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Stothart MR, McLoughlin PD, Medill SA, Greuel RJ, Wilson AJ, Poissant J. Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses. Nat Commun 2024; 15:6012. [PMID: 39039075 PMCID: PMC11263349 DOI: 10.1038/s41467-024-49963-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: 11/03/2023] [Accepted: 06/21/2024] [Indexed: 07/24/2024] Open
Abstract
Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.
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Affiliation(s)
- Mason R Stothart
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
- Department of Biology, University of Oxford, Oxford, United Kingdom.
| | - Philip D McLoughlin
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sarah A Medill
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ruth J Greuel
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter, Penryn, United Kingdom
| | - Jocelyn Poissant
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada.
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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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Zhang JS, Chen Z, Chu CH, Yu OY. Effect of silver diamine fluoride upon the microbial community of carious lesions: A scoping review. J Dent 2023; 134:104554. [PMID: 37220834 DOI: 10.1016/j.jdent.2023.104554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/15/2023] [Indexed: 05/25/2023] Open
Abstract
OBJECTIVES To explore the effects of silver diamine fluoride (SDF) on the microbial community of carious lesions. DATA Original studies evaluating the effect of SDF treatment on the microbial community of human carious lesions were included. SOURCES A systematic search of English-language publications was performed in PubMed, EMBASE, Scopus, and Web of Science. Gray literature was searched in ClinicalTrials.gov and Google Scholar. STUDY SELECTION/RESULTS This review included seven publications reporting the effects of SDF on microbial community of dental plaque or carious dentin, including the microbial biodiversity, relative abundance of microbial taxa, and predicted functional pathways of the microbial community. The studies on microbial community of dental plaque reported that SDF did not have a significant effect on both the within-community species diversity (alpha-diversity) and inter-community microbial compositional dissimilarity (beta-diversity) of the plaque microbial communities. However, SDF changed the relative abundance of 29 bacterial species of plaque community, inhibited carbohydrate transportation and interfered with the metabolic functions of the plaque microbial community. A study on the microbial community in dentin carious lesions reported that SDF affected its beta-diversity and changed the relative abundance of 14 bacterial species. CONCLUSION SDF showed no significant effects on the biodiversity of the plaque microbial community but changed the beta-diversity of the carious dentin microbial community. SDF could change the relative abundance of certain bacterial species in the dental plaque and the carious dentin. SDF could also affect the predicted functional pathways of the microbial community. CLINICAL SIGNIFICANCE This review provided comprehensive evidence on the potential effect of SDF treatment on the microbial community of carious lesions.
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Affiliation(s)
- Josie Shizhen Zhang
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong SAR, China
| | - Zigui Chen
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong SAR, China; Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chun-Hung Chu
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong SAR, China
| | - Ollie Yiru Yu
- Faculty of Dentistry, The University of Hong Kong, 34 Hospital Road, Hong Kong SAR, China.
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Stothart MR, McLoughlin PD, Poissant J. Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights. Mol Ecol Resour 2023; 23:549-564. [PMID: 36112078 DOI: 10.1111/1755-0998.13713] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/17/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022]
Abstract
Prevailing 16S rRNA gene-amplicon methods for characterizing the bacterial microbiome of wildlife are economical, but result in coarse taxonomic classifications, are subject to primer and 16S copy number biases, and do not allow for direct estimation of microbiome functional potential. While deep shotgun metagenomic sequencing can overcome many of these limitations, it is prohibitively expensive for large sample sets. Here we evaluated the ability of shallow shotgun metagenomic sequencing to characterize taxonomic and functional patterns in the faecal microbiome of a model population of feral horses (Sable Island, Canada). Since 2007, this unmanaged population has been the subject of an individual-based, long-term ecological study. Using deep shotgun metagenomic sequencing, we determined the sequencing depth required to accurately characterize the horse microbiome. In comparing conventional vs. high-throughput shotgun metagenomic library preparation techniques, we validate the use of more cost-effective laboratory methods. Finally, we characterize similarities between 16S amplicon and shallow shotgun characterization of the microbiome, and demonstrate that the latter recapitulates biological patterns first described in a published amplicon data set. Unlike for amplicon data, we further demonstrate how shallow shotgun metagenomic data provide useful insights regarding microbiome functional potential which support previously hypothesized diet effects in this study system.
