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Ma X, Brinker E, Lea CR, Delmain D, Chamorro ED, Martin DR, Graff EC, Wang X. Evaluation of fecal sample collection methods for feline gut microbiome profiling: fecal loop vs. litter box. Front Microbiol 2024; 15:1337917. [PMID: 38800749 PMCID: PMC11127567 DOI: 10.3389/fmicb.2024.1337917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 04/12/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Microbial population structures within fecal samples are vital for disease screening, diagnosis, and gut microbiome research. The two primary methods for collecting feline fecal samples are: (1) using a fecal loop, which retrieves a rectal sample using a small, looped instrument, and (2) using the litter box, which collects stool directly from the litter. Each method has its own advantages and disadvantages and is suitable for different research objectives. Methods and results Whole-genome shotgun metagenomic sequencing were performed on the gut microbiomes of fecal samples collected using these two methods from 10 adult cats housed in the same research facility. We evaluated the influence of collection methods on feline microbiome analysis, particularly their impact on DNA extraction, metagenomic sequencing yield, microbial composition, and diversity in subsequent gut microbiome analyses. Interestingly, fecal sample collection using a fecal loop resulted in a lower yield of microbial DNA compared to the litterbox method (p = 0.004). However, there were no significant differences between the two groups in the proportion of host contamination (p = 0.106), virus contamination (p = 0.232), relative taxonomy abundance of top five phyla (Padj > 0.638), or the number of microbial genes covered (p = 0.770). Furthermore, no significant differences were observed in alpha-diversity, beta-diversity, the number of taxa identified at each taxonomic level, and the relative abundance of taxonomic units. Discussion These two sample collection methods do not affect microbial population structures within fecal samples and collecting fecal samples directly from the litterbox within 6 hours after defecation can be considered a reliable approach for microbiome research.
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Affiliation(s)
- Xiaolei Ma
- School of Life Sciences and Technology, Tongji University, Shanghai, China
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Emily Brinker
- Department of Comparative Pathobiology, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States
| | - Christopher R. Lea
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Diane Delmain
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Erin D. Chamorro
- Department of Clinical Sciences, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Douglas R. Martin
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Department of Anatomy, Physiology, and Pharmacology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Emily C. Graff
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
| | - Xu Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Scott-Ritchey Research Center, College of Veterinary Medicine, Auburn University, Auburn, AL, United States
- Center for Advanced Science, Innovation, and Commerce, Alabama Agricultural Experiment Station, Auburn, AL, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
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Epidemiological Studies of Children's Gut Microbiota: Validation of Sample Collection and Storage Methods and Microbiota Analysis of Toddlers' Feces Collected from Diapers. Nutrients 2022; 14:nu14163315. [PMID: 36014821 PMCID: PMC9416069 DOI: 10.3390/nu14163315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/03/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
The composition of human gut microbiota influences human health and disease over the long term. Since the flora in specimens can easily change at ambient temperature outside the body, epidemiological studies need feasible methods of stool specimen collection and storage to be established. We aimed to validate two methods: feces frozen-stored in tubes containing guanidine thiocyanate solution for two months after collection (Method B), and feces excreted in diapers and frozen-stored (Method C). Validation was by comparison with a gold standard Method A. Bacterial flora of five adults were sampled and stored by all three methods. Bacterial composition was examined by amplicon sequencing analysis. Bland-Altman analyses showed that Methods B and C might change relative abundances of certain bacterial flora. Thereafter, we analyzed the bacterial flora of 76 toddlers (two age groups) in stools sampled and processed by Method C. The diversity indices of toddlers' flora were less than those of adults. The relative abundance of some bacteria differed significantly between children aged 1.5 and 3 years. The specimen collection and storage methods validated in this study are worth adopting in large-scale epidemiological studies, especially for small children, provided the limited accuracy for some specific bacteria is understood.
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Abstract
Integrative analysis of high-quality metagenomics and metabolomics data from fecal samples provides novel clues for the mechanism underpinning gut microbe-human interactions. However, data regarding the influence of fecal collection methods on both metagenomics and metabolomics are sparse. Six fecal collection methods (the gold standard [GS] [i.e., immediate freezing at −80°C with no solution], 95% ethanol, RNAlater, OMNIgene Gut, fecal occult blood test [FOBT] cards, and Microlution) were used to collect 88 fecal samples from eight healthy volunteers for whole-genome shotgun sequencing (WGSS) and untargeted metabolomic profiling. Metrics assessed included the abundances of predominant phyla and α- and β-diversity at the species, gene, and pathway levels. Intraclass correlation coefficients (ICCs) were calculated for microbes and metabolites to estimate (i) stability (day 4 versus day 0 within each method), (ii) concordance (day 0 for each method versus the GS), and (iii) reliability (day 4 for each method versus the GS). For the top 4 phyla and microbial diversity metrics at the species, gene, and pathway levels, generally high stability and reliability were observed for most methods except for 95% ethanol; similar concordances were seen for different methods. For metabolomics data, 95% ethanol showed the highest stability, concordance, and reliability (median ICCs = 0.71, 0.71, and 0.65, respectively). Taken together, OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles. We recommend using separate collecting methods for gut metagenomic sequencing and fecal metabolomic profiling in large population studies. IMPORTANCE The choice of fecal collection method is essential for studying gut microbe-human interactions in large-scale population-based research. In this study, we examined the effects of fecal collection methods and storage time at ambient temperature on variations in the gut microbiome community composition; microbial diversity metrics at the species, gene, and pathway levels; antibiotic resistance genes; and metabolome profiling. Our findings suggest using different fecal sample collection methods for different data generation purposes. OMNIgene Gut, FOBT cards, RNAlater, and Microlution, but not 95% ethanol, were reliable collection methods for gut metagenomic studies. However, 95% ethanol was the best for preserving fecal metabolite profiles.
