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Yamakawa M, Wada K, Hayashi M, Ezaki T, Nakashima Y, Nagata C, Sumoto Y. Milk and dairy product intakes, intestinal bacteria, and respiratory infections in children of elementary school age and older in Japan. Nutrition 2023; 115:112145. [PMID: 37517304 DOI: 10.1016/j.nut.2023.112145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/11/2023] [Accepted: 06/27/2023] [Indexed: 08/01/2023]
Abstract
OBJECTIVES The aim of this study was to examine the associations between milk and dairy product intakes, intestinal bacteria, and respiratory infections in children of elementary school age and older in Japan. METHODS We conducted cross-sectional surveys each year from 2013 to 2015 for grades 2, 5, and 8 students of an elementary and junior high school (n = 1020). Exclusion owing to ineligibility regarding data on dietary intake, respiratory infections, and intestinal bacteria led to 922 participants for the analyses. Dietary intake was assessed with a self-administered food frequency questionnaire. Respiratory infections occurring ≥ 4 episodes over the past year were determined based on the caregivers' reports. Intestinal bacteria (species and counts) were analyzed with real-time polymerase chain reaction. Logistic regression models were used to estimate the odds ratios (ORs) and 95% CIs. RESULTS The odds of ≥ 4 respiratory infection episodes decreased with higher milk intake after adjusting for potential confounders, and the ORs (95% CIs) for the second and third tertile categories, compared with the first tertile category, were 0.91 (0.58-1.42) and 0.48 (0.29-0.77), respectively (P for trend = 0.001). A decreasing trend in the ORs for lactic acid drink intake was observed only in those with a low count of intestinal Faecalibacterium prausnitzii. CONCLUSIONS We found that higher milk intake was inversely associated with respiratory infections in children older than preschool age. Higher lactic acid drink intake could be inversely associated only in children with a low F. prausnitzii count in the intestine.
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Affiliation(s)
- Michiyo Yamakawa
- Department of Epidemiology and Preventive Medicine, Gifu University Graduate School of Medicine, Gifu, Japan.
| | - Keiko Wada
- Department of Epidemiology and Preventive Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Masahiro Hayashi
- Division of Anaerobe Research, Life Science Research Center, Gifu University, Gifu, Japan; Center for Conservation of Microbial Genetic Resource, Gifu University, Gifu, Japan
| | - Takayuki Ezaki
- Center for Conservation of Microbial Genetic Resource, Gifu University, Gifu, Japan
| | - Yuma Nakashima
- Department of Epidemiology and Preventive Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Chisato Nagata
- Department of Epidemiology and Preventive Medicine, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yoshio Sumoto
- Department of Social Studies Education, Graduate School of Education, Gifu University, Gifu, Japan
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Chai W, Maskarinec G, Lim U, Boushey CJ, Wilkens LR, Setiawan VW, Le Marchand L, Randolph TW, Jenkins IC, Lampe JW, Hullar MA. Association of Habitual Intake of Probiotic Supplements and Yogurt with Characteristics of the Gut Microbiome in the Multiethnic Cohort Adiposity Phenotype Study. GUT MICROBIOME (CAMBRIDGE, ENGLAND) 2023; 4:e14. [PMID: 38468639 PMCID: PMC10927272 DOI: 10.1017/gmb.2023.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Consumption of probiotics and/or yogurt could be a solution for restoring the balance of the gut microbiota. This study examined associations of regular intake of probiotic supplements or yogurt with the gut microbiota among a diverse population of older adults (N=1,861; 60-72 years). Fecal microbial composition was obtained from 16S rRNA gene sequencing (V1-V3 region). General Linear Models were used to estimate the associations of probiotic supplement or yogurt intake with microbiome measures adjusting for covariates. Compared to non-yogurt consumers (N=1,023), regular yogurt consumers (≥once/week, N=818) had greater Streptococcus (β=0.29, P=0.0003) and lower Odoribacter (β=-0.33, P<0.0001) abundance. The directions of the above associations were consistent across the five ethnic groups but stronger among Japanese Americans (Streptococcus: β=0.56, P=0.0009; Odoribacter: β=-0.62, P=0.0005). Regular intake of probiotic supplements (N=175) was not associated with microbial characteristics (i.e., alpha diversity and the abundance of 152 bacteria genera). Streptococcus is one of the predominant bacteria genera in yogurt products, which may explain the positive association between yogurt consumption and Streptococcus abundance. Our analyses suggest that changes in Odoribacter were independent of changes in Streptococcus abundance. Future studies may investigate whether these microbial genera and their sub-level species mediate potential pathways between yogurt consumption and health.