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Affiliation(s)
- Mason R Stothart
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Philip D McLoughlin
- Department of Biology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Jocelyn Poissant
- Department of Ecosystem and Public Health, Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
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Impact of Freeze Storage on the Estimation of Phenotypic Antimicrobial Resistance Prevalence in Escherichia coli Collected from Faecal Samples from Healthy Humans and Chickens. Antibiotics (Basel) 2022; 11:antibiotics11111643. [DOI: 10.3390/antibiotics11111643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/13/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Many studies on phenotypic antimicrobial resistance (AMR) of bacteria from healthy populations are conducted on freeze-stored samples. However, the impact of this practice on phenotypic AMR is not known. We investigated the prevalence of phenotypic AMR in Escherichia coli from chicken (n = 10) and human (n = 11) faecal samples collected from healthy subjects, subject to freeze storage (−20 °C and −80 °C) for 1, 2, 3, and 6 months. We compared counts of E. coli and prevalence of phenotypic resistance against five antimicrobials commonly used in chicken farming (ciprofloxacin, enrofloxacin, doxycycline, gentamicin, and florfenicol) with samples processed within 24 h of collection. Prevalence of phenotypic AMR was estimated by performing differential counts on agar media with and without antimicrobials. At −20 °C, there was a considerable reduction in E. coli counts over time, and this reduction was greater for human samples (−0.630 log10 units per 100 days) compared with chicken samples (−0.178 log10 units per 100 days). For most antimicrobials, AMR prevalence estimates decreased in freeze-stored samples both in humans and chickens over time. Based on these results, we conclude that results on the prevalence of phenotypic AMR on samples from freeze-stored samples are unreliable, and only fresh samples should be used in such studies.
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Bensch HM, Tolf C, Waldenström J, Lundin D, Zöttl M. Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples. PeerJ 2022; 10:e13095. [PMID: 35310158 PMCID: PMC8932309 DOI: 10.7717/peerj.13095] [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: 11/30/2021] [Accepted: 02/20/2022] [Indexed: 01/12/2023] Open
Abstract
Background The transport and storage of samples in temperatures of minus 80 °C is commonly considered as the gold standard for microbiome studies. However, studies conducting sample collection at remote sites without a reliable cold-chain would benefit from a sample preservation method that allows transport and storage at ambient temperature. Methods In this study we compare alpha diversity and 16S microbiome composition of 20 fecal sample replicates from Damaraland mole-rats (Fukomys damarensis) preserved in a minus 80 °C freezer and transported on dry ice to freeze-dried samples that were stored and transported in ambient temperature until DNA extraction. Results We found strong correlations between relative abundances of Amplicon Sequence Variants (ASVs) between preservation treatments of the sample, no differences in alpha diversity measures between the two preservation treatments and minor effects of the preservation treatment on beta diversity measures. Our results show that freeze-drying samples can be a useful method for cost-effective transportation and storage of microbiome samples that yields quantitatively almost indistinguishable results in 16S microbiome analyses as those stored in minus 80 °C.
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Affiliation(s)
- Hanna M. Bensch
- Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Department of Biology and Environmental Science, Linnaeus University, Sweden,Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
| | - Conny Tolf
- Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Department of Biology and Environmental Science, Linnaeus University, Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Department of Biology and Environmental Science, Linnaeus University, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Department of Biology and Environmental Science, Linnaeus University, Sweden
| | - Markus Zöttl
- Centre for Ecology and Evolution in Microbial Model Systems (EEMIS), Department of Biology and Environmental Science, Linnaeus University, Sweden,Kalahari Research Centre, Kuruman River Reserve, Van Zylsrus, South Africa
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Bhattacharjee A, Dubey S, Sharma S. Storage of soil microbiome for application in sustainable agriculture: prospects and challenges. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:3171-3183. [PMID: 34718953 DOI: 10.1007/s11356-021-17164-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Soil microbiome is a dynamic micro-ecosystem driving and fine-tuning several biological processes in the global macro-ecosystems. Its tremendous potential towards mediating sustainability in the ecosystem necessitates the urgent need to store it optimally and efficiently as "next-generation biologicals" for future applications via soil transplantation. The challenge, therefore, is to devise a strategy for the storage of soil microbiome such that its "functionality" is preserved for later application. This review discusses the current endeavours made towards storage of the soil microbiome. The methods for assessing the integrity of soil microbiome by targeting the structural diversity and functional potential of the preserved microbiomes have also been discussed. Further, the success stories related to the storage of fecal microbiome for application in transplants have also been highlighted. This is done primarily with the objective of learning lessons, and parallel application of the knowledge gained, in bringing about improvement in the research domain of soil microbiome storage. Subsequently, the limitations of current techniques of preservation have also been delineated. Further, the open questions in the area have been critically discussed. In conclusion, possible alternatives for storage, comprehensive analyses of the composition of the stored microbiome and their potential have been presented.