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Kim HI, Hong SH, Lee SY, Ku JM, Kim MJ, Ko SG. Gardenia Jasminoides Ameliorates Antibiotic-Associated Aggravation of DNCB-Induced Atopic Dermatitis by Restoring the Intestinal Microbiome Profile. Nutrients 2021; 13:nu13041349. [PMID: 33919521 PMCID: PMC8072552 DOI: 10.3390/nu13041349] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/31/2022] Open
Abstract
The intestinal microbiome is considered one of the key regulators of health. Accordingly, the severity of atopic dermatitis (AD) is mediated by the skin and intestinal microbiome environment. In this study, while evaluating the aggravation in AD symptoms by the antibiotics cocktail (ABX)-induced depletion of the intestinal microbiome, we sought to verify the effect of Gardenia jasminoides (GJ), a medicinal herb used for inflammatory diseases, on AD regarding its role on the intestinal microbiome. To verify the aggravation in AD symptoms induced by the depletion of the intestinal microbiome, we established a novel mouse model by administrating an ABX to create a microbiome-free environment in the intestine, and then applied 2,4-dinitrochlorobenzene (DNCB) to induce an AD-like skin inflammatory response. While ABX treatment aggravated AD-like symptoms, the 2-week administration of GJ improved these pathological changes. DNCB application upregulated immune cell count and serum cytokine expression, which were alleviated by GJ. Moreover, pathological alterations by antibiotics and DNCB, including histological damage of the intestine and the intestinal expression of IL-17, were recovered in GJ-treated mice. The beneficial effect of GJ was due to the restoration of the intestinal microbiome composition. Overall, we suggest GJ as a potential therapeutic agent for AD due to its regulation of the intestinal microbiome.
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Affiliation(s)
- Hyo In Kim
- Department of Surgery, Beth Israel Deaconess Medical Center/Harvard Medical School, 330 Brookline Ave, Boston, MA 02215, USA;
| | - Se Hyang Hong
- Clinical Medicine Division, Korea Institute of Oriental Medicine, 1672 Yuseongdae-ro, Yuseong-gu, Daejeon 34054, Korea;
| | - Seo Yeon Lee
- Department of Science in Korean Medicine, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea; (S.Y.L.); (M.J.K.)
| | - Jin Mo Ku
- Department of Preventive Medicine, College of Korean Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
| | - Min Jeong Kim
- Department of Science in Korean Medicine, Graduate School, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea; (S.Y.L.); (M.J.K.)
| | - Seong-Gyu Ko
- Department of Preventive Medicine, College of Korean Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea;
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, 26 Kyungheedae-ro, Dongdaemun-gu, Seoul 02447, Korea
- Correspondence: ; Tel.: +82-2-961-0329; Fax: +82-2-966-1165
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Young C, Wood HM, Fuentes Balaguer A, Bottomley D, Gallop N, Wilkinson L, Benton SC, Brealey M, John C, Burtonwood C, Thompson KN, Yan Y, Barrett JH, Morris EJA, Huttenhower C, Quirke P. Microbiome Analysis of More Than 2,000 NHS Bowel Cancer Screening Programme Samples Shows the Potential to Improve Screening Accuracy. Clin Cancer Res 2021; 27:2246-2254. [PMID: 33658300 PMCID: PMC7610626 DOI: 10.1158/1078-0432.ccr-20-3807] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 12/05/2020] [Accepted: 02/12/2021] [Indexed: 02/03/2023]
Abstract
PURPOSE There is potential for fecal microbiome profiling to improve colorectal cancer screening. This has been demonstrated by research studies, but it has not been quantified at scale using samples collected and processed routinely by a national screening program. EXPERIMENTAL DESIGN Between 2016 and 2019, the largest of the NHS Bowel Cancer Screening Programme hubs prospectively collected processed guaiac fecal occult blood test (gFOBT) samples with subsequent colonoscopy outcomes: blood-negative [n = 491 (22%)]; colorectal cancer [n = 430 (19%)]; adenoma [n = 665 (30%)]; colonoscopy-normal [n = 300 (13%)]; nonneoplastic [n = 366 (16%)]. Samples were transported and stored at room temperature. DNA underwent 16S rRNA gene V4 amplicon sequencing. Taxonomic profiling was performed to provide features for classification via random forests (RF). RESULTS Samples provided 16S amplicon-based microbial profiles, which confirmed previously described colorectal cancer-microbiome associations. Microbiome-based RF models showed potential as a first-tier screen, distinguishing colorectal cancer or neoplasm (colorectal cancer or adenoma) from blood-negative with AUC 0.86 (0.82-0.89) and AUC 0.78 (0.74-0.82), respectively. Microbiome-based models also showed potential as a second-tier screen, distinguishing from among gFOBT blood-positive samples, colorectal cancer or neoplasm from colonoscopy-normal with AUC 0.79 (0.74-0.83) and AUC 0.73 (0.68-0.77), respectively. Models remained robust when restricted to 15 taxa, and performed similarly during external validation with metagenomic datasets. CONCLUSIONS Microbiome features can be assessed using gFOBT samples collected and processed routinely by a national colorectal cancer screening program to improve accuracy as a first- or second-tier screen. The models required as few as 15 taxa, raising the potential of an inexpensive qPCR test. This could reduce the number of colonoscopies in countries that use fecal occult blood test screening.