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Affiliation(s)
- Weiwen Chai
- Department of Nutrition and Health Sciences, University of Nebraska-Lincoln, Lincoln, NE
| | | | - Unhee Lim
- University of Hawai’i Cancer Center, Honolulu, HI
| | | | | | - V. Wendy Setiawan
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA
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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: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [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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Gut Microbiome Proteomics in Food Allergies. Int J Mol Sci 2023; 24:ijms24032234. [PMID: 36768555 PMCID: PMC9917015 DOI: 10.3390/ijms24032234] [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: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Food allergies (FA) have dramatically increased in recent years, particularly in developed countries. It is currently well-established that food tolerance requires the strict maintenance of a specific microbial consortium in the gastrointestinal (GI) tract microbiome as alterations in the gut microbiota can lead to dysbiosis, causing inflammation and pathogenic intestinal conditions that result in the development of FA. Although there is currently not enough knowledge to fully understand how the interactions between gut microbiota, host responses and the environment cause food allergies, recent advances in '-omics' technologies (i.e., proteomics, genomics, metabolomics) and in approaches involving systems biology suggest future headways that would finally allow the scientific understanding of the relationship between gut microbiome and FA. This review summarizes the current knowledge in the field of FA and insights into the future advances that will be achieved by applying proteomic techniques to study the GI tract microbiome in the field of FA and their medical treatment. Metaproteomics, a proteomics experimental approach of great interest in the study of GI tract microbiota, aims to analyze and identify all the proteins in complex environmental microbial communities; with shotgun proteomics, which uses liquid chromatography (LC) for separation and tandem mass spectrometry (MS/MS) for analysis, as it is the most promising technique in this field.
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Frankenfeld CL. Fecal Metabolome: New Addition to the Toolbox for Dietary Assessment? J Nutr 2023; 152:2643-2644. [PMID: 36288243 DOI: 10.1093/jn/nxac233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Mattes RD, Rowe SB, Ohlhorst SD, Brown AW, Hoffman DJ, Liska DJ, Feskens EJM, Dhillon J, Tucker KL, Epstein LH, Neufeld LM, Kelley M, Fukagawa NK, Sunde RA, Zeisel SH, Basile AJ, Borth LE, Jackson E. Valuing the Diversity of Research Methods to Advance Nutrition Science. Adv Nutr 2022; 13:1324-1393. [PMID: 35802522 PMCID: PMC9340992 DOI: 10.1093/advances/nmac043] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 12/13/2022] Open
Abstract
The ASN Board of Directors appointed the Nutrition Research Task Force to develop a report on scientific methods used in nutrition science to advance discovery, interpretation, and application of knowledge in the field. The genesis of this report was growing concern about the tone of discourse among nutrition professionals and the implications of acrimony on the productive study and translation of nutrition science. Too often, honest differences of opinion are cast as conflicts instead of areas of needed collaboration. Recognition of the value (and limitations) of contributions from well-executed nutrition science derived from the various approaches used in the discipline, as well as appreciation of how their layering will yield the strongest evidence base, will provide a basis for greater productivity and impact. Greater collaborative efforts within the field of nutrition science will require an understanding that each method or approach has a place and function that should be valued and used together to create the nutrition evidence base. Precision nutrition was identified as an important emerging nutrition topic by the preponderance of task force members, and this theme was adopted for the report because it lent itself to integration of many approaches in nutrition science. Although the primary audience for this report is nutrition researchers and other nutrition professionals, a secondary aim is to develop a document useful for the various audiences that translate nutrition research, including journalists, clinicians, and policymakers. The intent is to promote accurate, transparent, verifiable evidence-based communication about nutrition science. This will facilitate reasoned interpretation and application of emerging findings and, thereby, improve understanding and trust in nutrition science and appropriate characterization, development, and adoption of recommendations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Leonard H Epstein
