1
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Romanis CS, Timms VJ, Crosbie ND, Neilan BA. 16S rRNA gene amplicon sequencing data from an Australian wastewater treatment plant. Microbiol Resour Announc 2024:e0123723. [PMID: 38700348 DOI: 10.1128/mra.01237-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 04/20/2024] [Indexed: 05/05/2024] Open
Abstract
Amplicon sequencing data of the 16S rRNA (V1-V3) gene from 56 effluent and sediment samples from an Australian wastewater treatment plant are reported. Proteobacteria (3.50%-90.09%), Actinobacteria (0.02%-45.71%), and Cyanobacteria (0.05%-63.73%) were dominant in the effluent. The sediment samples were dominated by Proteobacteria (13.14%-84.83%), Chloroflexi (0.84%-42.52%), and Firmicutes (1.54%-17.21%).
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Affiliation(s)
- C S Romanis
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - V J Timms
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
- ARC Centre of Excellence for Synthetic Biology, Newcastle, Australia
| | - N D Crosbie
- Melbourne Water, Docklands, Victoria, Australia
| | - B A Neilan
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
- ARC Centre of Excellence for Synthetic Biology, Newcastle, Australia
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2
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Trecarten S, Fongang B, Liss M. Current Trends and Challenges of Microbiome Research in Prostate Cancer. Curr Oncol Rep 2024; 26:477-487. [PMID: 38573440 DOI: 10.1007/s11912-024-01520-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
PURPOSE OF REVIEW The role of the gut microbiome in prostate cancer is an emerging area of research interest. However, no single causative organism has yet been identified. The goal of this paper is to examine the role of the microbiome in prostate cancer and summarize the challenges relating to methodology in specimen collection, sequencing technology, and interpretation of results. RECENT FINDINGS Significant heterogeneity still exists in methodology for stool sampling/storage, preservative options, DNA extraction, and sequencing database selection/in silico processing. Debate persists over primer choice in amplicon sequencing as well as optimal methods for data normalization. Statistical methods for longitudinal microbiome analysis continue to undergo refinement. While standardization of methodology may help yield more consistent results for organism identification in prostate cancer, this is a difficult task due to considerable procedural variation at each step in the process. Further reproducibility and methodology research is required.
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Affiliation(s)
- Shaun Trecarten
- Department of Urology, UT Health San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA
| | - Bernard Fongang
- Glenn Biggs Institute for Alzheimer's & Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
- Department of Biochemistry and Structural Biology, UT Health San Antonio, San Antonio, TX, USA
- Department of Population Health Sciences, UT Health San Antonio, San Antonio, TX, USA
| | - Michael Liss
- Department of Urology, UT Health San Antonio, 7703 Floyd Curl Dr, San Antonio, TX, 78229, USA.
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3
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Maghini DG, Dvorak M, Dahlen A, Roos M, Kuersten S, Bhatt AS. Quantifying bias introduced by sample collection in relative and absolute microbiome measurements. Nat Biotechnol 2024; 42:328-338. [PMID: 37106038 DOI: 10.1038/s41587-023-01754-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 03/21/2023] [Indexed: 04/29/2023]
Abstract
To gain insight into the accuracy of microbial measurements, it is important to evaluate sources of bias related to sample condition, preservative method and bioinformatic analyses. There is increasing evidence that measurement of the total count and concentration of microbes in the gut, or 'absolute abundance', provides a richer source of information than relative abundance and can correct some conclusions drawn from relative abundance data. However, little is known about how preservative choice can affect these measurements. In this study, we investigated how two common preservatives and short-term storage conditions impact relative and absolute microbial measurements. OMNIgene GUT OMR-200 yields lower metagenomic taxonomic variation between different storage temperatures, whereas Zymo DNA/RNA Shield yields lower metatranscriptomic taxonomic variation. Absolute abundance quantification reveals two different causes of variable Bacteroidetes:Firmicutes ratios across preservatives. Based on these results, we recommend OMNIgene GUT OMR-200 preservative for field studies and Zymo DNA/RNA Shield for metatranscriptomics studies, and we strongly encourage absolute quantification for microbial measurements.
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Affiliation(s)
- Dylan G Maghini
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Mai Dvorak
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alex Dahlen
- Quantitative Sciences Unit, Stanford University, Stanford, CA, USA
| | | | | | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
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4
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Chiu O, Gomez DE, Obrego D, Dunfield K, MacNicol JL, Liversidge B, Verbrugghe A. Impact of fecal sample preservation and handling techniques on the canine fecal microbiota profile. PLoS One 2024; 19:e0292731. [PMID: 38285680 PMCID: PMC10824447 DOI: 10.1371/journal.pone.0292731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/27/2023] [Indexed: 01/31/2024] Open
Abstract
Canine fecal microbiota profiling provides insight into host health and disease. Standardization of methods for fecal sample storage for microbiomics is currently inconclusive, however. This study investigated the effects of homogenization, the preservative RNAlater, room temperature exposure duration, and short-term storage in the fridge prior to freezing on the canine fecal microbiota profile. Within 15 minutes after voiding, samples were left non-homogenized or homogenized and aliquoted, then kept at room temperature (20-22°C) for 0.5, 4, 8, or 24 hours. Homogenized aliquots then had RNAlater added or not. Following room temperature exposure, all aliquots were stored in the fridge (4°C) for 24 hours prior to storing in the freezer (-20°C), or stored directly in the freezer. DNA extraction, PCR amplification, then sequencing were completed on all samples. Alpha diversity (diversity, evenness, and richness), and beta diversity (community membership and structure), and relative abundances of bacterial genera were compared between treatments. Homogenization and RNAlater minimized changes in the microbial communities over time, although minor changes in relative abundances occurred. Non-homogenized samples had more inter-sample variability and greater changes in beta diversity than homogenized samples. Storage of canine fecal samples in the fridge for 24 h prior to storage in the freezer had little effect on the fecal microbiota profile. Our findings suggest that if immediate analysis of fecal samples is not possible, samples should at least be homogenized to preserve the existing microbiota profile.
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Affiliation(s)
- Olivia Chiu
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Diego E. Gomez
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Dasiel Obrego
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Kari Dunfield
- School of Environmental Sciences, University of Guelph, Guelph, Ontario, Canada
| | - Jennifer L. MacNicol
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Brooklynn Liversidge
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
| | - Adronie Verbrugghe
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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5
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Langon X. Validation of method for faecal sampling in cats and dogs for faecal microbiome analysis. BMC Vet Res 2023; 19:274. [PMID: 38102642 PMCID: PMC10724939 DOI: 10.1186/s12917-023-03842-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 12/03/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Reproducible and reliable studies of cat and dog faecal microbiomes are dependent on many methodology-based variables including how the faecal stools are sampled and stored prior to processing. The current study aimed to establish an appropriate method for sampling and storing faecal stools from cats and dogs which may also be applied to privately-owned pets. The approach investigated the effects of storing faeces for up to 12 h at room temperature and sampling from various locations within the stool in terms of microbial diversity, relative taxa abundances and DNA yield. Faeces were collected from 10 healthy cats and 10 healthy dogs and stored at room temperature (20 °C). Samples were taken from various locations within the stool (the first emitted part (i), the middle (ii) and the last emitted end (iii), at either surface or core) at 0, 0.5, 1, 2, 3, 6 and 12 h, stabilised and stored at -80 °C. DNA was extracted from all samples, using Illumina NovaSeq. RESULTS Faecal bacterial composition of dogs and cats shown no statistically significant differences in alpha diversity. Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria were the most prevalent phyla. Cat and dog samples were characterized by a dominance of Prevotella, and a lack of Fusobacterium in feline stools. Room temperature storage of cat and dog faecal samples generally had no significant effect on alpha diversity, relative taxa abundance or DNA yield for up to 12 h. Sampling from regions i, ii or iii of the stool at the surface or core did not significantly influence the outcome. However, surface cat faecal samples stored at room temperature for 12 h showed a significant increase in two measures of alpha diversity and there was a tendency for a similar effect in dogs. When comparing samples with beta diversity measures, it appeared that for dog and cat samples, individual effect has the strongest impact on the observed microbial diversity (R2 0.64 and 0.88), whereas sampling time, depth and horizontal locations significantly affected the microbial diversity but with less impact. CONCLUSION Cat and dog faeces were stable at room temperature for up to 12 h, with no significant changes in alpha diversity, relative taxa abundance and DNA concentration. Beta diversity analysis demonstrated that despite an impact of the sampling storing time and the surface of the sampling, we preserved the identity of the microbial structure linked to the individual. Finally, the data suggest that faecal stools stored for > 6 h at room temperature should be sampled at the core, not the surface.
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Affiliation(s)
- Xavier Langon
- Royal Canin Sas, 650 avenue de la Petite Camargue, AIMARGUES Cedex, CS, 10309, 30470, France.
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6
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Williams CE, Brown AE, Williams CL. The role of diet and host species in shaping the seasonal dynamics of the gut microbiome. FEMS Microbiol Ecol 2023; 99:fiad156. [PMID: 38070877 PMCID: PMC10750813 DOI: 10.1093/femsec/fiad156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 10/05/2023] [Accepted: 12/08/2023] [Indexed: 12/27/2023] Open
Abstract
The gut microbiome plays an important role in the health and fitness of hosts. While previous studies have characterized the importance of various ecological and evolutionary factors in shaping the composition of the gut microbiome, most studies have been cross-sectional in nature, ignoring temporal variation. Thus, it remains unknown how these same factors might affect the stability and dynamics of the gut microbiome over time, resulting in variation across the tree of life. Here, we used samples collected in each of four seasons for three taxa: the herbivorous southern white rhinoceros (Ceratotherium simum simum, n = 5); the carnivorous Sumatran tiger (Panthera tigris sumatrae, n = 5); and the red panda (Ailurus fulgens, n = 9), a herbivorous carnivore that underwent a diet shift in its evolutionary history from carnivory to a primarily bamboo-based diet. We characterize the variability of the gut microbiome among these three taxa across time to elucidate the influence of diet and host species on these dynamics. Altogether, we found that red pandas exhibit marked seasonal variation in their gut microbial communities, experiencing both high microbial community turnover and high variation in how individual red panda's gut microbiota respond to seasonal changes. Conversely, while the gut microbiota of rhinoceros change throughout the year, all individuals respond in the same way to seasonal changes. Tigers experience relatively low levels of turnover throughout the year, yet the ways in which individuals respond to seasonal transitions are highly varied. We highlight how the differences in microbiome richness and network connectivity between these three species may affect the level of temporal stability in the gut microbiota across the year.
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Affiliation(s)
- Claire E Williams
- Department of Biology, University of Nevada, Reno, Reno, NV 89557, United States
| | - Ashli E Brown
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS State, MS 39762, United States
| | - Candace L Williams
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, MS State, MS 39762, United States
- Beckman Center for Conservation Science, San Diego Zoo Wildlife Alliance, San Diego, CA 92027, United States
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7
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Spreckels JE, Fernández-Pato A, Kruk M, Kurilshikov A, Garmaeva S, Sinha T, Ghosh H, Harmsen H, Fu J, Gacesa R, Zhernakova A. Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques. ISME Commun 2023; 3:116. [PMID: 37945978 PMCID: PMC10636111 DOI: 10.1038/s43705-023-00325-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/18/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Human milk microbiome studies are currently hindered by low milk bacterial/human cell ratios and often rely on 16S rRNA gene sequencing, which limits downstream analyses. Here, we aimed to find a method to study milk bacteria and assess bacterial sharing between maternal and infant microbiota. We tested four DNA isolation methods, two bacterial enrichment methods and three sequencing methods on mock communities, milk samples and negative controls. Of the four DNA isolation kits, the DNeasy PowerSoil Pro (PS) and MagMAX Total Nucleic Acid Isolation (MX) kits provided consistent 16S rRNA gene sequencing results with low contamination. Neither enrichment method substantially decreased the human metagenomic sequencing read-depth. Long-read 16S-ITS-23S rRNA gene sequencing biased the mock community composition but provided consistent results for milk samples, with little contamination. In contrast to 16S rRNA gene sequencing, 16S-ITS-23S rRNA gene sequencing of milk, infant oral, infant faecal and maternal faecal DNA from 14 mother-infant pairs provided sufficient resolution to detect significantly more frequent sharing of bacteria between related pairs compared to unrelated pairs. In conclusion, PS or MX kit-DNA isolation followed by 16S rRNA gene sequencing reliably characterises human milk microbiota, and 16S-ITS-23S rRNA gene sequencing enables studies of bacterial transmission in low-biomass samples.