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Affiliation(s)
- Caroline Young
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom.
| | - Henry M Wood
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Alba Fuentes Balaguer
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Daniel Bottomley
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Niall Gallop
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Lyndsay Wilkinson
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Sally C Benton
- NHS Bowel Cancer Screening Programme - Southern Hub, Surrey Research Park, Guildford, United Kingdom
| | - Martin Brealey
- NHS Bowel Cancer Screening Programme - Southern Hub, Surrey Research Park, Guildford, United Kingdom
| | - Cerin John
- NHS Bowel Cancer Screening Programme - Southern Hub, Surrey Research Park, Guildford, United Kingdom
| | - Carole Burtonwood
- NHS Bowel Cancer Screening Programme - Southern Hub, Surrey Research Park, Guildford, United Kingdom
| | - Kelsey N Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Jennifer H Barrett
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
| | - Eva J A Morris
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
- Big Data Institute, Nuffield Department of Population Health, Old Road Campus, University of Oxford, Oxford, United Kingdom
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Philip Quirke
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Leeds, United Kingdom
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Young C, Wood HM, Seshadri RA, Van Nang P, Vaccaro C, Melendez LC, Bose M, Van Doi M, Piñero TA, Valladares CT, Arguero J, Balaguer AF, Thompson KN, Yan Y, Huttenhower C, Quirke P. The colorectal cancer-associated faecal microbiome of developing countries resembles that of developed countries. Genome Med 2021; 13:27. [PMID: 33593386 PMCID: PMC7887780 DOI: 10.1186/s13073-021-00844-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 02/04/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The incidence of colorectal cancer (CRC) is increasing in developing countries, yet limited research on the CRC- associated microbiota has been conducted in these areas, in part due to scarce resources, facilities, and the difficulty of fresh or frozen stool storage/transport. Here, we aimed (1) to establish a broad representation of diverse developing countries (Argentina, Chile, India, and Vietnam); (2) to validate a 'resource-light' sample-collection protocol translatable in these settings using guaiac faecal occult blood test (gFOBT) cards stored and, importantly, shipped internationally at room temperature; (3) to perform initial profiling of the collective CRC-associated microbiome of these developing countries; and (4) to compare this quantitatively with established CRC biomarkers from developed countries. METHODS We assessed the effect of international storage and transport at room temperature by replicating gFOBT from five UK volunteers, storing two in the UK, and sending replicates to institutes in the four countries. Next, to determine the effect of prolonged UK storage, DNA extraction replicates for a subset of samples were performed up to 252 days apart. To profile the CRC-associated microbiome of developing countries, gFOBT were collected from 41 treatment-naïve CRC patients and 40 non-CRC controls from across the four institutes, and V4 16S rRNA gene sequencing was performed. Finally, we constructed a random forest (RF) model that was trained and tested against existing datasets from developed countries. RESULTS The microbiome was stably assayed when samples were stored/transported at room temperature and after prolonged UK storage. Large-scale microbiome structure was separated by country and continent, with a smaller effect from CRC. Importantly, the RF model performed similarly to models trained using external datasets and identified similar taxa of importance (Parvimonas, Peptostreptococcus, Fusobacterium, Alistipes, and Escherichia). CONCLUSIONS This study demonstrates that gFOBT, stored and transported at room temperature, represents a suitable method of faecal sample collection for amplicon-based microbiome biomarkers in developing countries and suggests a CRC-faecal microbiome association that is consistent between developed and developing countries.