- University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | | | - Michael Kelley
- Michael Kelley Nutrition Science Consulting, Wauwatosa, WI, USA
| | - Naomi K Fukagawa
- USDA Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | | | - Steven H Zeisel
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Qian SJ, Liu B, Shi J, Zhang X, Deng K, Shen J, Tao Y, Qiao S, Lai HC, Yuan C, Tonetti MS. Effects of Dental Implants and Nutrition on Elderly Edentulous Subjects: Protocol for a Factorial Randomized Clinical Trial. Front Nutr 2022; 9:930023. [PMID: 35832045 PMCID: PMC9272417 DOI: 10.3389/fnut.2022.930023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
Background Loss of masticatory function consequent to tooth loss has been associated with changes in food choices and insufficient nutritional intake. To date, interventions based on dental prostheses alone did not significantly improve nutrient intake. Pilot studies have shown positive impacts of interventions combining implant-supported fixed dental prosthesis with brief dietary advice. The relative contribution and the potential synergy of the components of such interventions need to be determined as it has major public health implications for the community-dwelling aging population that continues to disproportionately suffer from tooth loss and its consequences. Objective To assess the effect of rehabilitation of masticatory function with fixed implant supported dentures and nutrition education in older subjects with terminal dentition (stage IV periodontitis) or full edentulism. Methods A 2 × 2 factorial randomized controlled trial with 16-month follow-up of eligible adults (≥60 years) with loss of masticatory function consequent to full arch edentulism or terminal dentition (n = 120) will be conducted to test whether the rehabilitation of masticatory function with fixed implant supported dentures, nutrition education and/or their combination improves intake of fresh fruits and vegetables for aging subjects. The study has been designed to detect changes in fresh fruits and fresh vegetables intake at 4 months using the 24-h dietary recall method. Changes in protein as percentage of total energy, nutritional biomarkers, plasma metabolomics, oral and gut microbiome, quality of life and masticatory function will also be assessed. Discussion We hypothesize that receiving rehabilitation of masticatory function with fixed implant dentures together with nutrition education is the most effective intervention for improving nutrient intake in aging community-dwelling subjects with extensive tooth loss. The results of this study will assist in designing better treatment regimens, guide medical care for individual subjects, and inform public health and policy. Clinical Trials Registration NCT05334407.
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Affiliation(s)
- Shu-Jiao Qian
- Shanghai PerioImplant Innovation Center, Department of Oral and Maxillofacial Implantology, National Clinical Research Center of Stomatology, Ninth People's Hospital, College of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Beilei Liu
- Shanghai PerioImplant Innovation Center, Department of Oral and Maxillofacial Implantology, National Clinical Research Center of Stomatology, Ninth People's Hospital, College of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Junyu Shi
- Shanghai PerioImplant Innovation Center, Department of Oral and Maxillofacial Implantology, National Clinical Research Center of Stomatology, Ninth People's Hospital, College of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Zhang
- Shanghai PerioImplant Innovation Center, Department of Oral and Maxillofacial Implantology, National Clinical Research Center of Stomatology, Ninth People's Hospital, College of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ke Deng