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Grants
- This study was supported by funds from the Dutch Research Council (NWO-VIDI grant 016.178.056 to A.Z., NWO-VICI grant VI.C.202.022 to J.F., NWO gravitation grant Exposome-NL 024.004.017 to A.K. and A.Z., NWO gravitation grant Netherlands Organ-on-Chip Initiative 024.003.001 to J.F.), the Dutch Heart Foundation (IN-CONTROL CVON2018-27 to J.F.), the European Research Council (ERC starting grant 715772 to A.Z., ERC consolidator grant 101001678 to J.F.), an EASI-Genomics grant (PID7780 to T.S. and A.Z.), the De-Cock Hadders foundation (2021-57 to J.E.S., 2021-08 to S.G.), the International Society for Research in Human Milk and Lactation (ISRHML, personal grant to J.E.S), the Winston Bakker Fonds (WB-08, granted to T.S.), and the European Union’s Horizon 2020 research innovation program (824110). S.G. and T.S. hold scholarships from the Graduate School of Medical Sciences and the Junior Scientific Masterclass of the University of Groningen, the Netherlands, respectively. The Lifelines NEXT cohort study received funds from the University Medical Center Groningen Hereditary Metabolic Diseases Fund, Health~Holland (Top Sector Life Sciences and Health), the Ubbo Emmius Foundation, the European Union, the Northern Netherlands Alliance (SNN), the provinces of Friesland and Groningen, the municipality of Groningen, Philips, and the Société des Produits Nestlé.
- De-Cock Hadders foundation (2021-57) International Society of Research in Human Milk and Lactation (ISRHML personal grant)
- Dutch Research Council (NWO gravitation grant Exposome-NL 024.004.017)
- De-Cock Hadders foundation (2021-08) University of Groningen Graduate School of Medical Sciences (scholarship)
- EASI-Genomics (grant PID7780) Winston Bakker Fonds (WB-08) University of Groningen Junior Scientific Masterclass (scholarship)
- Dutch Research Council (NWO-VICI grant VI.C.202.022) Dutch Research Council (NWO gravitation grant Netherlands Organ-on-Chip Initiative 024.003.001) European Research Council (ERC consolidator grant 101001678)
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Affiliation(s)
- Johanne E Spreckels
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Asier Fernández-Pato
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Marloes Kruk
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Alexander Kurilshikov
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Sanzhima Garmaeva
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Trishla Sinha
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Hiren Ghosh
- Medical Center - University of Freiburg, Institute for Infection Prevention and Hospital Epidemiology, Freiburg, Germany
| | - Hermie Harmsen
- Department of Medical Microbiology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Jingyuan Fu
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Ranko Gacesa
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
- Department of Gastroenterology and Hepatology, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen and University Medical Center Groningen, Groningen, the Netherlands.
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Ward AB, Harris PA, Argo CM, Watson C, Neacsu M, Russell WR, Ribeiro A, Collie-Duguid E, Heidari Z, Morrison PK. Homemade Nucleic Acid Preservation Buffer Proves Effective in Preserving the Equine Faecal Microbiota over Time at Ambient Temperatures. Animals (Basel) 2023; 13:3107. [PMID: 37835713 PMCID: PMC10572018 DOI: 10.3390/ani13193107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
The equine faecal microbiota is often assessed as a proxy of the microbial community in the distal colon, where the microbiome has been linked to states of health and disease in the horse. However, the microbial community structure may change over time if samples are not adequately preserved. This study stored equine faecal samples from n = 10 horses in four preservation treatments at room temperature for up to 150 h and assessed the resulting impact on microbial diversity and the differential abundance of taxa. Treatments included "COLD" (samples packaged with a cool pack), "CLX" (2% chlorhexidine digluconate solution), "NAP" (nucleic acid preservation buffer), and "FTA" (Whatman FTA™ cards). The samples were assessed using 16S rRNA gene sequencing after storage for 0, 24, 72, and 150 h at room temperature under the different treatments. The results showed effective preservation of diversity and community structure with NAP buffer but lower diversity (p = 0.001) and the under-representation of Fibrobacterota in the FTA card samples. The NAP treatment inhibited the overgrowth of bloom taxa that occurred by 72 h at room temperature. The COLD, CLX, and NAP treatments were effective in preserving the faecal microbiota for up to 24 h at room temperature, and the CLX and NAP treatments improved the yield of Patescibacteria and Fibrobacterota in some cases. The cold and CLX treatments were ineffective in preventing community shifts that occurred by 72 h at room temperature. These findings demonstrate the suitability of the COLD, NAP, and CLX treatments for the room temperature storage of equine faeces for up to 24 h and of NAP buffer for up to 150 h prior to processing.
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Affiliation(s)
- Ashley B. Ward
- School of Veterinary Medicine, Scotland’s Rural College, Aberdeen AB21 9YA, UK
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
- School of Medicine Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Patricia A. Harris
- Equine Studies Group, Waltham Petcare Science Institute, Leicestershire LE14 4RT, UK
| | - Caroline McG. Argo
- School of Veterinary Medicine, Scotland’s Rural College, Aberdeen AB21 9YA, UK
| | - Christine Watson
- Department of Rural Land Use, Scotland’s Rural College, Aberdeen AB21 9YA, UK
| | - Madalina Neacsu
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Wendy R. Russell
- The Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
| | - Antonio Ribeiro
- School of Medicine Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, King’s College, Aberdeen AB24 3FX, UK
| | - Elaina Collie-Duguid
- School of Medicine Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, King’s College, Aberdeen AB24 3FX, UK
| | - Zeynab Heidari
- School of Medicine Medical Sciences and Nutrition, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, UK
- Centre for Genome-Enabled Biology and Medicine, University of Aberdeen, King’s College, Aberdeen AB24 3FX, UK
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Widjaja F, Rietjens IMCM. From-Toilet-to-Freezer: A Review on Requirements for an Automatic Protocol to Collect and Store Human Fecal Samples for Research Purposes. Biomedicines 2023; 11:2658. [PMID: 37893032 PMCID: PMC10603957 DOI: 10.3390/biomedicines11102658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
The composition, viability and metabolic functionality of intestinal microbiota play an important role in human health and disease. Studies on intestinal microbiota are often based on fecal samples, because these can be sampled in a non-invasive way, although procedures for sampling, processing and storage vary. This review presents factors to consider when developing an automated protocol for sampling, processing and storing fecal samples: donor inclusion criteria, urine-feces separation in smart toilets, homogenization, aliquoting, usage or type of buffer to dissolve and store fecal material, temperature and time for processing and storage and quality control. The lack of standardization and low-throughput of state-of-the-art fecal collection procedures promote a more automated protocol. Based on this review, an automated protocol is proposed. Fecal samples should be collected and immediately processed under anaerobic conditions at either room temperature (RT) for a maximum of 4 h or at 4 °C for no more than 24 h. Upon homogenization, preferably in the absence of added solvent to allow addition of a buffer of choice at a later stage, aliquots obtained should be stored at either -20 °C for up to a few months or -80 °C for a longer period-up to 2 years. Protocols for quality control should characterize microbial composition and viability as well as metabolic functionality.
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Affiliation(s)
- Frances Widjaja
- Division of Toxicology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands;
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10
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Aizpurua O, Dunn RR, Hansen LH, Gilbert MTP, Alberdi A. Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data. Crit Rev Biotechnol 2023:1-19. [PMID: 37731336 DOI: 10.1080/07388551.2023.2254933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/27/2023] [Indexed: 09/22/2023]
Abstract
Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.
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Affiliation(s)
- Ostaizka Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Lars H Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - M T P Gilbert
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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11
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Zhang L, Feng Z, Li Y, Lv C, Li C, Hu Y, Fu M, Song L. Salivary and fecal microbiota: potential new biomarkers for early screening of colorectal polyps. Front Microbiol 2023; 14:1182346. [PMID: 37655344 PMCID: PMC10467446 DOI: 10.3389/fmicb.2023.1182346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Objective Gut microbiota plays an important role in colorectal cancer (CRC) pathogenesis through microbes and their metabolites, while oral pathogens are the major components of CRC-associated microbes. Multiple studies have identified gut and fecal microbiome-derived biomarkers for precursors lesions of CRC detection. However, few studies have used salivary samples to predict colorectal polyps. Therefore, in order to find new noninvasive colorectal polyp biomarkers, we searched into the differences in fecal and salivary microbiota between patients with colorectal polyps and healthy controls. Methods In this case-control study, we collected salivary and fecal samples from 33 patients with colorectal polyps (CP) and 22 healthy controls (HC) between May 2021 and November 2022. All samples were sequenced using full-length 16S rRNA sequencing and compared with the Nucleotide Sequence Database. The salivary and fecal microbiota signature of colorectal polyps was established by alpha and beta diversity, Linear discriminant analysis Effect Size (LEfSe) and random forest model analysis. In addition, the possibility of microbiota in identifying colorectal polyps was assessed by Receiver Operating Characteristic Curve (ROC). Results In comparison to the HC group, the CP group's microbial diversity increased in saliva and decreased in feces (p < 0.05), but there was no significantly difference in microbiota richness (p > 0.05). The principal coordinate analysis revealed significant differences in β-diversity of salivary and fecal microbiota between the CP and HC groups. Moreover, LEfSe analysis at the species level identified Porphyromonas gingivalis, Fusobacterium nucleatum, Leptotrichia wadei, Prevotella intermedia, and Megasphaera micronuciformis as the major contributors to the salivary microbiota, and Ruminococcus gnavus, Bacteroides ovatus, Parabacteroides distasonis, Citrobacter freundii, and Clostridium symbiosum to the fecal microbiota of patients with polyps. Salivary and fecal bacterial biomarkers showed Area Under ROC Curve of 0.8167 and 0.8051, respectively, which determined the potential of diagnostic markers in distinguishing patients with colorectal polyps from controls, and it increased to 0.8217 when salivary and fecal biomarkers were combined. Conclusion The composition and diversity of the salivary and fecal microbiota were significantly different in colorectal polyp patients compared to healthy controls, with an increased abundance of harmful bacteria and a decreased abundance of beneficial bacteria. A promising non-invasive tool for the detection of colorectal polyps can be provided by potential biomarkers based on the microbiota of the saliva and feces.
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Affiliation(s)
- Limin Zhang
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Ziying Feng
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Yinghua Li
- Central Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Cuiting Lv
- Central Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Chunchun Li
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Yue Hu
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Mingsheng Fu
- Department of Gastroenterology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
| | - Liang Song
- Department of Stomatology, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China
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12
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Jokela R, Ponsero AJ, Dikareva E, Wei X, Kolho KL, Korpela K, de Vos WM, Salonen A. Sources of gut microbiota variation in a large longitudinal Finnish infant cohort. EBioMedicine 2023; 94:104695. [PMID: 37399600 PMCID: PMC10328818 DOI: 10.1016/j.ebiom.2023.104695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Although the infant gut microbiota has been extensively studied, comprehensive assessment on the microbiota determinants including technical variables has not been performed in large infant cohorts. METHODS We studied the effect of 109 variables on the 16S rRNA gene amplicon-based gut microbiota profiles of infants sampled longitudinally from three weeks to two years of life in the Finnish HELMi birth cohort. Spot faecal samples from both parents were included for intra-family analyses, totalling to 7657 samples from 985 families that were evaluated for beta-diversity patterns using permutational multivariate analysis on Bray-Curtis distances, and differential abundance testing and alpha-diversity for variables of interest. We also assessed the effect of different taxonomic levels and distance methods. FINDINGS In time point-specific models, the largest share of variation explained, up to 2-6%, were seen in decreasing order for the DNA extraction batch, delivery mode and related perinatal exposures, defecation frequency and parity/siblings. Variables describing the infant gastrointestinal function were continuously important during the first two years, reflecting changes in e.g., feeding habits. The effect of parity/siblings on infant microbiota was modified by birth mode and exposure to intrapartum antibiotics, exemplifying the tight interlinkage of perinatal factors relevant for infant microbiota research. In total, up to 19% of the biological microbiota variation in the infant gut could be explained. Our results highlight the need to interpret variance partitioning results in the context of each cohort's characteristics and microbiota processing. INTERPRETATION Our study provides a comprehensive report of key factors associated with infant gut microbiota composition across the two first years of life in a homogenous cohort. The study highlights possible important future research areas and confounding factors to be considered. FUNDING This research was supported by Business Finland, Academy of Finland, Foundation for Nutrition Research and the Doctoral Program in Microbiology and Biotechnology, University of Helsinki, Finland.