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Affiliation(s)
- Caroline Young
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Level 4 Wellcome Trust Brenner Building, Leeds, LS9 7TF, UK.
| | - Henry M Wood
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Level 4 Wellcome Trust Brenner Building, Leeds, LS9 7TF, UK
| | | | - Pham Van Nang
- Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Carlos Vaccaro
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de buenos Aires (HIBA), Buenos Aires, Argentina
| | | | | | - Mai Van Doi
- Can Tho University of Medicine and Pharmacy, Can Tho, Vietnam
| | - Tamara Alejandra Piñero
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de buenos Aires (HIBA), Buenos Aires, Argentina
| | | | - Julieta Arguero
- Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB) - CONICET - Instituto Universitario del Hospital Italiano (IUHI), Hospital Italiano de buenos Aires (HIBA), Buenos Aires, Argentina
| | - Alba Fuentes Balaguer
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Level 4 Wellcome Trust Brenner Building, Leeds, LS9 7TF, UK
| | - Kelsey N Thompson
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Yan Yan
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Philip Quirke
- Pathology & Data Analytics, Leeds Institute of Medical Research at St James's University Hospital, University of Leeds, Level 4 Wellcome Trust Brenner Building, Leeds, LS9 7TF, UK
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Thomas R, Wong WSW, Saadon R, Vilboux T, Deeken J, Niederhuber J, Hourigan SK, Yang E. Gut microbial composition difference between pediatric ALL survivors and siblings. Pediatr Hematol Oncol 2020; 37:475-488. [PMID: 32427521 PMCID: PMC7701956 DOI: 10.1080/08880018.2020.1759740] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Acute lymphoblastic leukemia (ALL) is the most common childhood cancer with high cure rates leading to rising numbers of long-term survivors. Adult survivors of childhood ALL are at increased risk of obesity, cardiovascular disease, and other chronic illnesses. We hypothesize that ALL therapy is associated with long-term gut microbiome alterations that contribute to predisposition to chronic medical conditions. We conducted a pilot study to test whether differences can be detected between stool microbiota of pediatric ALL survivors and their siblings. Stool samples were collected from 38 individuals under age 19 who were at least 1 year after completion of therapy for ALL. Stool samples collected from 16 healthy siblings served as controls. 16S ribosomal RNA gene sequencing was performed on the stool samples. Comparing microbiota of survivors to sibling controls, no statistically significant differences were found in alpha or beta diversity. However, among the top 10 operational taxonomic units (OTUs) from component 1 in sparse partial least squares discriminant analysis (sPLS-DA) with different relative abundance in survivors versus siblings, OTUs mapping to the genus Faecalibacterium were depleted in survivors. Differences in gut microbial composition were found between pediatric survivors of childhood ALL and their siblings. Specifically, the protective Faecalibacterium is depleted in survivors, which is reminiscent of gut microbiota alteration found in adult survivors of childhood ALL and reported in obesity, suggesting that microbiota alterations in pediatric ALL survivors start in childhood and may play a role in predisposition to chronic illness in later years of survivorship.
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Affiliation(s)
- Ronay Thomas
- Pediatric Hematology-Oncology, Pediatric Specialists of Virginia, Falls Church, Virginia, USA
| | - Wendy S. W. Wong
- Inova Translational Medicine Institute, Inova Health Systems, Falls Church, Virginia, USA
| | - Reem Saadon
- Pediatric Hematology-Oncology, Pediatric Specialists of Virginia, Falls Church, Virginia, USA
| | - Thierry Vilboux
- Inova Translational Medicine Institute, Inova Health Systems, Falls Church, Virginia, USA
| | - John Deeken
- Inova Schar Cancer Institute, Falls Church, Virginia, USA
| | - John Niederhuber
- Inova Translational Medicine Institute, Inova Health Systems, Falls Church, Virginia, USA;,Surgery and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Suchitra K. Hourigan
- Inova Translational Medicine Institute, Inova Health Systems, Falls Church, Virginia, USA;,Pediatric Gastroenterology, Pediatric Specialists of Virginia, Falls Church, Virginia, USA;,Pediatrics, Inova Children’s Hospital, Falls Church, Virginia, USA
| | - Elizabeth Yang
- Pediatric Hematology-Oncology, Pediatric Specialists of Virginia, Falls Church, Virginia, USA;,Pediatrics, George Washington University School of Medicine, Washington, DC, USA;,Pediatrics, Virginia Commonwealth University School of Medicine Inova Campus, Falls Church, Virginia, USA
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Kinneman L, Zhu W, Wong WSW, Clemency N, Provenzano M, Vilboux T, Jane't K, Seo-Mayer P, Levorson R, Kou M, Ascher D, Niederhuber JE, Hourigan SK. Assessment of the Urinary Microbiome in Children Younger Than 48 Months. Pediatr Infect Dis J 2020; 39:565-570. [PMID: 32091499 DOI: 10.1097/inf.0000000000002622] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND The urinary tract was once thought to be sterile, and little is known about the urinary microbiome in children. This study aimed to examine the urinary microbiome of young children across demographic and clinical factors. METHODS Children <48 months, undergoing a urinary catheterization for clinical purposes in the Pediatric Emergency Department were recruited and urine samples collected. Detailed demographic and clinical information were recorded. Urine samples underwent DNA extraction and 16S ribosomal RNA gene sequencing, urinalysis and urine culture. RESULTS Eighty-five children were included; a urinary microbiome was identified in every child. Nine children had Escherichia coli urinary tract infections (UTIs) identified. Those with UTIs had a significantly decreased alpha diversity (t test, P < 0.001) and the composition of the microbiome clustered separately (P = 0.001) compared with those without UTIs. CONCLUSIONS A urinary microbiome was identified in every child, even neonates. Differences in microbiome diversity and composition were observed in patients with a standard culture positive UTI. The urinary microbiome has just begun to be explored, and the implications on long-term disease processes deserve further investigation.