- Shanghai PerioImplant Innovation Center, Department of Oral and Maxillofacial Implantology, National Clinical Research Center of Stomatology, Ninth People's Hospital, College of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jie Shen
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Yang Tao
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
| | - Shichong Qiao
- Shanghai PerioImplant Innovation Center, Department of Oral and Maxillofacial Implantology, National Clinical Research Center of Stomatology, Ninth People's Hospital, College of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hong-Chang Lai
- Shanghai PerioImplant Innovation Center, Department of Oral and Maxillofacial Implantology, National Clinical Research Center of Stomatology, Ninth People's Hospital, College of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Changzheng Yuan
- School of Public Health, Zhejiang University School of Medicine, Hangzhou, China
- Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, United States
- Changzheng Yuan
| | - Maurizio S. Tonetti
- Shanghai PerioImplant Innovation Center, Department of Oral and Maxillofacial Implantology, National Clinical Research Center of Stomatology, Ninth People's Hospital, College of Medicine, Shanghai Jiao Tong University, Shanghai, China
- European Research Group on Periodontology, Genova, Italy
- *Correspondence: Maurizio S. Tonetti
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Lozano CP, Wilkens LR, Shvetsov YB, Maskarinec G, Park SY, Shepherd JA, Boushey CJ, Hebert JR, Wirth MD, Ernst T, Randolph T, Lim U, Lampe JW, Le Marchand L, Hullar MAJ. Associations of the Dietary Inflammatory Index with total adiposity and ectopic fat through the gut microbiota, LPS, and C-reactive protein in the Multiethnic Cohort-Adiposity Phenotype Study. Am J Clin Nutr 2022; 115:1344-1356. [PMID: 34871345 PMCID: PMC9071464 DOI: 10.1093/ajcn/nqab398] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/29/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Mechanisms linking a proinflammatory diet to obesity remain under investigation. The ability of diet to influence the gut microbiome (GM) in creating chronic low-grade systemic inflammation provides a plausible connection to adiposity. OBJECTIVES Assess whether any associations seen between the Energy-Adjusted Dietary Inflammatory Index (E-DII score), total fat mass, visceral adipose tissue (VAT), or liver fat (percentage volume) operated through the GM or microbial related inflammatory factors, in a multiethnic cross-sectional study. METHODS In the Multiethnic Cohort-Adiposity Phenotype Study (812 men, 843 women, aged 60-77 y) we tested whether associations between the E-DII and total adiposity, VAT, and liver fat function through the GM, LPS, and high-sensitivity C-reactive protein (hs-CRP). DXA-derived total fat mass, MRI-measured VAT, and MRI-based liver fat were measured. Participants provided stool and fasting blood samples and completed an FFQ. Stool bacterial DNA was amplified and the 16S rRNA gene was sequenced at the V1-V3 region. E-DII score was computed from FFQ data, with a higher E-DII representing a more proinflammatory diet. The associations between E-DII score, GM (10 phyla, 28 genera, α diversity), and adiposity phenotypes were examined using linear regression and mediation analyses, adjusting for confounders. RESULTS There were positive total effects (c) between E-DII and total fat mass (c = 0.68; 95% CI: 0.47, 0.90), VAT (c = 4.61; 95% CI: 2.95, 6.27), and liver fat (c = 0.40; 95% CI: 0.27, 0.53). The association between E-DII score and total fat mass was mediated by LPS, Flavonifractor, [Ruminococcus] gnavus group, and Tyzzerella. The association between E-DII score and ectopic fat occurred indirectly through Fusobacteria, Christensenellaceae R-7 group, Coprococcus 2, Escherichia-Shigella, [Eubacterium] xylanophilum group, Flavonifractor, Lachnoclostridium, [Ruminococcus] gnavus group, Tyzzerella, [Ruminococcus] gnavus group (VAT only), and α diversity (liver fat only). There was no significant association between E-DII score and adiposity phenotype through hs-CRP. CONCLUSIONS Associations found between E-DII and adiposity phenotypes occurred through the GM and LPS.
