonia
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19
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Pribyl AL, Parks DH, Angel NZ, Boyd JA, Hasson AG, Fang L, MacDonald SL, Wills BA, Wood DLA, Krause L, Tyson GW, Hugenholtz P. Critical evaluation of faecal microbiome preservation using metagenomic analysis. ISME COMMUNICATIONS 2021; 1:14. [PMID: 37938632 PMCID: PMC9645250 DOI: 10.1038/s43705-021-00014-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/14/2021] [Accepted: 04/06/2021] [Indexed: 05/04/2023]
Abstract
The ability to preserve microbial communities in faecal samples is essential as increasing numbers of studies seek to use the gut microbiome to identify biomarkers of disease. Here we use shotgun metagenomics to rigorously evaluate the technical and compositional reproducibility of five room temperature (RT) microbial stabilisation methods compared to the best practice of flash-freezing. These methods included RNALater, OMNIGene-GUT, a dry BBL swab, LifeGuard, and a novel method for preserving faecal samples, a Copan FLOQSwab in an active drying tube (FLOQSwab-ADT). Each method was assessed using six replicate faecal samples from five participants, totalling 180 samples. The FLOQSwab-ADT performed best for both technical and compositional reproducibility, followed by RNAlater and OMNIgene-GUT. LifeGuard and the BBL swab had unpredictable outgrowth of Escherichia species in at least one replicate from each participant. We further evaluated the FLOQSwab-ADT in an additional 239 samples across 10 individuals after storage at -20 °C, RT, and 50 °C for four weeks compared to fresh controls. The FLOQSwab-ADT maintained its performance across all temperatures, indicating this method is an excellent alternative to existing RT stabilisation methods.
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Affiliation(s)
| | | | | | - Joel A Boyd
- Microba Life Sciences, Brisbane, QLD, Australia
| | | | - Liang Fang
- Microba Life Sciences, Brisbane, QLD, Australia
| | | | | | | | - Lutz Krause
- Microba Life Sciences, Brisbane, QLD, Australia
| | - Gene W Tyson
- Microba Life Sciences, Brisbane, QLD, Australia
- Centre for Microbiome Research, School of Biomedical Science, Translational Research Institute, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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20
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Swei A, Kwan JY. Response to Holmes - practical considerations for vector microbiome studies. Mol Ecol 2021; 30:2214-2219. [PMID: 33904214 DOI: 10.1111/mec.15922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/12/2021] [Indexed: 01/04/2023]
Affiliation(s)
- Andrea Swei
- Department of Biology, San Francisco State University, San Francisco, CA, USA
| | - Jessica Y Kwan
- School of Veterinary Medicine, University of California Davis, Davis, CA, USA
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21
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Gavriliuc S, Stothart MR, Henry A, Poissant J. Long-term storage of feces at -80 °C versus -20 °C is negligible for 16S rRNA amplicon profiling of the equine bacterial microbiome. PeerJ 2021; 9:e10837. [PMID: 33854827 PMCID: PMC7953882 DOI: 10.7717/peerj.10837] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/04/2021] [Indexed: 12/31/2022] Open
Abstract
The development of next-generation sequencing technologies has spurred a surge of research on bacterial microbiome diversity and function. But despite the rapid growth of the field, many uncertainties remain regarding the impact of differing methodologies on downstream results. Sample storage temperature is conventionally thought to be among the most important factors for ensuring reproducibility across marker gene studies, but to date much of the research on this topic has focused on short-term storage in the context of clinical applications. Consequently, it has remained unclear if storage at −80 °C, widely viewed as the gold standard for long-term archival of feces, is truly required for maintaining sample integrity in amplicon-based studies. A better understanding of the impacts of long-term storage conditions is important given the substantial cost and limited availability of ultra-low temperature freezers. To this end, we compared bacterial microbiome profiles inferred from 16S V3–V4 amplicon sequencing for paired fecal samples obtained from a feral horse population from Sable Island, Nova Scotia, Canada, stored at either −80 °C or −20 °C for 4 years. We found that storage temperature did not significantly affect alpha diversity measures, including amplicon sequence variant (ASV) richness and evenness, and abundance of rare sequence variants, nor presence/absence, relative abundances and phylogenetic diversity weighted measures of beta diversity. These results indicate that storage of equine feces at −20 °C for periods ranging from a few months to a few years is equivalent to storage at −80 °C for amplicon-based microbiome studies, adding to accumulating evidence indicating that standard domestic freezers are both economical and effective for microbiome research.