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Affiliation(s)
- Lauren Kinneman
- From the Department of Pediatrics and Department of Emergency Medicine, Inova Children's Hospital, Falls Church, VA.,Division of Emergency Medicine, Department of Pediatrics, University of Washington, Seattle, WA.,Seattle Children's Emergency Department, Seattle, WA
| | - Wei Zhu
- Seattle Children's Emergency Department, Seattle, WA
| | - Wendy S W Wong
- Inova Translational Medicine Institute, Falls Church, VA.,Seattle Children's Emergency Department, Seattle, WA
| | - Nicole Clemency
- Inova Translational Medicine Institute, Falls Church, VA.,Seattle Children's Emergency Department, Seattle, WA
| | - Marina Provenzano
- Inova Translational Medicine Institute, Falls Church, VA.,Seattle Children's Emergency Department, Seattle, WA
| | | | - Keary Jane't
- Inova Translational Medicine Institute, Falls Church, VA
| | - Patricia Seo-Mayer
- From the Department of Pediatrics and Department of Emergency Medicine, Inova Children's Hospital, Falls Church, VA.,Pediatric Specialists of Virginia, Falls Church, VA
| | - Rebecca Levorson
- From the Department of Pediatrics and Department of Emergency Medicine, Inova Children's Hospital, Falls Church, VA.,Pediatric Specialists of Virginia, Falls Church, VA
| | - Maybelle Kou
- From the Department of Pediatrics and Department of Emergency Medicine, Inova Children's Hospital, Falls Church, VA
| | - David Ascher
- From the Department of Pediatrics and Department of Emergency Medicine, Inova Children's Hospital, Falls Church, VA
| | - John E Niederhuber
- Inova Translational Medicine Institute, Falls Church, VA.,Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA
| | - Suchitra K Hourigan
- From the Department of Pediatrics and Department of Emergency Medicine, Inova Children's Hospital, Falls Church, VA.,Inova Translational Medicine Institute, Falls Church, VA.,Pediatric Specialists of Virginia, Falls Church, VA
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Maternal H. pylori is associated with differential fecal microbiota in infants born by vaginal delivery. Sci Rep 2020; 10:7305. [PMID: 32350392 PMCID: PMC7190710 DOI: 10.1038/s41598-020-64296-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 04/11/2020] [Indexed: 02/08/2023] Open
Abstract
Helicobacter pylori colonization may affect the mucosal immune system through modification of microbiota composition and their interactions with the host. We hypothesized that maternal H. pylori status affects the maternal intestinal microbiota of both mother and newborn. In this study, we determine the structure of the fecal microbiota in mothers and neonates according to maternal H. pylori status and delivery mode. We included 22 mothers and H. pylori infection was determined by fecal antigen test. Eleven mothers (50%) were H. pylori-positive (7 delivering vaginally and 4 by C-section), and 11 were negative (6 delivering vaginally and 5 by C-section). Stool samples were obtained from mothers and infants and the fecal DNA was sequenced. The fecal microbiota from mothers and their babies differed by the maternal H. pylori status, only in vaginal birth, not in C-section delivery. All 22 infants tested negative for fecal H. pylori at 15 days of age, but those born vaginally -and not those by C-section- showed differences in the infant microbiota by maternal H. pylori status (PERMANOVA, p = 0.01), with higher abundance of Enterobacteriaceae and Veillonella, in those born to H. pylori-positive mothers. In conclusion, the structure of the infant fecal microbiota is affected by the maternal H. pylori status only in infants born vaginally, suggesting that the effect could be mediated by labor and birth exposures.
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10
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Hourigan SK, Zhu W, S.W.Wong W, Clemency NC, Provenzano M, Vilboux T, Niederhuber JE, Deeken J, Chung S, McDaniel-Wiley K, Trump D. Studying the urine microbiome in superficial bladder cancer: samples obtained by midstream voiding versus cystoscopy. BMC Urol 2020; 20:5. [PMID: 31992287 PMCID: PMC6986141 DOI: 10.1186/s12894-020-0576-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 01/17/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Preliminary data suggest that the urinary microbiome may play a role in bladder cancer. Information regarding the most suitable method of collecting urine specimens is needed for the large population studies needed to address this. To compare microbiome metrics resulting from 16S ribosomal RNA gene sequencing between midstream, voided specimens and those obtained at cystoscopy. METHODS Adults, with a history of superficial urothelial cell carcinoma (non-muscle invasive bladder cancer) being followed with periodic surveillance cystoscopy had a urine sample collected by a mid-stream, voided technique and then from the bladder at cystoscopy. Urine samples underwent 16S ribosomal RNA gene sequencing on the Illumina MiSeq platform. RESULTS 22 subjects (8 female, 14 male) were included. There was no significant difference in beta diversity (diversity between samples) in all samples between collection methods. However, analysis by sex revealed a difference between voided and cystoscopy samples from the same individual in males (p = 0.006, Adonis test) but not in females (p = 0.317, Adonis test). No differences were seen by collection method in any alpha diversity (diversity within a sample) measurement or differential abundance of taxa. CONCLUSIONS Beta diversity of the urine microbiome did differ by collection method for males only. This suggests that the urinary microbiomes of the two collection methods are not equivalent to each other, at least in males, which is the sex that bladder cancer occurs most frequently in. Therefore, the same collection method within a given study should be used.