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Affiliation(s)
| | | | | | | | - Song-Yi Park
- University of Hawaii Cancer Center, Honolulu, HI, USA
| | | | | | - James R Hebert
- University of South Carolina,Cancer Prevention and Control Program, Department of Epidemiology and Biostatistics, Arnold School of Public Health, Columbia, SC, USA
| | - Michael D Wirth
- University of South Carolina,Cancer Prevention and Control Program, Department of Epidemiology and Biostatistics, Arnold School of Public Health, Columbia, SC, USA
| | - Thomas Ernst
- University of Maryland, Department of Diagnostic Radiology and Nuclear Medicine, Baltimore, MD, USA
| | - Timothy Randolph
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA, USA
| | - Unhee Lim
- University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Johanna W Lampe
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA, USA
| | | | - Meredith A J Hullar
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Seattle, WA, USA
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Dietary Intake Mediates Ethnic Differences in Gut Microbial Composition. Nutrients 2022; 14:nu14030660. [PMID: 35277019 PMCID: PMC8840192 DOI: 10.3390/nu14030660] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/16/2022] Open
Abstract
Background: The human gut microbiome (GM) has been observed to vary by race/ethnicity. Objective: Assess whether racial/ethnic GM variation is mediated by differences in diet. Design: Stool samples collected from 2013 to 2016 from 5267 healthy Multiethnic Cohort participants (age 59−98) were analyzed using 16S rRNA gene sequencing to estimate the relative abundance of 152 bacterial genera. For 63 prevalent genera (>50% in each ethnic group), we analyzed the mediation of GM differences among African Americans, Japanese Americans, Latinos, Native Hawaiians, and Whites by overall diet quality (Healthy Eating Index score (HEI-2015)) and intake amounts of 14 component foods/nutrients assessed from 2003 to 2008. For each significant mediation (p < 1.3 × 10−5), we determined the percent of the total ethnicity effect on genus abundance mediated by the dietary factor. Results: Ethnic differences in the abundance of 12 genera were significantly mediated by one or more of eight dietary factors, most frequently by overall diet quality and intakes of vegetables and red meat. Lower vegetable intake mediated differences in Lachnospira (36% in African Americans, 39% in Latinos) and Ruminococcus-1 (−35% in African Americans, −43% in Latinos) compared to Native Hawaiians who consumed the highest amount. Higher red meat intake mediated differences in Lachnospira (−41%) and Ruminococcus-1 (36%) in Native Hawaiians over African Americans, who consumed the least. Dairy and alcohol intakes appeared to mediate and counterbalance the difference in Bifidobacterium between Whites and Japanese Americans. Conclusions: Overall diet quality and component food intakes may contribute to ethnic differences in GM composition and to GM-related racial/ethnic health disparities.
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Wu F, Davey S, Clendenen TV, Koenig KL, Afanasyeva Y, Zhou B, Bedi S, Li H, Zeleniuch-Jacquotte A, Chen Y. Gut Microbiota and Subjective Memory Complaints in Older Women. J Alzheimers Dis 2022; 88:251-262. [PMID: 35570486 PMCID: PMC9987476 DOI: 10.3233/jad-220011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Epidemiological studies that investigate alterations in gut microbial composition associated with cognitive dysfunction are limited. OBJECTIVE To examine the association between the gut microbiota and subjective memory complaints (SMCs), a self-reported, validated indicator of cognitive dysfunction. METHODS In this cross-sectional study of 95 older women selected from the New York University Women's Health Study (NYUWHS), we characterized the gut microbial composition using 16S rRNA gene sequencing. We estimated odds ratio (OR) from beta regression which approximates the ratio of mean relative abundances of individual bacterial taxon from phylum to genus levels by binary (2+ versus < 2) and continuous SMCs. RESULTS Women reporting 2 or more SMCs had higher relative abundances of genus Holdemania and family Desulfovibrionaceae compared with those reporting one or no complaint. Compared with women with < 2 SMCs, the relative abundances of Holdemania and family Desulfovibrionaceae were 2.09 times (OR: 2.09, 95% confidence interval [CI]: 1.38-3.17) and 2.10 times (OR: 2.10, 95% CI: 1.43-3.09) higher in women with 2+ SMCs, respectively (false discovery rate (FDR)-adjusted p = 0.038 and 0.010, respectively). A dose-response association was observed for genus Sutterella and family Desulfovibrionaceae. Every one-unit increase in SMCs was associated with 25% and 27% higher relative abundances of Sutterella (OR: 1.25; 95% CI: 1.11-1.40) and Desulfovibrionaceae (OR: 1.27; 95% CI: 1.13-1.42), respectively (FDR-adjusted p = 0.018 and 0.006, respectively). CONCLUSION Our findings support an association between alterations in the gut bacterial composition and cognitive dysfunction.