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Affiliation(s)
- Annapurna Bhattacharjee
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shubham Dubey
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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Shi J, Yang Y, Xu W, Cai H, Wu J, Long J, Cai Q, Zheng W, Flynn CR, Shu XO, Yu D. Sex-Specific Associations between Gut Microbiome and Non-Alcoholic Fatty Liver Disease among Urban Chinese Adults. Microorganisms 2021; 9:microorganisms9102118. [PMID: 34683439 PMCID: PMC8537656 DOI: 10.3390/microorganisms9102118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) has been linked to altered gut microbiome; however, evidence from large population-based studies is limited. We compared gut microbiome profiles of 188 male and 233 female NAFLD cases with 571 male and 567 female controls from two longitudinal studies of urban Chinese adults. History of NAFLD was assessed during surveys administered in 2004-2017. Microbiota were assessed using 16S rRNA sequencing of stool samples collected in 2015-2018. Associations of NAFLD with microbiome diversity and composition were evaluated by generalized linear or logistic regression models. Compared with controls, male cases had lower microbial α-diversity, higher abundance of genera Dialister and Streptococcus and Bifidobacterium species, lower abundance of genus Phascolarctobacterium, and lower prevalence of taxa including order RF39 (all p < 0.05). In contrast, female cases had higher α-diversity, higher abundance of genus Butyricimonas and a family of order Clostridiales, lower abundance of Dialister and Bifidobacterium species, and higher prevalence of RF39. Significant NAFLD-sex interactions were found for α-diversity and above taxa (all false discovery rate < 0.1). In conclusion, we observed sex-specific gut microbiome features related to history of NAFLD. Further studies are needed to validate our findings and evaluate the health effects of NAFLD-related gut microbiota.
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Affiliation(s)
- Jiajun Shi
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Suite 600, Nashville, TN 37232, USA; (J.S.); (Y.Y.); (H.C.); (J.W.); (J.L.); (Q.C.); (W.Z.); (X.-O.S.)
| | - Yaohua Yang
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Suite 600, Nashville, TN 37232, USA; (J.S.); (Y.Y.); (H.C.); (J.W.); (J.L.); (Q.C.); (W.Z.); (X.-O.S.)
| | - Wanghong Xu
- Department of Epidemiology, School of Public Health, Fudan University, Shanghai 200433, China;
| | - Hui Cai
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Suite 600, Nashville, TN 37232, USA; (J.S.); (Y.Y.); (H.C.); (J.W.); (J.L.); (Q.C.); (W.Z.); (X.-O.S.)
| | - Jie Wu
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Suite 600, Nashville, TN 37232, USA; (J.S.); (Y.Y.); (H.C.); (J.W.); (J.L.); (Q.C.); (W.Z.); (X.-O.S.)
| | - Jirong Long
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Suite 600, Nashville, TN 37232, USA; (J.S.); (Y.Y.); (H.C.); (J.W.); (J.L.); (Q.C.); (W.Z.); (X.-O.S.)
| | - Qiuyin Cai
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Suite 600, Nashville, TN 37232, USA; (J.S.); (Y.Y.); (H.C.); (J.W.); (J.L.); (Q.C.); (W.Z.); (X.-O.S.)
| | - Wei Zheng
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Suite 600, Nashville, TN 37232, USA; (J.S.); (Y.Y.); (H.C.); (J.W.); (J.L.); (Q.C.); (W.Z.); (X.-O.S.)
| | - Charles R. Flynn
- Department of Surgery, Division of General Surgery, Vanderbilt University Medical Center, Suite 600, Nashville, TN 37232, USA;
| | - Xiao-Ou Shu
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Suite 600, Nashville, TN 37232, USA; (J.S.); (Y.Y.); (H.C.); (J.W.); (J.L.); (Q.C.); (W.Z.); (X.-O.S.)
| | - Danxia Yu
- Department of Medicine, Division of Epidemiology, Vanderbilt University Medical Center, Suite 600, Nashville, TN 37232, USA; (J.S.); (Y.Y.); (H.C.); (J.W.); (J.L.); (Q.C.); (W.Z.); (X.-O.S.)
- Correspondence: ; Tel.: +1-615-936-7389; Fax: +1-615-936-8291
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