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Affiliation(s)
- Suchitra K. Hourigan
- Inova Children’s Hospital, 3300 Gallows Road, Falls Church, VA 22042 USA
- Inova Translational Medicine Institute, 3300 Gallows Road, Falls Church, VA 22042 USA
| | - Wei Zhu
- Inova Translational Medicine Institute, 3300 Gallows Road, Falls Church, VA 22042 USA
| | - Wendy S.W.Wong
- Inova Translational Medicine Institute, 3300 Gallows Road, Falls Church, VA 22042 USA
| | - Nicole C. Clemency
- Inova Translational Medicine Institute, 3300 Gallows Road, Falls Church, VA 22042 USA
| | - Marina Provenzano
- Inova Translational Medicine Institute, 3300 Gallows Road, Falls Church, VA 22042 USA
| | - Thierry Vilboux
- Inova Translational Medicine Institute, 3300 Gallows Road, Falls Church, VA 22042 USA
| | - John E. Niederhuber
- Inova Translational Medicine Institute, 3300 Gallows Road, Falls Church, VA 22042 USA
- Public Health Sciences, Center for Genomics in Public Health, School of Medicine, University of Virginia, Charlottesville, VA 22908 USA
| | - John Deeken
- Inova Translational Medicine Institute, 3300 Gallows Road, Falls Church, VA 22042 USA
- Public Health Sciences, Center for Genomics in Public Health, School of Medicine, University of Virginia, Charlottesville, VA 22908 USA
- Inova Schar Cancer Institute, 3224 Gallows Road, Fairfax, VA 22031 USA
| | - Simon Chung
- Inova Schar Cancer Institute, 3224 Gallows Road, Fairfax, VA 22031 USA
- Department of Urology, Inova Fairfax Medical Center, 3300 Gallows Road, Falls Church, VA 22042 USA
| | - Kim McDaniel-Wiley
- Department of Urology, Inova Fairfax Medical Center, 3300 Gallows Road, Falls Church, VA 22042 USA
| | - Donald Trump
- Inova Schar Cancer Institute, 3224 Gallows Road, Fairfax, VA 22031 USA
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11
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Wong WS, Sabu P, Deopujari V, Levy S, Shah AA, Clemency N, Provenzano M, Saadoon R, Munagala A, Baker R, Baveja R, Mueller NT, Dominguez-Bello MG, Huddleston K, Niederhuber JE, Hourigan SK. Prenatal and Peripartum Exposure to Antibiotics and Cesarean Section Delivery Are Associated with Differences in Diversity and Composition of the Infant Meconium Microbiome. Microorganisms 2020; 8:E179. [PMID: 32012716 PMCID: PMC7074690 DOI: 10.3390/microorganisms8020179] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 01/11/2020] [Accepted: 01/19/2020] [Indexed: 12/16/2022] Open
Abstract
The meconium microbiome may provide insight into intrauterine and peripartum exposures and the very earliest intestinal pioneering microbes. Prenatal antibiotics have been associated with later obesity in children, which is thought to be driven by microbiome dependent mechanisms. However, there is little data regarding associations of prenatal or peripartum antibiotic exposure, with or without cesarean section (CS), with the features of the meconium microbiome. In this study, 16S ribosomal RNA gene sequencing was performed on bacterial DNA of meconium samples from 105 infants in a birth cohort study. After multivariable adjustment, delivery mode (p = 0.044), prenatal antibiotic use (p = 0.005) and peripartum antibiotic use (p < 0.001) were associated with beta diversity of the infant meconium microbiome. CS (vs. vaginal delivery) and peripartum antibiotics were also associated with greater alpha diversity of the meconium microbiome (Shannon and Simpson, p < 0.05). Meconium from infants born by CS (vs. vaginal delivery) had lower relative abundance of the genus Escherichia (p < 0.001). Prenatal antibiotic use and peripartum antibiotic use (both in the overall analytic sample and when restricting to vaginally delivered infants) were associated with differential abundance of several bacterial taxa in the meconium. Bacterial taxa in the meconium microbiome were also differentially associated with infant excess weight at 12 months of age, however, sample size was limited for this comparison. In conclusion, prenatal and peripartum antibiotic use along with CS delivery were associated with differences in the diversity and composition of the meconium microbiome. Whether or not these differences in the meconium microbiome portend risk for long-term health outcomes warrants further exploration.