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Affiliation(s)
- Fen Wu
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Samuel Davey
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Tess V Clendenen
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Karen L Koenig
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Yelena Afanasyeva
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Boyan Zhou
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Sukhleen Bedi
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | - Huilin Li
- Department of Population Health, New York University School of Medicine, New York, NY, USA
| | | | - Yu Chen
- Department of Population Health, New York University School of Medicine, New York, NY, USA
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Ma E, Maskarinec G, Lim U, Boushey CJ, Wilkens LR, Setiawan VW, Le Marchand L, Randolph TW, Jenkins IC, Curtis KR, Lampe JW, Hullar MA. Long-term association between diet quality and characteristics of the gut microbiome in the multiethnic cohort study. Br J Nutr 2021; 128:1-10. [PMID: 34369335 PMCID: PMC8825880 DOI: 10.1017/s0007114521002968] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As past usual diet quality may affect gut microbiome (GM) composition, we examined the association of the Healthy Eating Index (HEI)-2015 assessed 21 and 9 years before stool collection with measures of fecal microbial composition in a subset of the Multiethnic Cohort. A total of 5936 participants completed a validated quantitative FFQ (QFFQ) at cohort entry (Q1, 1993-1996), 5280 at follow-up (Q3, 2003-2008) and 1685 also at a second follow-up (Adiposity Phenotype Study (APS), 2013-2016). All participants provided a stool sample in 2013-2016. Fecal microbial composition was obtained from 16S rRNA gene sequencing (V1-V3 regions). HEI-2015 scores were computed based on each QFFQ. Using linear regression adjusted for relevant covariates, we calculated associations of HEI-2015 scores with gut microbial diversity and 152 individual genera. The mean HEI-2015 scores increased from Q1 (67 (sd 10)) to Q3 (71 (sd 11)) and APS (72 (sd 10)). Alpha diversity assessed by the Shannon Index was significantly higher with increasing tertiles of HEI-2015. Of the 152 bacterial genera tested, seven (Anaerostipes, Coprococcus_2, Eubacterium eligens, Lachnospira, Lachnospiraceae_ND3007, Ruminococcaceae_UCG-013 and Ruminococcus_1) were positively and five (Collinsella, Parabacteroides, Ruminiclostridium_5, Ruminococcus gnavus and Tyzzerella) were inversely associated with HEI-2015 assessed in Q1, Q3 and APS. The estimates of change per unit of the HEI-2015 score associated with the abundance of these twelve genera were consistent across the three questionnaires. The quality of past diet, assessed as far as ∼20 years before stool collection, is equally predictive of GM composition as concurrently assessed diet, indicative of the long-term consistency of this relation.