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Affiliation(s)
- Roosa Jokela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Alise J Ponsero
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Evgenia Dikareva
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Xiaodong Wei
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaija-Leena Kolho
- Children's Hospital, Paediatric Research Centre, University of Helsinki and HUS, Helsinki, Finland; Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Katri Korpela
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Laboratory of Microbiology, Wageningen University, Wageningen, the Netherlands
| | - Anne Salonen
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Nikodemova M, Holzhausen EA, Deblois CL, Barnet JH, Peppard PE, Suen G, Malecki KM. The effect of low-abundance OTU filtering methods on the reliability and variability of microbial composition assessed by 16S rRNA amplicon sequencing. Front Cell Infect Microbiol 2023; 13:1165295. [PMID: 37377642 PMCID: PMC10291178 DOI: 10.3389/fcimb.2023.1165295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/18/2023] [Indexed: 06/29/2023] Open
Abstract
PCR amplicon sequencing may lead to detection of spurious operational taxonomic units (OTUs), inflating estimates of gut microbial diversity. There is no consensus in the analytical approach as to what filtering methods should be applied to remove low-abundance OTUs; moreover, few studies have investigated the reliability of OTU detection within replicates. Here, we investigated the reliability of OTU detection (% agreement in detecting OTU in triplicates) and accuracy of their quantification (assessed by coefficient of variation (CV)) in human stool specimens. Stool samples were collected from 12 participants 22-55 years old. We applied several methods for filtering low-abundance OTUs and determined their impact on alpha-diversity and beta-diversity metrics. The reliability of OTU detection without any filtering was only 44.1% (SE=0.9) but increased after filtering low-abundance OTUs. After filtering OTUs with <0.1% abundance in the dataset, the reliability increased to 87.7% (SE=0.6) but at the expense of removing 6.97% reads from the dataset. When filtering was based on individual sample, the reliability increased to 73.1% after filtering OTUs with <10 copies while removing only 1.12% of reads. High abundance OTUs (>10 copies in sample) had lower CV, indicating better accuracy of quantification than low-abundance OTUs. Excluding very low-abundance OTUs had a significant impact on alpha-diversity metrics sensitive to the presence of rare species (observed OTUs, Chao1) but had little impact on relative abundance of major phyla and families and alpha-diversity metrics accounting for both richness and evenness (Shannon, Inverse Simpson). To increase the reliability of microbial composition, we advise removing OTUs with <10 copies in individual samples, particularly in studies where only one subsample per specimen is available for analysis.
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Affiliation(s)
- Maria Nikodemova
- Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- Department of Physical Therapy, University of Florida, Gainesville, FL, United States
| | - Elizabeth A. Holzhausen
- Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, United States
| | - Courtney L. Deblois
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, United States
| | - Jodi H. Barnet
- Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Paul E. Peppard
- Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, United States
| | - Kristen M. Malecki
- Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- Division of Environmental and Occupational Health Sciences, School of Public Health, University of Illinois at Chicago, Chicago, IL, United States
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15
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Burnham CM, McKenney EA, Heugten KA, Minter LJ, Trivedi S. Effect of fecal preservation method on captive southern white rhinoceros gut microbiome. WILDLIFE SOC B 2023. [DOI: 10.1002/wsb.1436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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16
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Zouiouich S, Byrd DA, Hua X, Karwa S, Wan Y, Shi J, Humphrey GC, Ackermann GL, Knight R, Abnet CC, Vogtmann E, Sinha R. Stability of the Fecal and Oral Microbiome over 2 Years at -80°C for Multiple Collection Methods. Cancer Epidemiol Biomarkers Prev 2023; 32:444-451. [PMID: 36649143 PMCID: PMC10498478 DOI: 10.1158/1055-9965.epi-22-0883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 11/18/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND In prospective cohorts, biological samples are generally stored over long periods before an adequate number of cases have accrued. We investigated the impact of sample storage at -80°C for 2 years on the stability of the V4 region of the 16S rRNA gene across seven different collection methods (i.e., no additive, 95% ethanol, RNAlater stabilization solution, fecal occult blood test cards, and fecal immunochemical test tubes for feces; OMNIgene ORAL tubes and Scope mouthwash for saliva) among 51 healthy volunteers. METHODS Intraclass correlation coefficients (ICC) were calculated for the relative abundance of the top three phyla, the 20 most abundant genera, three alpha-diversity metrics, and the first principal coordinates of three beta-diversity matrices. RESULTS The subject variability was much higher than the variability introduced by the sample collection type, and storage time. For fecal samples, microbial stability over 2 years was high across collection methods (range, ICCs = 0.70-0.99), except for the samples collected with no additive (range, ICCs = 0.23-0.83). For oral samples, most microbiome diversity measures were stable over time with ICCs above 0.74; however, ICCs for the samples collected with Scope mouthwash were lower for two alpha-diversity measures, Faith's phylogenetic diversity (0.23) and the observed number of operational taxonomic units (0.23). CONCLUSIONS Fecal and oral samples in most used collection methods are stable for microbiome analyses after 2 years at -80°C, except for fecal samples with no additive. IMPACT This study provides evidence that samples stored for an extended period from prospective studies are useful for microbiome analyses.
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Affiliation(s)
- Semi Zouiouich
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Doratha A Byrd
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Xing Hua
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Smriti Karwa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Yunhu Wan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Gregory C Humphrey
- Department of Pediatrics, University of California, San Diego, California
| | - Gail L Ackermann
- Department of Pediatrics, University of California, San Diego, California
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, California
| | - Christian C Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
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Alonzo-De la Rosa CM, Miard S, Taubert S, Picard F. Methods to extract and study the biological effects of murine gut microbiota using Caenorhabditis elegans as a screening host. PLoS One 2023; 18:e0281887. [PMID: 36821579 PMCID: PMC9949637 DOI: 10.1371/journal.pone.0281887] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 02/01/2023] [Indexed: 02/24/2023] Open
Abstract
Gut microbiota has been established as a main regulator of health. However, how changes in gut microbiota are directly associated with physiological and cellular alterations has been difficult to tackle on a large-scale basis, notably because of the cost and labor-extensive resources required for rigorous experiments in mammals. In the present study, we used the nematode Caenorhabditis elegans as a model organism to elucidate microbiota-host interactions. We developed a method to extract gut microbiota (MCB) from murine feces, and tested its potential as food source for and its impact on C. elegans biology compared to the standard bacterial diet Escherichia coli OP50. Although less preferred than OP50, MCB was not avoided but had a lower energy density (triglycerides and glucose). Consistently, MCB-fed worms exhibited smaller body length and size, lower fertility, and lower fat content than OP50-fed worms, but had a longer mean lifespan, which resembles the effects of calorie restriction in mammals. However, these outcomes were altered when bacteria were inactivated, suggesting an important role of symbiosis of MCB beyond nutrient source. Taken together, our findings support the effectiveness of gut MCB processing to test its effects in C. elegans. More work comparing MCB of differently treated mice or humans is required to further validate relevance to mammals before large-scale screening assays.
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Affiliation(s)
- Claudia Miriam Alonzo-De la Rosa
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
- Faculty of Pharmacy, Université Laval, Quebec, Canada
| | - Stéphanie Miard
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
| | - Stefan Taubert
- British Columbia Children’s Hospital Research Institute, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, The University of British Columbia, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Frédéric Picard
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Canada
- Faculty of Pharmacy, Université Laval, Quebec, Canada
- * E-mail:
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Jugan MC, KuKanich K, Freilich L. Clinical response in dogs with acute hemorrhagic diarrhea syndrome following randomized probiotic treatment or fecal microbiota transplant. Front Vet Sci 2023; 10:1050538. [PMID: 36816181 PMCID: PMC9932283 DOI: 10.3389/fvets.2023.1050538] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023] Open
Abstract
Probiotics and fecal microbiota transplants (FMTs) are two microbiome-targeted therapies that have been investigated for use in gastrointestinal diseases associated with dysbiosis. The aim of this study was to compare the effects of an oral multi-strain probiotic and enema-administered FMTs on clinical signs and serum lipopolysaccharide in dogs with acute hemorrhagic diarrhea syndrome (AHDS). A total of 18 client-owned dogs with a diagnosis of AHDS were enrolled in a randomized, blinded study at the time of hospital admission. The dogs were randomized into two groups: the probiotic group received a daily oral probiotic (200 × 109 CFU/10kg q 24 h) for 14 days and a single sham enema; the FMT group received a single FMT via retention enema (10 mL/kg) and placebo oral capsule for 14 days. All dogs received concurrent standard-of-care therapy, including intravenous fluids and anti-emetics; no dogs received antimicrobials. The fecal score, disease severity scores, and serum lipopolysaccharide were measured on days 0, 3, and 14. Fourteen of eighteen enrolled dogs completed the study (n = 9 probiotics; n = 5 FMT). Lipopolysaccharide decreased on days 3 and 14 from baseline and correlated with fecal and disease severity scores. There was no difference in the duration or severity of clinical signs in dogs with AHDS following an enema-administered FMT compared to probiotic treatment. Further evaluation of serum lipopolysaccharide as a marker of disease severity and recovery is warranted.
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Qiu B, Xi Y, Liu F, Li Y, Xie X, Guo J, Guo S, Wu Y, Wu L, Liang T, Ding Y, Zhang J, Wu Q, Liu H. Gut Microbiome Is Associated With the Response to Chemoradiotherapy in Patients With Non-small Cell Lung Cancer. Int J Radiat Oncol Biol Phys 2023; 115:407-18. [PMID: 35905860 DOI: 10.1016/j.ijrobp.2022.07.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/12/2022] [Accepted: 07/15/2022] [Indexed: 01/14/2023]
Abstract
PURPOSE To explore the dynamic change of gut microbiota and its predictive role in progression-free survival (PFS) in non-small cell lung cancer (NSCLC) after concurrent chemoradiotherapy (CCRT). METHODS AND MATERIALS Forty-one patients with NSCLC in 2 phase 2 trials (NCT02573506 and NCT03006575) were analyzed. A total of 102 fecal samples were collected at 3 time points (T0, before CCRT; T1, 2 weeks after the initiation of CCRT; and T2, the end of CCRT). Gut microbiota composition and functionality were analyzed by 16S rRNA gene sequencing and shotgun metagenomics, respectively. Alpha diversity, taxonomic composition, and KEGG functional pathways were compared between patients in the long-PFS group (PFS ≥11.0 months) and short-PFS group (PFS <11.0 months). A random forest classifier was constructed to identify microbial signature related to PFS. Clinical and microbial factors potentially predictive of PFS were assessed in the univariate and multivariate Cox regression analysis. RESULTS The abundance of Bacteroidota and Proteobacteria increased, while the abundance of Firmicutes decreased after CCRT. Shannon index (P = .006) and PD index (P = .022) were significantly higher in the long-PFS group than for those in the short-PFS group at T1. The PFS-prediction microbial signature at T1 included unclassified members of the Lanchospiraceae spp., such as NK4A136 and UCG-003 groups, Dorea sp., various strains from within the Eubacterium hallii and E. siraeum groups, and an unclassified member of the Muribaculaceae, which yielded an area under the ROC curve of 0.87. These discriminatory genera mostly belong to phylum Firmicutes/family Clostridia. Multivariate analysis indicated PD index (HR = 8.036, P = .016) and the abundance of Dorea sp. at T1 (HR = 4.186, P = .043) were independent predictors of PFS. The KEGG pathways at T1 overrepresented in the long-PFS group included fatty acid metabolism, fatty acid biosynthesis, and arginine biosynthesis. Those overrepresented in the short-PFS group included lipopolysaccharide biosynthesis, ascorbate and aldarate metabolism, and biosynthesis of vancomycin group antibiotics. CONCLUSIONS Gut microbiota composition and functionality at 2 weeks after the initiation of CCRT were associated with PFS in NSCLC. Further research is needed to confirm these results.
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Krukowski H, Valkenburg S, Madella AM, Garssen J, van Bergenhenegouwen J, Overbeek SA, Huys GRB, Raes J, Glorieux G. Gut microbiome studies in CKD: opportunities, pitfalls and therapeutic potential. Nat Rev Nephrol 2023; 19:87-101. [PMID: 36357577 DOI: 10.1038/s41581-022-00647-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2022] [Indexed: 11/12/2022]
Abstract
Interest in gut microbiome dysbiosis and its potential association with the development and progression of chronic kidney disease (CKD) has increased substantially in the past 6 years. In parallel, the microbiome field has matured considerably as the importance of host-related and environmental factors is increasingly recognized. Past research output in the context of CKD insufficiently considered the myriad confounding factors that are characteristic of the disease. Gut microbiota-derived metabolites remain an interesting therapeutic target to decrease uraemic (cardio)toxicity. However, future studies on the effect of dietary and biotic interventions will require harmonization of relevant readouts to enable an in-depth understanding of the underlying beneficial mechanisms. High-quality standards throughout the entire microbiome analysis workflow are also of utmost importance to obtain reliable and reproducible results. Importantly, investigating the relative composition and abundance of gut bacteria, and their potential association with plasma uraemic toxins levels is not sufficient. As in other fields, the time has come to move towards in-depth quantitative and functional exploration of the patient's gut microbiome by relying on confounder-controlled quantitative microbial profiling, shotgun metagenomics and in vitro simulations of microorganism-microorganism and host-microorganism interactions. This step is crucial to enable the rational selection and monitoring of dietary and biotic intervention strategies that can be deployed as a personalized intervention in CKD.