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Affiliation(s)
- Stefan Gavriliuc
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Mason R Stothart
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Astrid Henry
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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22
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Ammitzbøll N, Bau BPJ, Bundgaard-Nielsen C, Villadsen AB, Jensen AM, Leutscher PDC, Glavind K, Hagstrøm S, Arenholt LTS, Sørensen S. Pre- and postmenopausal women have different core urinary microbiota. Sci Rep 2021; 11:2212. [PMID: 33500504 PMCID: PMC7838182 DOI: 10.1038/s41598-021-81790-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 01/04/2021] [Indexed: 12/11/2022] Open
Abstract
Recent studies suggest that alterations in the female urinary microbiota is associated to development of bladder disease. However, the normal microbiota composition and variation in healthy women are poorly described. Moreover, the effects of hormonal changes on microbiota during menopause is not well understood. The aim of our study was to investigate the urinary microbiota in healthy pre- and postmenopausal women without urinary tract symptoms. Microbiota composition in catheterized urine samples was mapped using 16S rRNA gene sequencing. In total, 41 premenopausal and 42 postmenopausal women were initially included. Samples with first PCR amplification concentration below level of the negative control were excluded, resulting in 34 premenopausal and 20 postmenopausal women included in data analysis. Urine from postmenopausal women showed significantly higher alpha diversity compared to premenopausal women. Lactobacillus was the most abundant bacteria in both groups, however the relative abundance of Lactobacillus accounted for 77.8% in premenopausal versus 42.0% in postmenopausal women. In conclusion, urine from premenopausal mostly presented with Lactobacillus dominated urotypes, whereas urine from postmenopausal women presented a more diverse urinary microbiota with higher abundance of the genera Gardnerella and Prevotella. The clinical and pathophysiological implications of this difference remain to be elucidated.
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Affiliation(s)
- Nadia Ammitzbøll
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800 Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | | | - Caspar Bundgaard-Nielsen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800 Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Annemarie Brusen Villadsen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800 Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Ann-Maria Jensen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800 Hjørring, Denmark
| | - Peter Derek Christian Leutscher
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800 Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Karin Glavind
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Obstetrics and Gynecology, Aalborg University Hospital, Aalborg, Denmark
| | - Søren Hagstrøm
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800 Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Pediatrics, Aalborg University Hospital, Aalborg, Denmark
| | - Louise Thomsen Schmidt Arenholt
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800 Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Gynecology and Obstetrics, North Denmark Regional Hospital, Hjørring, Denmark
| | - Suzette Sørensen
- Centre for Clinical Research, North Denmark Regional Hospital, Bispensgade 37, 9800 Hjørring, Denmark. .,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.
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23
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Kang GU, Jung DR, Lee YH, Jeon SY, Han HS, Chong GO, Shin JH. Dynamics of Fecal Microbiota with and without Invasive Cervical Cancer and Its Application in Early Diagnosis. Cancers (Basel) 2020; 12:cancers12123800. [PMID: 33339445 PMCID: PMC7766064 DOI: 10.3390/cancers12123800] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary The fecal microbiome has been suggested to be linked to invasive cervical cancer (ICC). Considering that ICC is common in women, it is important to identify bacterial signatures from fecal microbiota that contribute in classifying cervical cancer. Although previous studies have suggested possible biomarkers based on fecal microbiota, limited information exists in terms of the diagnostic ability using gut microbiota-derived signatures for detecting early ICC. The purpose of this study was to investigate the potential association between early ICC and fecal microbiota and to examine whether fecal microbiota-derived markers can be utilized as a non-invasive tool to diagnose early ICC using machine learning (ML) techniques. Further studies to incorporate quantitative and qualitative characterization of identified individual bacterial genus and validate our model in larger cohorts are imperative in terms of causality for the association between cervical cancer and microbes. Abstract The fecal microbiota is being increasingly implicated in the diagnosis of various diseases. However, evidence on changes in the fecal microbiota in invasive cervical cancer (ICC) remains scarce. Here, we aimed to investigate the fecal microbiota of our cohorts, develop a diagnostic model for predicting early ICC, and identify potential fecal microbiota-derived biomarkers using amplicon sequencing data. We obtained fecal samples from 29 healthy women (HC) and 17 women with clinically confirmed early ICC (CAN). Although Shannon’s diversity index was not reached at statistical significance, the Chao1 and Observed operational taxonomic units (OTUs) in fecal microbiota was significantly different between CAN and HC group. Furthermore, there were significant differences in the taxonomic profiles between HC and CAN; Prevotella was significantly more abundant in the CAN group and Clostridium in the HC group. Linear discriminant analysis effect size (LEfSe) analysis was applied to validate the taxonomic differences at the genus level. Furthermore, we identified a set of seven bacterial genera that were used to construct a machine learning (ML)-based classifier model to distinguish CAN from patients with HC. The model had high diagnostic utility (area under the curve [AUC] = 0.913) for predicting early ICC. Our study provides an initial step toward exploring the fecal microbiota and helps clinicians diagnose.