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Affiliation(s)
- Wendy S.W. Wong
- Inova Translational Medicine Institute, Falls Church, Inova Fairfax Hospital, Falls Church, VA 22042, USA (V.D.); (S.L.); (N.C.); (M.P.); (R.S.); (A.M.); (K.H.); (J.E.N.)
| | - Priya Sabu
- School of Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Varsha Deopujari
- Inova Translational Medicine Institute, Falls Church, Inova Fairfax Hospital, Falls Church, VA 22042, USA (V.D.); (S.L.); (N.C.); (M.P.); (R.S.); (A.M.); (K.H.); (J.E.N.)
| | - Shira Levy
- Inova Translational Medicine Institute, Falls Church, Inova Fairfax Hospital, Falls Church, VA 22042, USA (V.D.); (S.L.); (N.C.); (M.P.); (R.S.); (A.M.); (K.H.); (J.E.N.)
| | - Ankit A. Shah
- Division of Maternal Fetal Medicine, Department of Ob/Gyn, Inova Fairfax Hospital, Falls Church, VA 22042, USA;
| | - Nicole Clemency
- Inova Translational Medicine Institute, Falls Church, Inova Fairfax Hospital, Falls Church, VA 22042, USA (V.D.); (S.L.); (N.C.); (M.P.); (R.S.); (A.M.); (K.H.); (J.E.N.)
| | - Marina Provenzano
- Inova Translational Medicine Institute, Falls Church, Inova Fairfax Hospital, Falls Church, VA 22042, USA (V.D.); (S.L.); (N.C.); (M.P.); (R.S.); (A.M.); (K.H.); (J.E.N.)
| | - Reem Saadoon
- Inova Translational Medicine Institute, Falls Church, Inova Fairfax Hospital, Falls Church, VA 22042, USA (V.D.); (S.L.); (N.C.); (M.P.); (R.S.); (A.M.); (K.H.); (J.E.N.)
| | - Akhil Munagala
- Inova Translational Medicine Institute, Falls Church, Inova Fairfax Hospital, Falls Church, VA 22042, USA (V.D.); (S.L.); (N.C.); (M.P.); (R.S.); (A.M.); (K.H.); (J.E.N.)
| | - Robin Baker
- Fairfax Neonatal Associates, Falls Church, VA 22042, USA; (R.B.); (R.B.)
| | - Rajiv Baveja
- Fairfax Neonatal Associates, Falls Church, VA 22042, USA; (R.B.); (R.B.)
| | - Noel T. Mueller
- Department of Epidemiology, Johns Hopkins School of Public Health, Baltimore, MD 21205, USA;
| | | | - Kathi Huddleston
- Inova Translational Medicine Institute, Falls Church, Inova Fairfax Hospital, Falls Church, VA 22042, USA (V.D.); (S.L.); (N.C.); (M.P.); (R.S.); (A.M.); (K.H.); (J.E.N.)
- College of Health and Human Services, George Mason University, Fairfax, VA 22030, USA
| | - John E. Niederhuber
- Inova Translational Medicine Institute, Falls Church, Inova Fairfax Hospital, Falls Church, VA 22042, USA (V.D.); (S.L.); (N.C.); (M.P.); (R.S.); (A.M.); (K.H.); (J.E.N.)
- Public Health Sciences, School of Medicine, University of Virginia, Charlottesville, VA 22908, USA
- Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Suchitra K. Hourigan
- Inova Children’s Hospital, Inova Fairfax Hospital, Falls Church, VA 22042, USA
- Pediatric Specialists of Virginia, Fairfax, VA 22031, USA
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12
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Moossavi S, Engen PA, Ghanbari R, Green SJ, Naqib A, Bishehsari F, Merat S, Poustchi H, Keshavarzian A, Malekzadeh R. Assessment of the impact of different fecal storage protocols on the microbiota diversity and composition: a pilot study. BMC Microbiol 2019; 19:145. [PMID: 31253096 PMCID: PMC6599303 DOI: 10.1186/s12866-019-1519-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 06/17/2019] [Indexed: 01/05/2023] Open
Abstract
Background Fecal samples are currently the most commonly studied proxy for gut microbiota. The gold standard of sample handling and storage for microbiota analysis is maintaining the cold chain during sample transfer and immediate storage at − 80 °C. Gut microbiota studies in large-scale, population-based cohorts require a feasible sample collection protocol. We compared the effect of three different storage methods and mock shipment: immediate freezing at − 80 °C, in 95% ethanol stored at room temperature (RT) for 48 h, and on blood collection card stored at RT for 48 h, on the measured composition of fecal microbiota of eight healthy, female volunteers by sequencing the V4 region of the 16S rRNA gene on an Illumina MiSeq. Results Shared operational taxonomic units (OTUs) between different methods were 68 and 3% for OTUs > 0.01 and < 0.01% mean relative abundance within each group, respectively. α and β-diversity measures were not significantly impacted by different storage methods. With the exception of Actinobacteria, fecal microbiota profiles at the phylum level were not significantly affected by the storage method. Actinobacteria was significantly higher in samples collected on card compared to immediate freezing (1.6 ± 1.1% vs. 0.4 ± 0.2%, p = 0.005) mainly driven by expansion of Actinobacteria relative abundance in fecal samples stored on card in two individuals. There was no statistically significant difference at lower taxonomic levels tested. Conclusion Consistent results of the microbiota composition and structure for different storage methods were observed. Fecal collection on card could be a suitable alternative to immediate freezing for fecal microbiota analysis using 16S rRNA gene amplicon sequencing. Electronic supplementary material The online version of this article (10.1186/s12866-019-1519-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shirin Moossavi
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Phillip A Engen
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL, USA
| | - Reza Ghanbari