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21
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Eisenhofer R, Brice KL, Blyton MDJ, Bevins SE, Leigh K, Singh BK, Helgen KM, Hough I, Daniels CB, Speight N, Moore BD. Individuality and stability of the koala ( Phascolarctos cinereus) faecal microbiota through time. PeerJ 2023; 11:e14598. [PMID: 36710873 PMCID: PMC9879153 DOI: 10.7717/peerj.14598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/29/2022] [Indexed: 01/24/2023] Open
Abstract
Gut microbiota studies often rely on a single sample taken per individual, representing a snapshot in time. However, we know that gut microbiota composition in many animals exhibits intra-individual variation over the course of days to months. Such temporal variations can be a confounding factor in studies seeking to compare the gut microbiota of different wild populations, or to assess the impact of medical/veterinary interventions. To date, little is known about the variability of the koala (Phascolarctos cinereus) gut microbiota through time. Here, we characterise the gut microbiota from faecal samples collected at eight timepoints over a month for a captive population of South Australian koalas (n individuals = 7), and monthly over 7 months for a wild population of New South Wales koalas (n individuals = 5). Using 16S rRNA gene sequencing, we found that microbial diversity was stable over the course of days to months. Each koala had a distinct faecal microbiota composition which in the captive koalas was stable across days. The wild koalas showed more variation across months, although each individual still maintained a distinct microbial composition. Per koala, an average of 57 (±16) amplicon sequence variants (ASVs) were detected across all time points; these ASVs accounted for an average of 97% (±1.9%) of the faecal microbial community per koala. The koala faecal microbiota exhibits stability over the course of days to months. Such knowledge will be useful for future studies comparing koala populations and developing microbiota interventions for this regionally endangered marsupial.
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Affiliation(s)
- Raphael Eisenhofer
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kylie L. Brice
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Michaela DJ Blyton
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, Brisbane, Queensland, Australia
| | - Scott E. Bevins
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Kellie Leigh
- Science for Wildlife Ltd, Sydney, New South Wales, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia,Global Centre for Land Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Kristofer M. Helgen
- Australian Museum Research Institute, Sydney, New South Wales, Australia,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of New South Wales, Sydney, New South Wales, Australia,Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Ian Hough
- Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Christopher B. Daniels
- Koala Life Foundation, Cleland Wildlife Park, Department for Environment and Water, 365c Mt Lofty Summit Road, Adelaide, South Australia, Australia
| | - Natasha Speight
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ben D. Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
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22
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Kim JH, Jeon JY, Im YJ, Ha N, Kim JK, Moon SJ, Kim MG. Long-term taxonomic and functional stability of the gut microbiome from human fecal samples. Sci Rep 2023; 13:114. [PMID: 36596832 PMCID: PMC9810722 DOI: 10.1038/s41598-022-27033-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023] Open
Abstract
Appropriate storage of fecal samples is a critical step for unbiased analysis in human microbiome studies. The purpose of this study was to evaluate the stability of the fecal microbial community for up to 18 months. Ten healthy volunteers provided fecal samples at the Jeonbuk National University Hospital. Stool samples were stored under the following six conditions: four different storage temperatures (- 70 °C, - 20 °C, 4 °C, and room temperature [20-25 °C]) and two different collection tubes (OMNIgene-Gut and DNA/RNA shield-fecal collection tubes). The gut microbiome was analyzed with 16S rRNA sequencing. We compared the taxonomic composition, alpha diversity, beta diversity and inferred pathway abundance between the baseline and 18 months after storage. Samples collected in the DNA/RNA Shield-fecal collection tubes showed the best performance in preservation of the taxonomic composition at 18 months. Pairwise differences in alpha diversity metrics showed the least deviation from zero. The PERMANOVA test showed non-significant change of beta diversity metrics (Unweighted Unifrac: q-value 0.268; Weighted Unifrac: q-value 0.848). The functional stability was significantly well preserved in the DNA/RNA Shield-fecal collection tubes (adjusted p value < 0.05). Our results demonstrate the use of the DNA/RNA Shield-fecal collection tube as an alternative storage method for fecal samples to preserve the taxonomic and functional stability of the microbiome over a long term.
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Affiliation(s)
- Jae Hyun Kim
- grid.411545.00000 0004 0470 4320School of Pharmacy and Institute of New Drug Development, Jeonbuk National University, Jeonju, Republic of Korea
| | - Ji-Young Jeon
- grid.411545.00000 0004 0470 4320Center for Clinical Pharmacology and Biomedical Research Institute, Jeonbuk National University Hospital, 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do 54907 Republic of Korea
| | - Yong-Jin Im
- grid.411545.00000 0004 0470 4320Center for Clinical Pharmacology and Biomedical Research Institute, Jeonbuk National University Hospital, 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do 54907 Republic of Korea
| | - Na Ha
- grid.411545.00000 0004 0470 4320Center for Clinical Pharmacology and Biomedical Research Institute, Jeonbuk National University Hospital, 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do 54907 Republic of Korea
| | - Jeon-Kyung Kim
- grid.411545.00000 0004 0470 4320School of Pharmacy and Institute of New Drug Development, Jeonbuk National University, Jeonju, Republic of Korea
| | - Seol Ju Moon
- grid.411545.00000 0004 0470 4320Center for Clinical Pharmacology and Biomedical Research Institute, Jeonbuk National University Hospital, 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do 54907 Republic of Korea ,grid.411545.00000 0004 0470 4320Department of Pharmacology, Medical School, Jeonbuk National University, Jeonju, Republic of Korea
| | - Min-Gul Kim
- grid.411545.00000 0004 0470 4320Center for Clinical Pharmacology and Biomedical Research Institute, Jeonbuk National University Hospital, 20, Geonji-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do 54907 Republic of Korea ,grid.411545.00000 0004 0470 4320Department of Pharmacology, Medical School, Jeonbuk National University, Jeonju, Republic of Korea ,grid.411545.00000 0004 0470 4320Research Institute of Clinical Medicine of Jeonbuk National University, Jeonju, Republic of Korea
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23
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Brezina S, Borkovec M, Baierl A, Bastian F, Futschik A, Gasche N, Gruenberger T, Hallas M, Jannsen C, Leeb G, Lutz R, Sladek B, Gsur A. Using fecal immmunochemical cartridges for gut microbiome analysis within a colorectal cancer screening program. Gut Microbes 2023; 15:2176119. [PMID: 36794815 PMCID: PMC9980522 DOI: 10.1080/19490976.2023.2176119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
The colorectal cancer (CRC) screening program B-PREDICT is an invited two-stage screening project using a fecal immunochemical test (FIT) for initial screening followed by a colonoscopy for those with a positive FIT. Since the gut microbiome likely plays a role in the etiology of CRC, microbiome-based biomarkers in combination with FIT could be a promising tool for optimizing CRC screening. Therefore, we evaluated the usability of FIT cartridges for microbiome analysis and compared it to Stool Collection and Preservation Tubes. Corresponding FIT cartridges as well as Stool Collection and Preservation Tubes were collected from participants of the B-PREDICT screening program to perform 16S rRNA gene sequencing. We calculated intraclass correlation coefficients (ICCs) based on center log ratio transformed abundances and used ALDEx2 to test for significantly differential abundant taxa between the two sample types. Additionally, FIT and Stool Collection and Preservation Tube triplicate samples were obtained from volunteers to estimate variance components of microbial abundances. FIT and Preservation Tube samples produce highly similar microbiome profiles which cluster according to subject. Significant differences between the two sample types can be found for abundances of some bacterial taxa (e.g. 33 genera) but are minor compared to the differences between the subjects. Analysis of triplicate samples revealed slightly worse repeatability of results for FIT than for Preservation Tube samples. Our findings indicate that FIT cartridges are appropriate for gut microbiome analysis nested within CRC screening programs.
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Affiliation(s)
- Stefanie Brezina
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Martin Borkovec
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Andreas Baierl
- Department of Statistics and Operations Research, University of Vienna, Vienna, Austria
| | | | - Andreas Futschik
- Department of Applied Statistics, Johannes Kepler University Linz, Linz, Austria
| | | | | | - Michael Hallas
- Institute of Pathology and Bacteriology, Clinic Favoriten, Vienna, Austria
| | | | - Gernot Leeb
- Department of Internal Medicine, Hospital Oberpullendorf, Oberpullendorf, Austria
| | - Rebecca Lutz
- Department of Surgery, Clinic Favoriten, Vienna, Austria
| | | | - Andrea Gsur
- Center for Cancer Research, Medical University of Vienna, Vienna, Austria,CONTACT Andrea Gsur Center for Cancer Research, Medical University of Vienna, Vienna, Austria
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24
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Adams VJ, LeBlanc N, Penell J. Results of a Clinical Trial Showing Changes to the Faecal Microbiome in Racing Thoroughbreds after Feeding a Nutritional Supplement. Vet Sci 2022; 10. [PMID: 36669028 DOI: 10.3390/vetsci10010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Next-generation sequencing (NGS) has been used to evaluate the effect of various interventions on the equine microbiome. The aim of this randomised blinded clinical trial was to determine if a prebiotic nutritional supplement would result in a change from baseline in the faecal microbiome composition of racing Thoroughbred horses in training being fed a high concentrate/grain-based diet to be more similar to that found in forage fed/pasture grazed horses. Thirty-two horses on one training yard were randomised to either receive the supplement or not. Faecal samples were collected at baseline, 6 and 12 weeks for NGS of the 16S ribosomal subunit gene. Twenty-two horses completed the trial, met the inclusion criteria and were included in the intention to treat analysis; 20 horses were included in the per protocol analysis. The mean and median percent decreases in Bacteroidetes, increases in Firmicutes and the Firmicutes:Bacteroidetes ratio were significantly greater than zero for the treated horses only. Supplemented horses (8/10) were more likely than control horses (2/10) to show an increase in Firmicutes of a ≥9% with ≥24% increase in Clostridia, ≥5% decrease in Bacteroidetes, ≥16% increase in the F:B ratio and ≥2% increase in Actinobacteria (RR = 4, 95% CI: 1.1-14.4, p = 0.01). This provides useful information for further investigations on long-term effects on the microbiome and on health and racing-related outcomes.
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25
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Gou W, Chen Y, Pan A, Wang H, Zhang K, Pan X, He Y, Fu Y, Jiang Z, Miao Z, Su C, Zhang J, Hu W, Zeng F, Ma W, Cheng G, Zhu Y, Zhou H, Zhang B, Zheng J. Westlake Gut Project: A consortium of microbiome epidemiology for the gut microbiome and health research in China. Medicine in Microecology 2022; 14:100064. [DOI: 10.1016/j.medmic.2022.100064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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26
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Priscilla C, Kumar S, Kumar CG, Parameswaran S, Viswanathan P, Ganesh RN. Pre-transplant Ratio of Firmicutes/Bacteroidetes of Gut Microbiota as a Potential Biomarker of Allograft Rejection in Renal Transplant Recipients. J Pure Appl Microbiol 2022; 16:1799-1808. [DOI: 10.22207/jpam.16.3.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The advent of technologies has made allogenic transplantation a potential curative therapy for end-stage renal diseases, but the episodes of rejection still remain as one of the challenges in the post-transplant scenario. In the recent years, several human and animal studies have elucidated that gut microbial dysbiosis is closely linked with allogenic transplantation and post-transplant complications. But most of the studies focused on the use of high through-put sequencing technologies to analyze gut microbiota despite of its high cost, analysis and time constraints. Hence, in this work we aimed to study the impact of the two dominant gut phyla Firmicutes and Bacteroidetes on 38 renal transplant recipients, before and after transplantation and to find its association with allograft rejection. Significant changes (p<0.01) were observed in the relative abundances of the phyla Firmicutes and Bacteroidetes at pre- and post-transplant period. We have also found that the recipients who had an increase in Firmicutes/Bacteroidetes (F/B) ratio before transplant were highly prone to rejection in the first-year post-transplant. The Receiver Operating Characteristic (ROC) curve analysis has shown that the ratio of F/B were able to discriminate between rejection and non-rejection cases with an Area under the ROC Curve (AUC) of 0.91. Additionally, we observed that the ratio of F/B have reduced during the time of rejection postulating that gut microbial dysbiosis has more association with rejection. Thus, the assessment of F/B ratio using qPCR would be of a more practical approach for diagnosis and monitoring of graft function in a cost-effective and timely manner.
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27
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Hua H, Meydan C, Afshin EE, Lili LN, D’Adamo CR, Rickard N, Dudley JT, Price ND, Zhang B, Mason CE. A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling. Front Immunol 2022; 13:889702. [PMID: 35711426 PMCID: PMC9196042 DOI: 10.3389/fimmu.2022.889702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/03/2022] [Indexed: 11/13/2022] Open
Abstract
While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and a dissolvable wipe used with DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, bacterial metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R2 of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R2 of 0.98), and samples consistently clustered by subject across each method. These data support that the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.