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Affiliation(s)
- Gi-Ung Kang
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
| | - Da-Ryung Jung
- Department of Biomedical Convergence Science & Technology, Kyungpook National University, Daegu 41566, Korea
| | - Yoon Hee Lee
- Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Daegu 41404, Korea
- Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41940, Korea
| | - Se Young Jeon
- Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41940, Korea
| | - Hyung Soo Han
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41940, Korea
- Department of Physiology, School of Medicine, Kyungpook National University, Daegu 41405, Korea
| | - Gun Oh Chong
- Department of Obstetrics and Gynecology, School of Medicine, Kyungpook National University, Daegu 41404, Korea
- Department of Obstetrics and Gynecology, Kyungpook National University Chilgok Hospital, Daegu 41404, Korea
- Clinical Omics Research Center, School of Medicine, Kyungpook National University, Daegu 41940, Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
- Department of Biomedical Convergence Science & Technology, Kyungpook National University, Daegu 41566, Korea
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24
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Bundgaard-Nielsen C, Knudsen J, Leutscher PDC, Lauritsen MB, Nyegaard M, Hagstrøm S, Sørensen S. Gut microbiota profiles of autism spectrum disorder and attention deficit/hyperactivity disorder: A systematic literature review. Gut Microbes 2020; 11:1172-1187. [PMID: 32329656 PMCID: PMC7524304 DOI: 10.1080/19490976.2020.1748258] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Accumulating evidence has implicated an involvement of the gut-brain axis in autism spectrum disorder (ASD) and attention-deficit hyperactivity disorder (ADHD), however with highly diverse results. This systematic review aims to describe and evaluate studies investigating the gut microbiota composition in individuals with ASD or ADHD and to evaluate if variations in gut microbiota are associated with these disorders. Twenty-four articles were identified in a systematic literature search of PubMed and Embase up to July 22, 2019. They consisted of 20 studies investigating ASD and four studies investigating ADHD. For ASD, several studies agreed on an overall difference in β-diversity, although no consistent bacterial variation between all studies was reported. For ADHD, the results were more diverse, with no clear differences observed. Several common characteristics in gut microbiota function were identified for ASD compared to controls. In contrast, highly heterogeneous results were reported for ADHD, and thus the association between gut microbiota composition and ADHD remains unclear. For both disorders, methodological differences hampered the comparison of studies.