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran.,Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stefan J Green
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - Ankur Naqib
- Sequencing Core, Research Resources Center, University of Illinois at Chicago, Chicago, IL, USA
| | - Faraz Bishehsari
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL, USA
| | - Shahin Merat
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran.,Liver and Pancreatobiliary Diseases Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Kargar Shomali Avenue, Tehran, Iran
| | - Hossein Poustchi
- Liver and Pancreatobiliary Diseases Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Kargar Shomali Avenue, Tehran, Iran
| | - Ali Keshavarzian
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical Center, Chicago, IL, USA.,Department of Pharmacology, Rush University Medical Center, Chicago, IL, USA.,Department of Physiology, Rush University Medical Center, Chicago, IL, USA.,Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, Netherlands
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran. .,Liver and Pancreatobiliary Diseases Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Kargar Shomali Avenue, Tehran, Iran.
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13
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Wang Z, Zolnik CP, Qiu Y, Usyk M, Wang T, Strickler HD, Isasi CR, Kaplan RC, Kurland IJ, Qi Q, Burk RD. Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies. Front Cell Infect Microbiol 2018; 8:301. [PMID: 30234027 PMCID: PMC6127643 DOI: 10.3389/fcimb.2018.00301] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 08/07/2018] [Indexed: 12/24/2022] Open
Abstract
Background: Integrated microbiome and metabolomics analyses hold the potential to reveal interactions between host and microbiota in relation to disease risks. However, there are few studies evaluating how field methods influence fecal microbiome characterization and metabolomics profiling. Methods: Five fecal collection methods [immediate freezing at -20°C without preservative, OMNIgene GUT, 95% ethanol, RNAlater, and Flinders Technology Associates (FTA) cards] were used to collect 40 fecal samples from eight healthy volunteers. We performed gut microbiota 16S rRNA sequencing, untargeted metabolomics profiling, and targeted metabolomics focusing on short chained fatty acids (SCFAs). Metrics included α-diversity and β-diversity as well as distributions of predominant phyla. To evaluate the concordance with the "gold standard" immediate freezing, the intraclass correlation coefficients (ICCs) for alternate fecal collection systems were calculated. Correlations between SCFAs and gut microbiota were also examined. Results: The FTA cards had the highest ICCs compared to the immediate freezing method for α-diversity indices (ICCs = 0.96, 0.96, 0.76 for Shannon index, Simpson's Index, Chao-1 Index, respectively), followed by OMNIgene GUT, RNAlater, and 95% ethanol. High ICCs (all >0.88) were observed for all methods for the β-diversity metric. For untargeted metabolomics, in comparison to immediate freezing which detected 621 metabolites at ≥75% detectability level, 95% ethanol showed the largest overlapping set of metabolites (n = 430; 69.2%), followed by FTA cards (n = 330; 53.1%) and OMNIgene GUT (n = 213; 34.3%). Both OMNIgene GUT (ICCs = 0.82, 0.93, 0.64) and FTA cards (ICCs = 0.87, 0.85, 0.54) had acceptable ICCs for the top three predominant SCFAs (butyric acid, propionic acid and acetic acid). Nominally significant correlations between bacterial genera and SCFAs (P < 0.05) were observed in fecal samples collected by different methods. Of note, a high correlation between the genus Blautia (known butyrate producer) and butyric acid was observed for both immediate freezing (r = 0.83) and FTA cards (r = 0.74). Conclusions: Four alternative fecal collection methods are generally comparable with immediate freezing, but there are differences in certain measures of the gut microbiome and fecal metabolome across methods. Choice of method depends on the research interests, simplicity of fecal collection procedures and ease of transportation to the lab, especially for large epidemiological studies.
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Affiliation(s)
- Zheng Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Christine P. Zolnik
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Biology, Long Island University, Brooklyn, NY, United States
| | - Yunping Qiu
- Department of Medicine, Stable Isotope and Metabolomics Core Facility, Diabetes Center, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Mykhaylo Usyk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Howard D. Strickler
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Carmen R. Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Irwin J. Kurland
- Department of Medicine, Stable Isotope and Metabolomics Core Facility, Diabetes Center, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
| | - Robert D. Burk
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, United States
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, United States
- Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, United States
- Obstetrics, Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, United States
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