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Affiliation(s)
- Hui Hua
- Thorne HealthTech, New York, NY, United States
- *Correspondence: Hui Hua, ; Christopher E. Mason,
| | - Cem Meydan
- Thorne HealthTech, New York, NY, United States
| | | | | | - Christopher R. D’Adamo
- Department of Family and Community Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | | | | | - Nathan D. Price
- Thorne HealthTech, New York, NY, United States
- Institute for Systems Biology, Seattle, WA, United States
| | - Bodi Zhang
- Thorne HealthTech, New York, NY, United States
| | - Christopher E. Mason
- Thorne HealthTech, New York, NY, United States
- The WorldQuant Initiative for Quantitative Prediction, New York, NY, United States
- *Correspondence: Hui Hua, ; Christopher E. Mason,
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28
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Szóstak N, Szymanek A, Havránek J, Tomela K, Rakoczy M, Samelak-Czajka A, Schmidt M, Figlerowicz M, Majta J, Milanowska-Zabel K, Handschuh L, Philips A. The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling. Sci Rep 2022; 12:8470. [PMID: 35589762 DOI: 10.1038/s41598-022-12037-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/29/2022] [Indexed: 11/12/2022] Open
Abstract
In recent years, the number of metagenomic studies increased significantly. Wide range of factors, including the tremendous community complexity and variability, is contributing to the challenge in reliable microbiome community profiling. Many approaches have been proposed to overcome these problems making hardly possible to compare results of different studies. The significant differences between procedures used in metagenomic research are reflected in a variation of the obtained results. This calls for the need for standardisation of the procedure, to reduce the confounding factors originating from DNA isolation, sequencing and bioinformatics analyses in order to ensure that the differences in microbiome composition are of a true biological origin. Although the best practices for metagenomics studies have been the topic of several publications and the main aim of the International Human Microbiome Standard (IHMS) project, standardisation of the procedure for generating and analysing metagenomic data is still far from being achieved. To highlight the difficulties in the standardisation of metagenomics methods, we thoroughly examined each step of the analysis of the human gut microbiome. We tested the DNA isolation procedure, preparation of NGS libraries for next-generation sequencing, and bioinformatics analysis, aimed at identifying microbial taxa. We showed that the homogenisation time is the leading factor impacting sample diversity, with the recommendation for a shorter homogenisation time (10 min). Ten minutes of homogenisation allows for better reflection of the bacteria gram-positive/gram-negative ratio, and the obtained results are the least heterogenous in terms of beta-diversity of samples microbial composition. Besides increasing the homogenisation time, we observed further potential impact of the library preparation kit on the gut microbiome profiling. Moreover, our analysis revealed that the choice of the library preparation kit influences the reproducibility of the results, which is an important factor that has to be taken into account in every experiment. In this study, a tagmentation-based kit allowed for obtaining the most reproducible results. We also considered the choice of the computational tool for determining the composition of intestinal microbiota, with Kraken2/Bracken pipeline outperforming MetaPhlAn2 in our in silico experiments. The design of an experiment and a detailed establishment of an experimental protocol may have a serious impact on determining the taxonomic profile of the intestinal microbiome community. Results of our experiment can be helpful for a wide range of studies that aim to better understand the role of the gut microbiome, as well as for clinical purposes.
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29
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Su W, Du Y, Lian F, Wu H, Zhang X, Yang W, Duan Y, Pan Y, Liu W, Wu A, Zhao B, Wu C, Wu S. Standards for Collection, Preservation, and Transportation of Fecal Samples in TCM Clinical Trials. Front Cell Infect Microbiol 2022; 12:783682. [PMID: 35521221 PMCID: PMC9065286 DOI: 10.3389/fcimb.2022.783682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 03/28/2022] [Indexed: 12/21/2022] Open
Abstract
Background Unlike chemical drugs with a single or a few kinds of active compounds, traditional Chinese medicines (TCMs)uses herbal formulas composed of numerous kinds of chemical constituents. Therefore, TCM clinical trials require unique and stricter standards for collecting, preserving, and transporting fecal samples than those used for chemical drugs. Unfortunately, there are no special standards for processing fecal samples in TCM clinical trials. Methods We invited interdisciplinary experts within TCM clinical trials and gut microbiome research to help formulate this standard. After more than a year’s in-depth discussion and amendments, we achieved a standard via expert interviews, literature research, questionnaire surveys, and public opinion solicitation. This standard has been reviewed and approved by the Standards Office of China of the Association of Chinese medicine. Results We established a sample information processing method prior to TCM clinical sample collection, which is adapted to the unique features of TCM. The method formulates detailed processing requirements for TCM information in addition to the factors that may disturb the gut microbiome. We also constructed a set of methods for collecting, preserving, and transporting fecal samples that meet the characteristics of TCM. These methods formulate detailed operating specifications on the collection approaches, storage conditions, transportation requirements, and management of fecal samples. Conclusions This standard guides the information processing prior to sample collection and the standard operating procedures for the collection, preservation, and transportation of fecal samples in TCM clinical trials, which also can be used as a reference by clinicians and researchers in modern medicines.
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Affiliation(s)
- Wenquan Su
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yawei Du
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Fengmei Lian
- Department of Endocrinology, Guang’anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China
| | - Hui Wu
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xinrong Zhang
- Fangshan Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Wenli Yang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Yunfeng Duan
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuanming Pan
- The 7th Medical Center, Chinese People’s Liberation Army General Hospital, Beijing, China
| | - Weijng Liu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Aiming Wu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
| | - Bowen Zhao
- Beijing QuantiHealth Technology Co, Ltd, Beijing, China
| | - Chongming Wu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- *Correspondence: Shengxian Wu, ; Chongming Wu,
| | - Shengxian Wu
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, China
- *Correspondence: Shengxian Wu, ; Chongming Wu,
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30
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Plauzolles A, Toumi E, Bonnet M, Pénaranda G, Bidaut G, Chiche L, Allardet-Servent J, Retornaz F, Goutorbe B, Halfon P. Human Stool Preservation Impacts Taxonomic Profiles in 16S Metagenomics Studies. Front Cell Infect Microbiol 2022; 12:722886. [PMID: 35211421 PMCID: PMC8860989 DOI: 10.3389/fcimb.2022.722886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022] Open
Abstract
Microbiotas play critical roles in human health, yet in most cases scientists lack standardized and reproducible methods from collection and preservation of samples, as well as the choice of omic analysis, up to the data processing. To date, stool sample preservation remains a source of technological bias in metagenomic sequencing, despite newly developed storage solutions. Here, we conducted a comparative study of 10 storage methods for human stool over a 14-day period of storage at fluctuating temperatures. We first compared the performance of each stabilizer with observed bacterial composition variation within the same specimen. Then, we identified the nature of the observed variations to determine which bacterial populations were more impacted by the stabilizer. We found that DNA stabilizers display various stabilizing efficacies and affect the recovered bacterial profiles thus highlighting that some solutions are more performant in preserving the true gut microbial community. Furthermore, our results showed that the bias associated with the stabilizers can be linked to the phenotypical traits of the bacterial populations present in the studied samples. Although newly developed storage solutions have improved our capacity to stabilize stool microbial content over time, they are nevertheless not devoid of biases hence requiring the implantation of standard operating procedures. Acknowledging the biases and limitations of the implemented method is key to better interpret and support true associated microbiome patterns that will then lead us towards personalized medicine, in which the microbiota profile could constitute a reliable tool for clinical practice.
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Affiliation(s)
- Anne Plauzolles
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
- *Correspondence: Anne Plauzolles,
| | - Eya Toumi
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
- MEPHI, IHU Méditerranée Infection, Aix Marseille Université, Marseille, France
| | - Marion Bonnet
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
| | - Guillaume Pénaranda
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
| | - Ghislain Bidaut
- CRCM, Aix‐Marseille Univ U105, Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Marseille, France
| | - Laurent Chiche
- Infectious and Internal Medicine Department, Hôpital Européen Marseille, Marseille, France
| | | | - Frédérique Retornaz
- Infectious and Internal Medicine Department, Hôpital Européen Marseille, Marseille, France
| | - Benoit Goutorbe
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
- CRCM, Aix‐Marseille Univ U105, Inserm U1068, CNRS UMR7258, Institut Paoli‐Calmettes, Marseille, France
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Philippe Halfon
- Clinical Research and R&D Department, Laboratoire Européen Alphabio, Marseille, France
- Infectious and Internal Medicine Department, Hôpital Européen Marseille, Marseille, France
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31
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Blyton MDJ, Soo RM, Hugenholtz P, Moore BD. Characterization of the juvenile koala gut microbiome across wild populations. Environ Microbiol 2022; 24:4209-4219. [PMID: 35018700 DOI: 10.1111/1462-2920.15884] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/21/2021] [Indexed: 11/03/2022]
Abstract
In this study we compared the faecal microbiomes of wild joey koalas (Phascolarctos cinereus) to those of adults, including their mothers, to establish whether gut microbiome maturation and inheritance in the wild is comparable to that seen in captivity. Our findings suggest that joey koala microbiomes slowly shift towards an adult assemblage between 6 and 12 months of age, as the microbiomes of 9-month-old joeys were more similar to those of adults than those of 7-month-olds, but still distinct. At the phylum level, differences between joeys and adults were broadly consistent with those in captivity, with Firmicutes increasing in relative abundance over the joeys' development and Proteobacteria decreasing. Of the fibre-degrading genes that increased in abundance over the development of captive joeys, those involved in hemicellulose and cellulose degradation, but not pectin degradation, were also generally found in higher abundance in adult wild koalas compared to 7-month-olds. Greater maternal inheritance of the faecal microbiome was seen in wild than in captive koalas, presumably due to the more solitary nature of wild koalas. This strong maternal inheritance of the gut microbiome could contribute to the development of localized differences in microbiome composition, population health and diet through spatial clustering of relatives.
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Affiliation(s)
- Michaela D J Blyton
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Rochelle M Soo
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, St Lucia, Qld, 4072, Australia
| | - Ben D Moore
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, 2753, Australia
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Westaway JAF, Huerlimann R, Kandasamy Y, Miller CM, Norton R, Staunton KM, Watson D, Rudd D. The bacterial gut microbiome of probiotic-treated very-preterm infants: changes from admission to discharge. Pediatr Res 2022; 92:142-150. [PMID: 34621029 PMCID: PMC9411061 DOI: 10.1038/s41390-021-01738-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 08/23/2021] [Accepted: 08/31/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Preterm birth is associated with the development of acute and chronic disease, potentially, through the disruption of normal gut microbiome development. Probiotics may correct for microbial imbalances and mitigate disease risk. Here, we used amplicon sequencing to characterise the gut microbiome of probiotic-treated premature infants. We aimed to identify and understand variation in bacterial gut flora from admission to discharge and in association with clinical variables. METHODS Infants born <32 weeks gestation and <1500 g, and who received probiotic treatment, were recruited in North Queensland Australia. Meconium and faecal samples were collected at admission and discharge. All samples underwent 16S rRNA short amplicon sequencing, and subsequently, a combination of univariate and multivariate analyses. RESULTS 71 admission and 63 discharge samples were collected. Univariate analyses showed significant changes in the gut flora from admission to discharge. Mixed-effects modelling showed significantly lower alpha diversity in infants diagnosed with either sepsis or retinopathy of prematurity (ROP) and those fed formula. In addition, chorioamnionitis, preeclampsia, sepsis, necrotising enterocolitis and ROP were also all associated with the differential abundance of several taxa. CONCLUSIONS The lower microbial diversity seen in infants with diagnosed disorders or formula-fed, as well as differing abundances of several taxa across multiple variables, highlights the role of the microbiome in the development of health and disease. This study supports the need for promoting healthy microbiome development in preterm neonates. IMPACT Low diversity and differing taxonomic abundances in preterm gut microbiota demonstrated in formula-fed infants and those identified with postnatal conditions, as well as differences in taxonomy associated with preeclampsia and chorioamnionitis, reinforcing the association of the microbiome composition changes due to maternal and infant disease. The largest study exploring an association between the preterm infant microbiome and ROP. A novel association between the preterm infant gut microbiome and preeclampsia in a unique cohort of very-premature probiotic-supplemented infants.