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Affiliation(s)
- Caspar Bundgaard-Nielsen
- Centre for Clinical Research, North Denmark Regional Hospital, Aalborg, Denmark,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark,CONTACT Caspar Bundgaard-Nielsen Centre for Clinical Research North Denmark Regional Hospital and Department of Clinical Medicine, Aalborg University, Aalborg, Denmark Bispensgade 37, 9800 Hjoerring, Denmark
| | - Julie Knudsen
- Centre for Clinical Research, North Denmark Regional Hospital, Aalborg, Denmark,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Peter D. C. Leutscher
- Centre for Clinical Research, North Denmark Regional Hospital, Aalborg, Denmark,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Marlene B. Lauritsen
- Research Unit for Child and Adolescent Psychiatry, Aalborg University Hospital, Aalborg, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Søren Hagstrøm
- Centre for Clinical Research, North Denmark Regional Hospital, Aalborg, Denmark,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark,Department of Pediatrics, Aalborg University Hospital, Aalborg, Denmark
| | - Suzette Sørensen
- Centre for Clinical Research, North Denmark Regional Hospital, Aalborg, Denmark,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
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25
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Bundgaard-Nielsen C, Ammitzbøll N, Isse YA, Muqtar A, Jensen AM, Leutscher PDC, Arenholt LTS, Hagstrøm S, Sørensen S. Voided Urinary Microbiota Is Stable Over Time but Impacted by Post Void Storage. Front Cell Infect Microbiol 2020; 10:435. [PMID: 32984068 PMCID: PMC7477311 DOI: 10.3389/fcimb.2020.00435] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 07/16/2020] [Indexed: 12/18/2022] Open
Abstract
Background: New sensitive techniques have revealed a thriving bacterial community in the human urinary tract, challenging the perception that urine in healthy humans is sterile. While the functional role of this urinary microbiota is unknown, dysbiosis has been linked to urgency urinary incontinence and risk of urinary tract infections. When comparing studies, it is crucial to account for possible confounders introduced due to methodological differences. Here we investigated whether collection and storage conditions had any impact on the urinary microbial composition. Results: For comparison of different storage conditions, midstream urine was collected from five healthy adult female donors and analyzed by 16S rRNA gene sequencing. Samples stored at -80 and -20°C, but not 4°C, were found to be comparable to freshly handled voided urine. Using the same methods, the daily or day-to-day variation in urinary microbiota was investigated in 19 healthy donors, including four women, five men, five girls, and five boys. Apart from two male adult donors, none of the tested conditions gave rise to significant differences in alpha and beta diversities between individuals. Conclusion: The composition of voided urinary microbiota was found to be effectively maintained by freezing, but not storage at 4°C. In addition, we did not observe any intrapersonal daily or day-to-day variations in microbiota composition in women, girls or boys. Together our study supports present methodologies that can be used in future studies investigating the urinary microbiota.
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Affiliation(s)
- Caspar Bundgaard-Nielsen
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Nadia Ammitzbøll
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Yusuf Abdi Isse
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Abdisalam Muqtar
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Ann-Maria Jensen
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark
| | - Peter D C Leutscher
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Steno Diabetes Center North Jutland, Aalborg, Denmark
| | - Louise Thomsen Schmidt Arenholt
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Gynecology and Obstetrics, North Denmark Regional Hospital, Hjørring, Denmark
| | - Søren Hagstrøm
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Steno Diabetes Center North Jutland, Aalborg, Denmark.,Department of Pediatrics, Aalborg University Hospital, Aalborg, Denmark
| | - Suzette Sørensen
- Centre for Clinical Research, North Denmark Regional Hospital, Hjørring, Denmark.,Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Steno Diabetes Center North Jutland, Aalborg, Denmark
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26
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Abstract
BACKGROUND During the past decade, breakthroughs in sequencing technology and computational biology have provided the basis for studies of the myriad ways in which microbial communities ("microbiota") in and on the human body influence human health and disease. In almost every medical specialty, there is now a growing interest in accurate and replicable profiling of the microbiota for use in diagnostic and therapeutic application. CONTENT This review provides an overview of approaches, challenges, and considerations for diagnostic applications borrowing from other areas of molecular diagnostics, including clinical metagenomics. Methodological considerations and evolving approaches for microbiota profiling from mitochondrially encoded 16S rRNA-based amplicon sequencing to metagenomics and metatranscriptomics are discussed. To improve replicability, at least the most vulnerable steps in testing workflows will need to be standardized and continuous efforts needed to define QC standards. Challenges such as purity of reagents and consumables, improvement of reference databases, and availability of diagnostic-grade data analysis solutions will require joint efforts across disciplines and with manufacturers. SUMMARY The body of literature supporting important links between the microbiota at different anatomic sites with human health and disease is expanding rapidly and therapeutic manipulation of the intestinal microbiota is becoming routine. The next decade will likely see implementation of microbiome diagnostics in diagnostic laboratories to fully capitalize on technological and scientific advances and apply them in routine medical practice.
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Affiliation(s)
- Robert Schlaberg
- Department of Pathology, University of Utah, Salt Lake City, UT.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT.,IDbyDNA Inc., San Francisco, CA
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27
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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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28
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Cumpanas AA, Bratu OG, Bardan RT, Ferician OC, Cumpanas AD, Horhat FG, Licker M, Pricop C, Cretu OM. Urinary Microbiota-Are We Ready for Prime Time? A Literature Review of Study Methods' Critical Steps in Avoiding Contamination and Minimizing Biased Results. Diagnostics (Basel) 2020; 10:diagnostics10060343. [PMID: 32471022 PMCID: PMC7345871 DOI: 10.3390/diagnostics10060343] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 05/20/2020] [Accepted: 05/25/2020] [Indexed: 12/11/2022] Open
Abstract
Within the last few years, there have been an increased number of clinical studies involving urinary microbiota. Low-biomass microbiome sequencing (e.g., urine, lung, placenta, blood) is easily biased by contamination or cross-contamination. So far, a few critical steps, from sampling urine to processing and analyzing, have been described (e.g., urine collection modality, sample volume size, snap freezing, negative controls usage, laboratory risks for contamination assessment, contamination of negative results reporting, exploration and discussion of the impact of contamination for the final results, etc.) We performed a literature search (Pubmed, Scopus and Embase) and reviewed the published articles related to urinary microbiome, evaluating how the aforementioned critical steps to obtain unbiased, reliable results have been taken or have been reported. We identified different urinary microbiome evaluation protocols, with non-homogenous reporting systems, which can make gathering results into consistent data for similar topics difficult and further burden the already so complex emerging field of urinary microbiome. We concluded that to ease the progress in this field, a joint approach from researchers, authors and publishers would be necessary in order to create mandatory reporting systems which would allow to recognize pitfalls and avoid compromising a promising field of research.
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Affiliation(s)
- Alin Adrian Cumpanas
- Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (A.A.C.); (R.T.B.); (O.C.F.)
| | - Ovidiu Gabriel Bratu
- Department of Urology, Emergency Military Central Hospital, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania;
| | - Razvan Tiberiu Bardan
- Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (A.A.C.); (R.T.B.); (O.C.F.)
| | - Ovidiu Catalin Ferician
- Department of Urology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (A.A.C.); (R.T.B.); (O.C.F.)
| | - Andrei Dragos Cumpanas
- Faculty of Medicine, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania
- Correspondence:
| | - Florin George Horhat
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (F.G.H.); (M.L.)
| | - Monica Licker
- Department of Microbiology, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania; (F.G.H.); (M.L.)
| | - Catalin Pricop
- Department of Urology, Gr.Tr.Popa University of Medicine and Pharmacy, 700115 Iasi, Romania;
| | - Octavian Marius Cretu
- Department of Surgery, “Victor Babes” University of Medicine and Pharmacy, 300041 Timisoara, Romania;
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Byrd DA, Sinha R, Hoffman KL, Chen J, Hua X, Shi J, Chia N, Petrosino J, Vogtmann E. Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing. mSphere 2020; 5:e00827-19. [PMID: 32250964 PMCID: PMC7045388 DOI: 10.1128/msphere.00827-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/12/2020] [Indexed: 12/16/2022] Open
Abstract
Few previous studies have assessed stability and "gold-standard" concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies.IMPORTANCE A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies.