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Affiliation(s)
- Jacob A. F. Westaway
- grid.1011.10000 0004 0474 1797College of Public Health, Medical and Veterinary Science, James Cook University, 1/14-88 McGregor Road, Smithfield, QLD 4878 Australia ,grid.1011.10000 0004 0474 1797Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, 1 James Cook Drive, Douglas, QLD 4811 Australia
| | - Roger Huerlimann
- grid.1011.10000 0004 0474 1797Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, 1 James Cook Drive, Douglas, QLD 4811 Australia ,grid.250464.10000 0000 9805 2626Marine Climate Change Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son Okinawa, 904-0495 Japan ,grid.1011.10000 0004 0474 1797College of Science and Engineering, James Cook University, 1 James Cook Drive, Douglas, QLD 4811 Australia
| | - Yoga Kandasamy
- grid.1011.10000 0004 0474 1797College of Public Health, Medical and Veterinary Science, James Cook University, 1 James Cook Drive, Douglas, QLD 4811 Australia ,grid.417216.70000 0000 9237 0383Department of neonatology, Townsville University Hospital, 100 Angus Smith Drive, Douglas, QLD 4814 Australia
| | - Catherine M. Miller
- grid.1011.10000 0004 0474 1797College of Public Health, Medical and Veterinary Science, James Cook University, 1/14-88 McGregor Road, Smithfield, QLD 4878 Australia ,grid.1011.10000 0004 0474 1797Australian Institute for Tropical Health and Medicine, James Cook University, 1/14-88 McGregor Road, Smithfield, QLD 4878 Australia
| | - Robert Norton
- Department of Microbiology, Pathology Queensland, 100 Angus Smith Drive, Douglas, QLD 4814 Australia
| | - Kyran M. Staunton
- grid.1011.10000 0004 0474 1797Australian Institute for Tropical Health and Medicine, James Cook University, 1/14-88 McGregor Road, Smithfield, QLD 4878 Australia
| | - David Watson
- grid.417216.70000 0000 9237 0383Department of Maternal-Fetal Medicine, Townsville University Hospital, 100 Angus Smith Drive, Douglas, 4814 Australia
| | - Donna Rudd
- grid.1011.10000 0004 0474 1797College of Public Health, Medical and Veterinary Science, James Cook University, 1 James Cook Drive, Douglas, QLD 4811 Australia
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Mordant A, Kleiner M. Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes. Microbiol Spectr 2021; 9:e0187721. [PMID: 34908431 PMCID: PMC8672883 DOI: 10.1128/spectrum.01877-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 10/31/2021] [Indexed: 12/20/2022] Open
Abstract
A critical step in studies of the intestinal microbiome using meta-omics approaches is the preservation of samples before analysis. Preservation is essential for approaches that measure gene expression, such as metaproteomics, which is used to identify and quantify proteins in microbiomes. Intestinal microbiome samples are typically stored by flash-freezing and storage at -80°C, but some experimental setups do not allow for immediate freezing of samples. In this study, we evaluated methods to preserve fecal microbiome samples for metaproteomics analyses when flash-freezing is not possible. We collected fecal samples from C57BL/6 mice and stored them for 1 and 4 weeks using the following methods: flash-freezing in liquid nitrogen, immersion in RNAlater, immersion in 95% ethanol, immersion in a RNAlater-like buffer, and combinations of these methods. After storage, we extracted protein and prepared peptides for liquid chromatography with tandem mass spectrometry (LC-MS/MS) analysis to identify and quantify peptides and proteins. All samples produced highly similar metaproteomes, except for ethanol-preserved samples that were distinct from all other samples in terms of protein identifications and protein abundance profiles. Flash-freezing and RNAlater (or RNAlater-like treatments) produced metaproteomes that differed only slightly, with less than 0.7% of identified proteins differing in abundance. In contrast, ethanol preservation resulted in an average of 9.5% of the identified proteins differing in abundance between ethanol and the other treatments. Our results suggest that preservation at room temperature in RNAlater or an RNAlater-like solution performs as well as freezing for the preservation of intestinal microbiome samples before metaproteomics analyses. IMPORTANCE Metaproteomics is a powerful tool to study the intestinal microbiome. By identifying and quantifying a large number of microbial, dietary, and host proteins in microbiome samples, metaproteomics provides direct evidence of the activities and functions of microbial community members. A critical step for metaproteomics workflows is preserving samples before analysis because protein profiles are susceptible to fast changes in response to changes in environmental conditions (air exposure, temperature changes, etc.). This study evaluated the effects of different preservation treatments on the metaproteomes of intestinal microbiome samples. In contrast to prior work on preservation of fecal samples for metaproteomics analyses, we ensured that all steps of sample preservation were identical so that all differences could be attributed to the preservation method.
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Affiliation(s)
- Angie Mordant
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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Holzhausen EA, Nikodemova M, Deblois CL, Barnet JH, Peppard PE, Suen G, Malecki KM. Assessing the impact of storage time on the stability of stool microbiota richness, diversity, and composition. Gut Pathog 2021; 13:75. [PMID: 34930464 PMCID: PMC8686582 DOI: 10.1186/s13099-021-00470-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/01/2021] [Indexed: 12/30/2022] Open
Abstract
Background New technologies like next-generation sequencing have led to a proliferation of studies investigating the role of the gut microbiome in human health, particularly population-based studies that rely upon participant self-collection of samples. However, the impact of methodological differences in sample shipping, storage, and processing are not well-characterized for these types of studies, especially when transit times may exceed 24 h. The aim of this study was to experimentally assess microbiota stability in stool samples stored at 4 °C for durations of 6, 24, 48, 72, and 96 h with no additives to better understand effects of variable shipping times in population-based studies. These data were compared to a baseline sample that was immediately stored at − 80 °C after stool production. Results Compared to the baseline sample, we found that the alpha-diversity metrics Shannon’s and Inverse Simpson’s had excellent intra-class correlations (ICC) for all storage durations. Chao1 richness had good to excellent ICC. We found that the relative abundances of bacteria in the phyla Verrucomicrobia, Actinobacteria, and Proteobacteria had excellent ICC with baseline for all storage durations, while Firmicutes and Bacteroidetes ranged from moderate to good. We interpreted the ICCs as follows: poor: ICC < 0.50, moderate: 0.50 < ICC < 0.75, good: 0.75 < ICC < 0.90, and excellent: ICC > 0.90. Using the Bray–Curtis dissimilarity index, we found that the greatest change in community composition occurred between 0 and 24 h of storage, while community composition remained relatively stable for subsequent storage durations. Samples showed strong clustering by individual, indicating that inter-individual variability was greater than the variability associated with storage time. Conclusions The results of this analysis suggest that several measures of alpha diversity, relative abundance, and overall community composition are robust to storage at 4 °C for up to 96 h. We found that the overall community richness was influenced by storage duration in addition to the relative abundances of sequences within the Firmicutes and Bacteroidetes phyla. Finally, we demonstrate that inter-individual variability in microbiota composition was greater than the variability due to changing storage durations.
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Affiliation(s)
- Elizabeth A Holzhausen
- Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, USA.
| | - Maria Nikodemova
- Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, USA
| | - Courtney L Deblois
- Department of Bacteriology, University of Wisconsin-Madison, Madison, USA.,Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, USA
| | - Jodi H Barnet
- Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, USA
| | - Paul E Peppard
- Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, USA
| | - Kristen M Malecki
- Population Health Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, USA.
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35
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Bernard R, Hourigan SK, Nicholson MR. Fecal Microbiota Transplantation and Microbial Therapeutics for the Treatment of Clostridioides difficile Infection in Pediatric Patients. J Pediatric Infect Dis Soc 2021; 10:S58-S63. [PMID: 34791396 PMCID: PMC8600035 DOI: 10.1093/jpids/piab056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Clostridioides difficile infection (CDI) is the most common cause of antibiotic-associated diarrhea and has high rates of recurrent disease. As a disease associated with intestinal dysbiosis, gastrointestinal microbiome manipulation and fecal microbiota transplantation (FMT) have evolved as effective, although relatively unregulated therapeutics and not without safety concerns. FMT for the treatment of CDI has been well studied in adults with increasing data reported in children. In this review, we discuss the current body of literature on the use of FMT in children including effectiveness, safety, risk factors for a failed FMT, and the role of FMT in children with comorbidities. We also review emerging microbial therapeutics for the treatment of rCDI.
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Affiliation(s)
- Rachel Bernard
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Monroe Carell Jr. Vanderbilt Children’s Hospital, Nashville, Tennessee, USA,Corresponding Author: Rachel Bernard, DO MS, Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Monroe Carell Jr. Vanderbilt Children’s Hospital, 2200 Children’s Way, Suite 11226 Doctors’ Office Tower, Nashville, TN 38201, USA. E-mail:
| | - Suchitra K Hourigan
- Division of Pediatric Gastroenterology, Pediatric Specialists of Virginia, Fairfax, Virginia, USA
| | - Maribeth R Nicholson
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Monroe Carell Jr. Vanderbilt Children’s Hospital, Nashville, Tennessee, USA
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Sorensen JW, Zinke LA, ter Horst AM, Santos-Medellín C, Schroeder A, Emerson JB. DNase Treatment Improves Viral Enrichment in Agricultural Soil Viromes. mSystems 2021; 6:e0061421. [PMID: 34491084 PMCID: PMC8547471 DOI: 10.1128/msystems.00614-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/11/2021] [Indexed: 11/20/2022] Open
Abstract
The small genomes of most viruses make it difficult to fully capture viral diversity in metagenomes dominated by DNA from cellular organisms. Viral size fraction metagenomics (viromics) protocols facilitate the enrichment of viral DNA from environmental samples, and these protocols typically include DNase treatment of the post-0.2-μm-filtered viromic fraction to remove contaminating free DNA prior to virion lysis. However, DNase may also remove desirable viral genomic DNA (e.g., contained in virions compromised due to frozen storage or laboratory processing), suggesting that DNase-untreated viromes might be useful in some cases. In order to understand how virome preparation with and without DNase treatment influences the resultant data, here, we compared 15 soil viromes (7 DNase treated and 8 untreated) from 8 samples collected from agricultural fields prior to tomato planting. DNase-treated viromes yielded significantly more assembled viral contigs, contained significantly less nonviral microbial DNA, and recovered more viral populations (viral operational taxonomic units [vOTUs]) through read mapping. However, DNase-treated and untreated viromes were statistically indistinguishable in terms of ecological patterns across viral communities. Although the results suggest that DNase treatment is preferable where possible, in comparison to previously reported total metagenomes from the same samples, both DNase-treated and untreated viromes were significantly enriched in viral signatures by all metrics compared, including a 225-times-higher proportion of viral reads in untreated viromes compared to total metagenomes. Thus, even without DNase treatment, viromics was preferable to total metagenomics for capturing viral diversity in these soils, suggesting that preparation of DNase-untreated viromes can be worthwhile when DNase treatment is not possible. IMPORTANCE Viromics is becoming an increasingly popular method for characterizing soil viral communities. DNase treatment of the viral size fraction prior to DNA extraction is meant to reduce contaminating free DNA and is a common step within viromics protocols to ensure that sequences are of viral origin. However, some samples may not be amenable to DNase treatment due to viral particles being compromised either in storage (i.e., frozen) or during other sample processing steps. To date, the effect of DNase treatment on the recovery of viruses and downstream ecological interpretations of soil viral communities is not thoroughly understood. This work sheds light on these questions and indicates that while DNase treatment of soil viromes improves the recovery of viral populations, this improvement is modest in comparison to the gains made by viromics over total soil metagenomics. Furthermore, DNase treatment may not be necessary to observe the ecological patterns structuring soil viral communities.
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Affiliation(s)
- Jackson W. Sorensen
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Laura A. Zinke
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Anneliek M. ter Horst
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | | | - Alena Schroeder
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
| | - Joanne B. Emerson
- Department of Plant Pathology, University of California, Davis, Davis, California, USA
- Genome Center, University of California, Davis, Davis, California, USA
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37
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Zhang B, Brock M, Arana C, Dende C, van Oers NS, Hooper LV, Raj P. Impact of Bead-Beating Intensity on the Genus- and Species-Level Characterization of the Gut Microbiome Using Amplicon and Complete 16S rRNA Gene Sequencing. Front Cell Infect Microbiol 2021; 11:678522. [PMID: 34660333 PMCID: PMC8517478 DOI: 10.3389/fcimb.2021.678522] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/14/2021] [Indexed: 12/26/2022] Open
Abstract
Bead-beating within a DNA extraction protocol is critical for complete microbial cell lysis and accurate assessment of the abundance and composition of the microbiome. While the impact of bead-beating on the recovery of OTUs at the phylum and class level have been studied, its influence on species-level microbiome recovery is not clear. Recent advances in sequencing technology has allowed species-level resolution of the microbiome using full length 16S rRNA gene sequencing instead of smaller amplicons that only capture a few hypervariable regions of the gene. We sequenced the v3-v4 hypervariable region as well as the full length 16S rRNA gene in mouse and human stool samples and discovered major clusters of gut bacteria that exhibit different levels of sensitivity to bead-beating treatment. Full length 16S rRNA gene sequencing unraveled vast species diversity in the mouse and human gut microbiome and enabled characterization of several unclassified OTUs in amplicon data. Many species of major gut commensals such as Bacteroides, Lactobacillus, Blautia, Clostridium, Escherichia, Roseburia, Helicobacter, and Ruminococcus were identified. Interestingly, v3-v4 amplicon data classified about 50% of Ruminococcus reads as Ruminococcus gnavus species which showed maximum abundance in a 9 min beaten sample. However, the remaining 50% of reads could not be assigned to any species. Full length 16S rRNA gene sequencing data showed that the majority of the unclassified reads were Ruminococcus albus species which unlike R. gnavus showed maximum recovery in the unbeaten sample instead. Furthermore, we found that the Blautia hominis and Streptococcus parasanguinis species were differently sensitive to bead-beating treatment than the rest of the species in these genera. Thus, the present study demonstrates species level variations in sensitivity to bead-beating treatment that could only be resolved with full length 16S rRNA sequencing. This study identifies species of common gut commensals and potential pathogens that require minimum (0-1 min) or extensive (4-9 min) bead-beating for their maximal recovery.