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Affiliation(s)
- Doratha A Byrd
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Jun Chen
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Xing Hua
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, USA
- Biomedical Engineering and Physiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Joseph Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Webale MK, Wanjala C, Guyah B, Shaviya N, Munyekenye GO, Nyanga PL, Marwa IN, Kagoiyo S, Wangai LN, Webale SK, Kamau K, Kitungulu N. Epidemiological patterns and antimicrobial resistance of bacterial diarrhea among children in Nairobi City, Kenya. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2020; 13:238-246. [PMID: 32821354 PMCID: PMC7417493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AIM Determine the prevalence of enteric bacterial pathogens and their antimicrobial resistance among diarrheic children in Nairobi City, Kenya. BACKGROUND Regardless of enteric bacterial pathogens being a major cause of gastroenteritis in children, their occurrence and antimicrobial resistance patterns reveals regional spatial and temporal variation. METHODS In a cross-sectional study, a total of 374 children below five years presenting with diarrhea at Mbagathi County Hospital were recruited. Stool microbiology test was used to detect enteric bacterial infection. Antimicrobial resistance was determined using the disk diffusion method. RESULTS Diarrheagenic E. coli (36.4%) was the leading species followed by Shigella (3.2%), Salmonella (2.4%), Campylobacter (1.6%), Yersinia (1.3%) and Aeromonas (1.1%) species. Escherichia coli pathotyping revealed that 20.9%, 4.0%, 10.2% and 0.5% of the study participants were infected with enteroaggregative E. coli (EAEC), enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC) and enteroinvasive E. coli (EIEC) pure isolates while the prevalence of mixed pathotype infections was 0.3% for EAEC/EPEC/ETEC and 0.5% for EAEC/ETEC. Shigella sero-grouping revealed that 0.5%, 0.3%, 1.9%, and 0.5% were infected with Shigella boydii, Shigella dysentriae, Shigella flexneri and Shigella sonnei pure isolates. Shigella species and E. coli co-infection was detected in 2.4% of the children, specifically, 1.1% for EAEC/Shigella boydii, 0.5% for EAEC/Shigella dysentriae and 0.3% in each case of EAEC/Shigella sonnei, EPEC/Shigella flexneri and ETEC/Shigella flexneri co-infections. Most of the isolates were resistant to commonly prescribed antibiotics. CONCLUSION There was a high prevalence of enteric bacterial pathogens and co-infection alters epidemiological dynamics of bacterial diarrhea in children. Continuous antibiotic resistance surveillance is justified because the pathogens were highly resistant to commonly prescribed antimicrobials.
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Affiliation(s)
| | - Christine Wanjala
- School of Public Health, Biomedical Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Bernard Guyah
- School of Public Health, Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Nathan Shaviya
- School of Public Health, Biomedical Sciences and Technology, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | | | | | | | - Sammy Kagoiyo
- School of Health Sciences, Kirinyaga University, Kutus, Kenya
| | | | - Sella K. Webale
- School of Public Health, Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Kenny Kamau
- School of Health Sciences, Kirinyaga University, Kutus, Kenya
| | - Nicholas Kitungulu
- School of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
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Marques FZ, Jama HA, Tsyganov K, Gill PA, Rhys-Jones D, Muralitharan RR, Muir J, Holmes A, Mackay CR. Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension. Hypertension 2019; 74:1279-1293. [DOI: 10.1161/hypertensionaha.119.13079] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Hypertension is a complex and modifiable condition in which environmental factors contribute to both onset and progression. Recent evidence has accumulated for roles of diet and the gut microbiome as environmental factors in blood pressure regulation. However, this is complex because gut microbiomes are a unique feature of each individual reflecting that individual’s developmental and environmental history creating caveats for both experimental models and human studies. Here, we describe guidelines for conducting gut microbiome studies in experimental and clinical hypertension. We provide a complete guide for authors on proper design, analyses, and reporting of gut microbiota/microbiome and metabolite studies and checklists that can be used by reviewers and editors to support robust reporting and interpretation. We discuss factors that modulate the gut microbiota in animal (eg, cohort, controls, diet, developmental age, housing, sex, and models used) and human studies (eg, blood pressure measurement and medication, body mass index, demographic characteristics including age, cultural identification, living structure, sex and socioeconomic environment, and exclusion criteria). We also provide best practice advice on sampling, storage of fecal/cecal samples, DNA extraction, sequencing methods (including metagenomics and 16S rRNA), and computational analyses. Finally, we discuss the measurement of short-chain fatty acids, metabolites produced by the gut microbiota, and interpretation of data. These guidelines should support better transparency, reproducibility, and translation of findings in the field of gut microbiota/microbiome in hypertension and cardiovascular disease.