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Affiliation(s)
- Bo Zhang
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Microbiome Research Laboratory (MRL), Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Matthew Brock
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Microbiome Research Laboratory (MRL), Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Carlos Arana
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Microbiome Research Laboratory (MRL), Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Chaitanya Dende
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | | | - Lora V Hooper
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Microbiome Research Laboratory (MRL), Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
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Bokoliya SC, Dorsett Y, Panier H, Zhou Y. Procedures for Fecal Microbiota Transplantation in Murine Microbiome Studies. Front Cell Infect Microbiol 2021; 11:711055. [PMID: 34621688 PMCID: PMC8490673 DOI: 10.3389/fcimb.2021.711055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/24/2021] [Indexed: 12/11/2022] Open
Abstract
Fecal microbiota transplantation (FMT) has been widely recognized as an approach to determine the microbiome’s causal role in gut dysbiosis-related disease models and as a novel disease-modifying therapy. Despite potential beneficial FMT results in various disease models, there is a variation and complexity in procedural agreement among research groups for performing FMT. The viability of the microbiome in feces and its successful transfer depends on various aspects of donors, recipients, and lab settings. This review focuses on the technical practices of FMT in animal studies. We first document crucial factors required for collecting, handling, and processing donor fecal microbiota for FMT. Then, we detail the description of gut microbiota depletion methods, FMT dosages, and routes of FMT administrations in recipients. In the end, we describe assessments of success rates of FMT with sustainability. It is critical to work under the anaerobic condition to preserve as much of the viability of bacteria. Utilization of germ- free mice or depletion of recipient gut microbiota by antibiotics or polyethylene glycol are two common recipient preparation approaches to achieve better engraftment. Oral-gastric gavage preferred by most researchers for fast and effective administration of FMT in mice. Overall, this review highlights various methods that may lead to developing the standard and reproducible protocol for FMT.
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Affiliation(s)
- Suresh C Bokoliya
- Department of Medicine, University of Connecticut (UConn) Health, Farmington, CT, United States
| | - Yair Dorsett
- Department of Medicine, University of Connecticut (UConn) Health, Farmington, CT, United States
| | - Hunter Panier
- Department of Medicine, University of Connecticut (UConn) Health, Farmington, CT, United States
| | - Yanjiao Zhou
- Department of Medicine, University of Connecticut (UConn) Health, Farmington, CT, United States
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39
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Karlsen TR, Kong XY, Holm S, Quiles-Jiménez A, Dahl TB, Yang K, Sagen EL, Skarpengland T, S Øgaard JD, Holm K, Vestad B, Olsen MB, Aukrust P, Bjørås M, Hov JR, Halvorsen B, Gregersen I. NEIL3-deficiency increases gut permeability and contributes to a pro-atherogenic metabolic phenotype. Sci Rep 2021; 11:19749. [PMID: 34611194 PMCID: PMC8492623 DOI: 10.1038/s41598-021-98820-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/09/2021] [Indexed: 12/12/2022] Open
Abstract
Atherosclerosis and its consequences cause considerable morbidity and mortality world-wide. We have previously shown that expression of the DNA glycosylase NEIL3 is regulated in human atherosclerotic plaques, and that NEIL3-deficiency enhances atherogenesis in Apoe-/- mice. Herein, we identified a time point prior to quantifiable differences in atherosclerosis between Apoe-/-Neil3-/- mice and Apoe-/- mice. Mice at this age were selected to explore the metabolic and pathophysiological processes preceding extensive atherogenesis in NEIL3-deficient mice. Untargeted metabolomic analysis of young Apoe-/-Neil3-/- mice revealed significant metabolic disturbances as compared to mice expressing NEIL3, particularly in metabolites dependent on the gut microbiota. 16S rRNA gene sequencing of fecal bacterial DNA indeed confirmed that the NEIL3-deficient mice had altered gut microbiota, as well as increased circulating levels of the bacterially derived molecule LPS. The mice were challenged with a FITC-conjugated dextran to explore gut permeability, which was significantly increased in the NEIL3-deficient mice. Further, immunohistochemistry showed increased levels of the proliferation marker Ki67 in the colonic epithelium of NEIL3-deficient mice, suggesting increased proliferation of intestinal cells and gut leakage. We suggest that these metabolic alterations serve as drivers of atherosclerosis in NEIL3-deficient mice.
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Affiliation(s)
- Tom Rune Karlsen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Xiang Yi Kong
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Sverre Holm
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Ana Quiles-Jiménez
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Tuva B Dahl
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Research and Development, Division of Emergencies and Critical Care, Oslo University Hospital HF, Rikshospitalet, Oslo, Norway
| | - Kuan Yang
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ellen L Sagen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Tonje Skarpengland
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Jonas D S Øgaard
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Kristian Holm
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Beate Vestad
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Maria B Olsen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Pål Aukrust
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Clinical Immunology and Infectious Diseases, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Johannes R Hov
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Oslo University Hospital, Oslo, Norway
| | - Bente Halvorsen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Ida Gregersen
- Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway.
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40
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Tuddenham S, Stennett CA, Cone RA, Ravel J, Macintyre AN, Ghanem KG, He X, Brotman RM. Vaginal cytokine profile and microbiota before and after lubricant use compared with condomless vaginal sex: a preliminary observational study. BMC Infect Dis 2021; 21:973. [PMID: 34537015 PMCID: PMC8449901 DOI: 10.1186/s12879-021-06512-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/18/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Limited data suggest that personal lubricants may damage the vaginal mucosal epithelium, alter the vaginal microbiota, and increase inflammation. We compared vaginal cytokine profiles and microbiota before and after vaginal lubricant use and condomless vaginal sex. METHODS Reproductive-age women were recruited to a 10-week observational cohort study and were asked to self-collect vaginal samples and behavioral diaries daily. This nested case-control analysis utilized samples collected before and after self-reported condomless sexual activity with lubricants (22 case participants) and without lubricants (22 control participants). Controls were matched to cases on race/ethnicity. Microbiota composition was characterized by sequencing amplicons of the 16S rRNA gene V3-V4 regions. Cytokine concentrations were quantified using a magnetic bead 41-plex panel assay and read using a Bio-Plex 200 array reader. Wilcoxon signed-rank tests were used to assess baseline differences in vaginal cytokines between cases and controls as well as differences pre- and post-exposure. Linear mixed effects models were used to examine differences in relative post-to-pre change in each individual cytokine between matched cases and controls. Similar analyses were conducted for the microbiota data. RESULTS Mean age was 29.8 years (SD 6.8), and 63.6% were African American. There were few statistically significant changes in cytokines or microbiota before and after exposure in cases or controls. In mixed-effects modeling, the mean relative post-to-pre change of cytokines was higher in cases vs. controls for macrophage derived chemokine (MDC) (p = 0.03). The microbiota data revealed no significant changes when measured by similarity scores, diversity indexes and descriptive community state types (CST) transition analyses. However, post sexual activity, the mean relative abundance of L. crispatus decreased for those who used lubricants (particularly those who were L. iners-dominated prior to exposure). CONCLUSIONS Although there were overall few differences in the vaginal microbiota and cytokine profiles of lubricant users and controls before and after condomless vaginal sex, there was a trend toward decreases in relative abundance of L. crispatus following use of lubricant. Future larger studies that take into account osmolarity and composition of lubricants may provide additional insights.
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Affiliation(s)
- Susan Tuddenham
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christina A Stennett
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Richard A Cone
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrew N Macintyre
- Department of Medicine, Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC, USA
| | - Khalil G Ghanem
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xin He
- School of Public Health, University of Maryland College Park, College Park, MD, USA
| | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
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41
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Abstract
Sample preservation is a critical procedure in any research that relies on molecular tools and is conducted in remote areas. Sample preservation options include low and room temperature storage, which require freezing equipment and specific buffering solutions, respectively. The aim of the present study was to investigate whether DNA/RNA Shield 1x from Zymo Research and DESS (Dimethyl sulfoxide, Ethylenediamine tetraacetic acid, Saturated Salt) solution performed similarly to snap freezing in liquid nitrogen. Soil samples were stored for 1 month in each of the buffers and without any solution at a range of temperatures: –20, +4, and +23°C. All treatments were compared to the “optimal treatment”, namely, snap freezing in liquid nitrogen. The quality and quantity of DNA were analyzed, and the microbial community structure was investigated in all samples. The results obtained indicated that the quantity and integrity of DNA was preserved well in all samples; however, the taxonomic distribution was skewed in samples stored without any solution at ambient temperatures, particularly when analyses were performed at lower taxonomic levels. Although both solutions performed equally well, sequencing output and OTU numbers in DESS-treated samples were closer to those snap frozen with liquid nitrogen. Furthermore, DNA/RNA Shield-stored samples performed better for the preservation of rare taxa.
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Affiliation(s)
- Mariia Pavlovska
- State Institution National Antarctic Scientific Center.,National University of Life and Environmental Sciences of Ukraine
| | | | | | - Evgen Dykyi
- State Institution National Antarctic Scientific Center
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Pérez-Burillo S, Hinojosa-Nogueira D, Navajas-Porras B, Blasco T, Balzerani F, Lerma-Aguilera A, León D, Pastoriza S, Apaolaza I, Planes FJ, Francino MP, Rufián-Henares JÁ. Effect of Freezing on Gut Microbiota Composition and Functionality for In Vitro Fermentation Experiments. Nutrients 2021; 13:nu13072207. [PMID: 34199047 PMCID: PMC8308218 DOI: 10.3390/nu13072207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/17/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
The gut microbiota has a profound effect on human health and is modulated by food and bioactive compounds. To study such interaction, in vitro batch fermentations are performed with fecal material, and some experimental designs may require that such fermentations be performed with previously frozen stools. Although it is known that freezing fecal material does not alter the composition of the microbial community in 16S rRNA gene amplicon and metagenomic sequencing studies, it is not known whether the microbial community in frozen samples could still be used for in vitro fermentations. To explore this, we undertook a pilot study in which in vitro fermentations were performed with fecal material from celiac, cow’s milk allergic, obese, or lean children that was frozen (or not) with 20% glycerol. Before fermentation, the fecal material was incubated in a nutritious medium for 6 days, with the aim of giving the microbial community time to recover from the effects of freezing. An aliquot was taken daily from the stabilization vessel and used for the in vitro batch fermentation of lentils. The microbial community structure was significantly different between fresh and frozen samples, but the variation introduced by freezing a sample was always smaller than the variation among individuals, both before and after fermentation. Moreover, the potential functionality (as determined in silico by a genome-scaled metabolic reconstruction) did not differ significantly, possibly due to functional redundancy. The most affected genus was Bacteroides, a fiber degrader. In conclusion, if frozen fecal material is to be used for in vitro fermentation purposes, our preliminary analyses indicate that the functionality of microbial communities can be preserved after stabilization.
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Affiliation(s)
- Sergio Pérez-Burillo
- Centro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, Spain; (S.P.-B.); (D.H.-N.); (B.N.-P.); (S.P.)
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Daniel Hinojosa-Nogueira
- Centro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, Spain; (S.P.-B.); (D.H.-N.); (B.N.-P.); (S.P.)
| | - Beatriz Navajas-Porras
- Centro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, Spain; (S.P.-B.); (D.H.-N.); (B.N.-P.); (S.P.)
| | - Telmo Blasco
- Tecnun, University of Navarra, Manuel de Lardizábal 13, 20018 San Sebastián, Spain; (T.B.); (F.B.); (I.A.); (F.J.P.)
| | - Francesco Balzerani
- Tecnun, University of Navarra, Manuel de Lardizábal 13, 20018 San Sebastián, Spain; (T.B.); (F.B.); (I.A.); (F.J.P.)
| | - Alberto Lerma-Aguilera
- Area de Genòmica i Salut, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO-Salut Pública), 46020 València, Spain; (A.L.-A.); (D.L.); (M.P.F.)
| | - Daniel León
- Area de Genòmica i Salut, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO-Salut Pública), 46020 València, Spain; (A.L.-A.); (D.L.); (M.P.F.)
| | - Silvia Pastoriza
- Centro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, Spain; (S.P.-B.); (D.H.-N.); (B.N.-P.); (S.P.)
| | - Iñigo Apaolaza
- Tecnun, University of Navarra, Manuel de Lardizábal 13, 20018 San Sebastián, Spain; (T.B.); (F.B.); (I.A.); (F.J.P.)
| | - Francisco J. Planes
- Tecnun, University of Navarra, Manuel de Lardizábal 13, 20018 San Sebastián, Spain; (T.B.); (F.B.); (I.A.); (F.J.P.)
| | - Maria Pilar Francino
- Area de Genòmica i Salut, Fundació per al Foment de la Investigació Sanitària i Biomèdica de la Comunitat Valenciana (FISABIO-Salut Pública), 46020 València, Spain; (A.L.-A.); (D.L.); (M.P.F.)
- CIBER en Epidemiología y Salud Pública, 28001 Madrid, Spain
| | - José Ángel Rufián-Henares
- Centro de Investigación Biomédica, Departamento de Nutrición y Bromatología, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Granada, 18071 Granada, Spain; (S.P.-B.); (D.H.-N.); (B.N.-P.); (S.P.)