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Affiliation(s)
- Francine Z. Marques
- From the Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science (F.Z.M., H.A.J., K.T., D.R.-J., R.R.M.), Monash University, Melbourne, Australia
- Heart Failure Research Group, Baker Heart and Diabetes Institute, Melbourne, Australia (F.Z.M., H.A.J.)
| | - Hamdi A. Jama
- From the Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science (F.Z.M., H.A.J., K.T., D.R.-J., R.R.M.), Monash University, Melbourne, Australia
- Heart Failure Research Group, Baker Heart and Diabetes Institute, Melbourne, Australia (F.Z.M., H.A.J.)
| | - Kirill Tsyganov
- From the Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science (F.Z.M., H.A.J., K.T., D.R.-J., R.R.M.), Monash University, Melbourne, Australia
| | - Paul A. Gill
- Translational Nutrition Science in the Department of Gastroenterology, Central Clinical School (P.A.G., J.M., D.R-J.), Monash University, Melbourne, Australia
| | - Dakota Rhys-Jones
- From the Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science (F.Z.M., H.A.J., K.T., D.R.-J., R.R.M.), Monash University, Melbourne, Australia
| | - Rikeish R. Muralitharan
- From the Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science (F.Z.M., H.A.J., K.T., D.R.-J., R.R.M.), Monash University, Melbourne, Australia
- Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur, Malaysia (R.R.M.)
| | - Jane Muir
- Translational Nutrition Science in the Department of Gastroenterology, Central Clinical School (P.A.G., J.M., D.R-J.), Monash University, Melbourne, Australia
| | - Andrew Holmes
- Charles Perkin Centre and School of Life and Environmental Sciences, University of Sydney, Australia (A.H.)
| | - Charles R. Mackay
- Infection and Immunity Program, Monash Biomedicine Discovery Institute (C.R.M.), Monash University, Melbourne, Australia
- Department of Biochemistry and Molecular Biology (C.R.M.), Monash University, Melbourne, Australia
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Byrd DA, Chen J, Vogtmann E, Hullings A, Song SJ, Amir A, Kibriya MG, Ahsan H, Chen Y, Nelson H, Knight R, Shi J, Chia N, Sinha R. Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations. PLoS One 2019; 14:e0224757. [PMID: 31738775 PMCID: PMC6860998 DOI: 10.1371/journal.pone.0224757] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/20/2019] [Indexed: 12/30/2022] Open
Abstract
The gut microbiome likely plays a role in the etiology of multiple health conditions, especially those affecting the gastrointestinal tract. Little consensus exists as to the best, standard methods to collect fecal samples for future microbiome analysis. We evaluated three distinct populations (N = 132 participants) using 16S rRNA gene amplicon sequencing data to investigate the reproducibility, stability, and accuracy of microbial profiles in fecal samples collected and stored via fecal occult blood test (FOBT) or Flinders Technology Associates (FTA) cards, fecal immunochemical tests (FIT) tubes, 70% and 95% ethanol, RNAlater, or with no solution. For each collection method, based on relative abundance of select phyla and genera, two alpha diversity metrics, and four beta diversity metrics, we calculated intraclass correlation coefficients (ICCs) to estimate reproducibility and stability, and Spearman correlation coefficients (SCCs) to estimate accuracy of the fecal microbial profile. Comparing duplicate samples, reproducibility ICCs for all collection methods were excellent (ICCs ≥75%). After 4–7 days at ambient temperature, ICCs for microbial profile stability were excellent (≥75%) for most collection methods, except those collected via no-solution and 70% ethanol. SCCs comparing each collection method to immediately-frozen no-solution samples ranged from fair to excellent for most methods; however, accuracy of genus-level relative abundances differed by collection method. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT/FTA cards, FIT tubes, 95% ethanol, and RNAlater are excellent choices for fecal sample collection methods in future microbiome studies. Furthermore, establishing standard collection methods across studies is highly desirable.