- Instituto de Investigación Biosanitaria ibs.GRANADA, Universidad de Granada, 18071 Granada, Spain
- Correspondence: ; Tel.: +34-958-24-28-41; Fax: +34-958-24-95-77
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Hosseinkhani F, Dubbelman AC, Karu N, Harms AC, Hankemeier T. Towards Standards for Human Fecal Sample Preparation in Targeted and Untargeted LC-HRMS Studies. Metabolites 2021; 11:364. [PMID: 34200487 DOI: 10.3390/metabo11060364] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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44
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Hanssen NMJ, de Vos WM, Nieuwdorp M. Fecal microbiota transplantation in human metabolic diseases: From a murky past to a bright future? Cell Metab 2021; 33:1098-110. [PMID: 34077717 DOI: 10.1016/j.cmet.2021.05.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/26/2021] [Accepted: 05/05/2021] [Indexed: 12/15/2022]
Abstract
Fecal microbiota transplantation (FMT) is gaining considerable traction as a therapeutic approach to influence the course of a plethora of chronic conditions, ranging from metabolic syndrome and malignancies to auto-immune and neurological diseases, and helped to establish the contribution of the gut microbiome to these conditions. Although FMT procedures have yielded important mechanistic insights, their use in clinical practice may be limited due to practical objections in the setting of metabolic diseases. While its applicability is established to treat recurrent Clostridiodes difficile, FMT is emerging in ulcerative colitis and various other diseases. A particularly new insight is that FMTs may not only alter insulin sensitivity but may also alter the course of type 1 diabetes by attenuating underlying auto-immunity. In this review, we will outline the major principles and pitfalls of FMT and where optimization of study design and the procedure itself will further advance the field of cardiometabolic medicine.
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45
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Everett C, Li C, Wilkinson JE, Nguyen LH, McIver LJ, Ivey K, Izard J, Palacios N, Eliassen AH, Willett WC, Ascherio A, Sun Q, Tworoger SS, Chan AT, Garrett WS, Huttenhower C, Rimm EB, Song M. Overview of the Microbiome Among Nurses study (Micro-N) as an example of prospective characterization of the microbiome within cohort studies. Nat Protoc 2021; 16:2724-2731. [PMID: 33883746 DOI: 10.1038/s41596-021-00519-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/16/2021] [Indexed: 02/06/2023]
Abstract
A lack of prospective studies has been a major barrier for assessing the role of the microbiome in human health and disease on a population-wide scale. To address this significant knowledge gap, we have launched a large-scale collection targeting fecal and oral microbiome specimens from 20,000 women within the Nurses' Health Study II cohort (the Microbiome Among Nurses study, or Micro-N). Leveraging the rich epidemiologic data that have been repeatedly collected from this cohort since 1989; the established biorepository of archived blood, urine, buccal cell, and tumor tissue specimens; the available genetic and biomarker data; the cohort's ongoing follow-up; and the BIOM-Mass microbiome research platform, Micro-N furnishes unparalleled resources for future prospective studies to interrogate the interplay between host, environmental factors, and the microbiome in human health. These prospectively collected materials will provide much-needed evidence to infer causality in microbiome-associated outcomes, paving the way toward development of microbiota-targeted modulators, preventives, diagnostics and therapeutics. Here, we describe a generalizable, scalable and cost-effective platform used for stool and oral microbiome specimen and metadata collection in the Micro-N study as an example of how prospective studies of the microbiome may be carried out.
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Affiliation(s)
- Christine Everett
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Chengchen Li
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jeremy E Wilkinson
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Lauren J McIver
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Kerry Ivey
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,South Australian Health and Medical Research Institute, Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia.,Department of Nutrition and Dietetics, College of Nursing and Health Sciences, Flinders University, Adelaide, South Australia, Australia
| | - Jacques Izard
- Food Science and Technology Department, Institute of Agriculture and Natural Resources, University of Nebraska, Lincoln, NE, USA.,Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Natalia Palacios
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Public Health, Zuckerberg College of Health Sciences, University of Massachusetts Lowell, Lowell, MA, USA
| | - A Heather Eliassen
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Walter C Willett
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Alberto Ascherio
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Qi Sun
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Shelley S Tworoger
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA
| | - Andrew T Chan
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Wendy S Garrett
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Medicine, Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eric B Rimm
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Mingyang Song
- Harvard Chan Microbiome in Public Health Center, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. .,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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Randall S, Cartozzo C, Simmons T, Swall JL, Singh B. Prediction of minimum postmortem submersion interval (PMSI min) based on eukaryotic community succession on skeletal remains recovered from a lentic environment. Forensic Sci Int 2021; 323:110784. [PMID: 33864992 DOI: 10.1016/j.forsciint.2021.110784] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 01/01/2021] [Accepted: 04/05/2021] [Indexed: 01/05/2023]
Abstract
Although recent studies explored using microbial succession during decomposition to estimate the postmortem interval (PMI) and postmortem submersion interval (PMSI), there is currently no published research using aquatic eukaryotic community succession to estimate the minimum postmortem submersion interval (PMSImin). The goals of this study were to determine whether eukaryotic community succession occurs on porcine skeletal remains in a lentic environment, and, if so, to develop a statistical model for PMSImin prediction. Fresh porcine bones (rib N = 100, scapula N = 100) were placed in cages (10'' x 10'') attached to floatation devices and submerged in a fresh water lake (Crozet, VA), using waterproof loggers and a YSI Sonde to record temperature and water quality variables, respectively. In addition to baseline samples, one cage, containing five ribs and five scapulae, and water samples (500 mL) were collected approximately every 250 accumulated degree days (ADD). Nineteen sample cohorts were collected over a period of 5200 ADD (579 Days). Variable region nine (V9) of the 18S ribosomal DNA (rDNA) was amplified and sequenced using a dual-index strategy on the MiSeq FGx sequencing platform. Resulting sequences underwent quality control parameters and analysis in mothur v 1.42.3, R v 3.5.3, and R v 3.6.0. Permutational multivariate analysis of variance (PERMANOVA) revealed a significant difference in phylogenetic β-diversity among ribs, scapulae and water (p = 0.001) and among ADD (p ≤ 0.011), which was supported by distinct clustering of samples associated with each ADD in UniFrac distance based non-metric multidimensional scaling (NMDS) ordinations. Using similarity percentage (SIMPER) analysis of class and family level taxa, differences observed between bone types were attributed to Peronosporomycetes_cl, Eukaryota_unclassified, and Intramacronucleata (e.g., Armophorida), however these differences were not statistically significant. Alpha diversity revealed a non-linear increase in phylogenetic diversity with an increase in ADD. Random forest models for ribs and scapulae predicted PMSImin with an error rate within±104 days (937 ADD) and±63 days (564 ADD), respectively. In conclusion, this study suggests that eukaryotic succession is capable of predicting long term PMSImin in lentic systems.
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Affiliation(s)
- Sala Randall
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA 23284, United States.
| | - Claire Cartozzo
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA 23284, United States; Department of Integrative Life Science, Virginia Commonwealth University, Richmond, VA 23284, United States
| | - Tal Simmons
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA 23284, United States
| | - Jenise L Swall
- Department of Statistical Sciences & Operations Research, Virginia Commonwealth University, Richmond, VA 23284, United States
| | - Baneshwar Singh
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA 23284, United States.
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47
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Sciavilla P, Strati F, Di Paola M, Modesto M, Vitali F, Cavalieri D, Prati GM, Di Vito M, Aragona G, De Filippo C, Mattarelli P. Gut microbiota profiles and characterization of cultivable fungal isolates in IBS patients. Appl Microbiol Biotechnol 2021; 105:3277-88. [PMID: 33839797 DOI: 10.1007/s00253-021-11264-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 03/25/2021] [Accepted: 04/04/2021] [Indexed: 02/06/2023]
Abstract
Studies so far conducted on irritable bowel syndrome (IBS) have been focused mainly on the role of gut bacterial dysbiosis in modulating the intestinal permeability, inflammation, and motility, with consequences on the quality of life. Limited evidences showed a potential involvement of gut fungal communities. Here, the gut bacterial and fungal microbiota of a cohort of IBS patients have been characterized and compared with that of healthy subjects (HS). The IBS microbial community structure differed significantly compared to HS. In particular, we observed an enrichment of bacterial taxa involved in gut inflammation, such as Enterobacteriaceae, Streptococcus, Fusobacteria, Gemella, and Rothia, as well as depletion of health-promoting bacterial genera, such as Roseburia and Faecalibacterium. Gut microbial profiles in IBS patients differed also in accordance with constipation. Sequence analysis of the gut mycobiota showed enrichment of Saccharomycetes in IBS. Culturomics analysis of fungal isolates from feces showed enrichment of Candida spp. displaying from IBS a clonal expansion and a distinct genotypic profiles and different phenotypical features when compared to HS of Candida albicans isolates. Alongside the well-characterized gut bacterial dysbiosis in IBS, this study shed light on a yet poorly explored fungal component of the intestinal ecosystem, the gut mycobiota. Our results showed a differential fungal community in IBS compared to HS, suggesting potential for new insights on the involvement of the gut mycobiota in IBS. KEY POINTS: • Comparison of gut microbiota and mycobiota between IBS and healthy subjects • Investigation of cultivable fungi in IBS and healthy subjects • Candida albicans isolates result more virulent in IBS subjects compared to healthy subjects.
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48
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Cartozzo C, Singh B, Swall J, Simmons T. Postmortem submersion interval (PMSI) estimation from the microbiome of sus scrofa bone in a freshwater lake. J Forensic Sci 2021; 66:1334-1347. [PMID: 33818789 DOI: 10.1111/1556-4029.14692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/13/2021] [Accepted: 02/01/2021] [Indexed: 01/22/2023]
Abstract
While many studies have developed microbial succession-based models for the prediction of postmortem interval (PMI) in terrestrial systems, similar well-replicated long-term decomposition studies are lacking for aquatic systems. Therefore, this study sought to identify temporal changes in bacterial community structure associated with porcine skeletal remains (n = 198) for an extended period in a fresh water lake. Every ca. 250 ADD, one cage, containing 5 ribs and 5 scapulae, was removed from the lake for a total of nineteen collections. Water was also sampled at each interval. Variable region 4 (V4) of 16S rDNA was amplified and sequenced for all collected samples using Illumina MiSeq FGx Sequencing platform; resulting data were analyzed with the mothur (v1.39.5) and R (v3.6.0). Bacterial communities associated with ribs differed significantly from those associated with scapulae. This difference was mainly attributed to Clostridia, Holophagae, and Spirochaete relative abundances. For each bone type, α-diversity increased with ADD; similarly, β-diversity bacterial community structure changed significantly with ADD and were explained using environmental parameters and inferred functional pathways. Models developed using 24 rib and 34 scapula family-level taxa allowed the prediction of PMSI with root mean square error of 522.97 ADD (~57 days) and 333.8 ADD (~37 days), respectively.
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Affiliation(s)
- Claire Cartozzo
- Integrative Life Sciences, Virginia Commonwealth University, Richmond, VA, USA.,Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Baneshwar Singh
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Jenise Swall
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, Richmond, VA, USA
| | - Tal Simmons
- Department of Forensic Science, Virginia Commonwealth University, Richmond, VA, USA
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Martin de Bustamante M, Plummer C, MacNicol J, Gomez D. Impact of Ambient Temperature Sample Storage on the Equine Fecal Microbiota. Animals (Basel) 2021; 11:ani11030819. [PMID: 33803934 PMCID: PMC8001224 DOI: 10.3390/ani11030819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 11/16/2022] Open
Abstract
Sample storage conditions are an important factor in fecal microbiota analyses in general. The objective of this study was to investigate the effect of sample storage at room temperature on the equine fecal microbiota composition. Fecal samples were collected from 11 healthy horses. Each sample was divided into 7 sealed aliquots. One aliquot was immediately frozen at -80 °C; the remaining aliquots were stored at room temperature (21 to 22 °C) with one transferred to the freezer at each of the following time points: 6, 12, 24, 48, 72 and 96 h. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene. Fibrobacteraceae (Fibrobacter) and Ruminococcaceae (Ruminococcus) were enriched in samples from 0 h and 6 h, whereas taxa from the families Bacillaceae, Planococcaceae, Enterobacteriaceae and Moraxellaceae were enriched in samples stored at room temperature for 24 h or greater. Samples frozen within the first 12 h after collection shared similar community membership. The community structure was similar for samples collected at 0 h and 6 h, but it was significantly different between samples frozen at 0 h and 12 h or greater. In conclusion, storage of equine fecal samples at ambient temperature for up to 6 h before freezing following sample collection had minimal effect on the microbial composition. Longer-term storage at ambient temperature resulted in alterations in alpha-diversity, community membership and structure and the enrichment of different taxa when compared to fecal samples immediately frozen at -80 °C.
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Affiliation(s)
- Michelle Martin de Bustamante
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA; (M.M.d.B.); (C.P.)
| | - Caryn Plummer
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA; (M.M.d.B.); (C.P.)
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Jennifer MacNicol
- Department of Animal Biosciences, Ontario Agriculture College, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Diego Gomez
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL 32610, USA
- Department of Clinical Studies, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
- Correspondence:
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50
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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