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Affiliation(s)
- Doratha A. Byrd
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Jun Chen
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Autumn Hullings
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Muhammad G. Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - Habibul Ahsan
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - Yu Chen
- New York School of Medicine, New York, New York, United States of America
| | - Heidi Nelson
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, California, United States of America
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
- Biomedical Engineering and Physiology, Mayo College, Rochester, Minnesota, United States of America
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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33
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De La Torre U, Henderson JD, Furtado KL, Pedroja M, Elenamarie O, Mora A, Pechanec MY, Maga EA, Mienaltowski MJ. Utilizing the fecal microbiota to understand foal gut transitions from birth to weaning. PLoS One 2019; 14:e0216211. [PMID: 31039168 PMCID: PMC6490953 DOI: 10.1371/journal.pone.0216211] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 04/16/2019] [Indexed: 12/20/2022] Open
Abstract
A healthy gastrointestinal (GI) tract with a properly established microbiota is necessary for a foal to develop into a healthy weanling. A foal's health can be critically impacted by aberrations in the microbiome such as with diarrhea which can cause great morbidity and mortality in foals. In this study, we hypothesized that gut establishment in the foal transitioning from a diet of milk to a diet of grain, forage, and pasture would be detectable through analyses of the fecal microbiotas. Fecal samples from 37 sets of foals and mares were collected at multiple time points ranging from birth to weaning. Bacterial DNA was isolated from the samples, and the V4 domain of bacterial 16S rRNA genes were amplified via polymerase chain reaction. Next generation sequencing was then performed on the resulting amplicons, and analyses were performed to characterize the microbiome as well as the relative abundance of microbiota present. We found that bacterial population compositions followed a pattern throughout the early life of the foal in an age-dependent manner. As foals transitioned from milk consumption to a forage and grain diet, there were recognizable changes in fecal microbial compositions from initial populations predominant in the ability to metabolize milk to populations capable of utilizing fibrous plant material. We were also able to recognize differences in microbial populations amongst diarrheic foals as well as microbial population differences associated with differences in management styles between facilities. Future efforts will gauge the effects of lesser abundant bacterial populations that could also be essential to GI health, as well as to determine how associations between microbial population profiles and animal management practices can be used to inform strategies for improving upon the health and growth of horses overall.
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Affiliation(s)
- Ubaldo De La Torre
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - John D. Henderson
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - Kathleen L. Furtado
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - Madeleine Pedroja
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - O’Malley Elenamarie
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - Anthony Mora
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - Monica Y. Pechanec
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - Elizabeth A. Maga
- Department of Animal Science, University of California Davis, Davis, California, United States of America
| | - Michael J. Mienaltowski
- Department of Animal Science, University of California Davis, Davis, California, United States of America
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Fricker AM, Podlesny D, Fricke WF. What is new and relevant for sequencing-based microbiome research? A mini-review. J Adv Res 2019; 19:105-112. [PMID: 31341676 PMCID: PMC6630040 DOI: 10.1016/j.jare.2019.03.006] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/20/2019] [Accepted: 03/20/2019] [Indexed: 02/07/2023] Open
Abstract
Sample storage and nucleic acid isolation influence microbiota compositions. Error-corrected amplicon sequence variants (ASVs) improve 16S rRNA analysis. Contamination and host cells confound and complicate microbiota analysis. Quantitative and active microbiota analyses can complement existing methods. Open data and protocol sharing increases transparency and reproducibility.
Microbiome research has transformed the scientific landscape, as reflected by the exponential increase in microbiome-related publications from many different disciplines. Host-associated microbial communities play a role for almost all aspects of human, animal and plant biology and health. Consequently, there are tremendous expectations for the development of new clinical, agricultural and biotechnological applications of microbiome research. However, the field continues to be largely shaped by descriptive studies, the mechanistic understanding of microbiome functions for their hosts remains fragmentary, and direct applications of microbiome research are lacking. The aim of this review is therefore to provide a general introduction to the technical opportunities and challenges of microbiome research, as well as to make experimental and bioinformatic recommendations, i.e. (i) to avoid, reduce and assess the confounding effects of sample storage, nucleic acid isolation and microbial contamination; (ii) to minimize non-microbial contributions in host-associated microbiome samples; (iii) to sharpen the focus on physiologically relevant microbiome features by distinguishing signals from metabolically active and inactive or dead microbes and by adopting quantitative methods; and (iv) to enforce open data and protocol policies in order increase the transparency, reproducibility and credibility of the field.
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Affiliation(s)
- Alena M Fricker
- Dept. of Microbiome Research and Applied Bioinformatics, Institute for Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - Daniel Podlesny
- Dept. of Microbiome Research and Applied Bioinformatics, Institute for Nutritional Sciences, University of Hohenheim, Stuttgart, Germany
| | - W Florian Fricke
- Dept. of Microbiome Research and Applied Bioinformatics, Institute for Nutritional Sciences, University of Hohenheim, Stuttgart, Germany.,Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
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