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Affiliation(s)
- Erica Ma
- University of Hawai’i Cancer Center, Honolulu, HI
| | | | - Unhee Lim
- University of Hawai’i Cancer Center, Honolulu, HI
| | | | | | - V. Wendy Setiawan
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA
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Newland GAI, Gibson GR, Jackson FL, Wijeyesekera A. Assessment of stool collection and storage conditions for in vitro human gut model studies. J Microbiol Methods 2021; 185:106230. [PMID: 33933521 DOI: 10.1016/j.mimet.2021.106230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND The role of the gut microbiota in health and disease is becoming increasingly apparent. Faeces is the most accessible sample to collect from human volunteers for studying the gut microbiota. However, the impact of stool collection and storage conditions on microbial and metabolic profiles have not been fully evaluated. By understanding the effect of different stool collection and storage conditions on microbial and metabolic composition, we can consider these parameters in the design of in vitro fermentation studies. METHODS Stool samples from 3 volunteers were stored under 5 different conditions to mimic methods that researchers may use to collect and store stool samples for study of the gut microbiota, including: fresh sample used within 10 min; stored on wet ice (4 °C) for 60 min; stored in an anaerobic chamber in a temperature-controlled bag (4 °C) for 60 min; freezing at -20 °C for 60 min and freezing at -20 °C for 60 min and then at -80 °C for 2 weeks. The stored samples were added to basal medium in batch culture fermenters alone (negative control) or with 5 g 2'-Fucosyllactose (2'FL) Human Milk Oligosaccharide (HMO) (as a positive fermentation control). Samples were collected at 3 timepoints (0, 12 and 24 h) for analysis by Flow Cytometry-Fluorescent In Situ Hybridisation (FC-FISH) and 1H-Nuclear Magnetic Resonance (NMR) spectroscopy to assess the impact on microbial and metabolic profiles, respectively. RESULTS Freezing stool significantly impacted microbial numbers and activity during in vitro fermentations, whereas storing the stool on wet ice (4 °C) or in an anaerobic chamber at 4 °C for 60 min had minimal effects on microbial and metabolic profiles throughout the 24 h batch culture fermentation experiments. DISCUSSION For in vitro batch culture fermentation studies where it may not be practical or possible to use fresh stool, either storing the stool on wet ice (4 °C) or in an anaerobic chamber at 4 °C for 60 min could be plausible alternatives to maintain microbial and metabolic profiles for analysis.
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Affiliation(s)
- Grace A I Newland
- Food Microbial Sciences Unit, Department of Food and Nutritional Sciences, University of Reading, Reading RG6 6AP, UK
| | - Glenn R Gibson
- Food Microbial Sciences Unit, Department of Food and Nutritional Sciences, University of Reading, Reading RG6 6AP, UK
| | - Frances L Jackson
- Food Microbial Sciences Unit, Department of Food and Nutritional Sciences, University of Reading, Reading RG6 6AP, UK
| | - Anisha Wijeyesekera
- Food Microbial Sciences Unit, Department of Food and Nutritional Sciences, University of Reading, Reading RG6 6AP, UK.
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13
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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] [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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14
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McCann SE, Hullar MA, Tritchler DL, Cortes-Gomez E, Yao S, Davis W, O’Connor T, Erwin D, Thompson LU, Yan L, Lampe JW. Enterolignan Production in a Flaxseed Intervention Study in Postmenopausal US Women of African Ancestry and European Ancestry. Nutrients 2021; 13:nu13030919. [PMID: 33809130 PMCID: PMC8001909 DOI: 10.3390/nu13030919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/08/2021] [Accepted: 03/10/2021] [Indexed: 12/22/2022] Open
Abstract
Lignans are phytochemicals studied extensively as dietary factors in chronic disease etiology. Our goal was to examine associations between the gut microbiota and lignan metabolism and whether these associations differ by ethnicity. We conducted a flaxseed (FS) dietary intervention in 252 healthy, postmenopausal women of African ancestry (AA) and European ancestry (EA). Participants consumed ~10 g/d ground flaxseed for 6 weeks and provided overnight urine collections and fecal samples before and after intervention. The gut microbiota was characterized using 16S rRNA gene sequencing and differences in microbial community composition compared by ethnicity and intervention status. We observed a significant difference in the composition of the microbiota measured as beta diversity (p < 0.05) between AA and EA at baseline that was attenuated with FS consumption. Genera that were significantly associated with ENL production (e.g., Klebsiella, Lactobacillus, Slackia, Senegalimassilia) were unique to each group. Bacteria (e.g., Fusobacteria, Pyramidobacter and Odoribacter) previously associated with colorectal cancer and cardiovascular disease, both diet-related chronic diseases, were unique to either AA or EA and were significantly reduced in the FS intervention. This study suggests that ethnic variation in ENL metabolism may be linked to gut microbiota composition, and its impact on disease risk deserves future investigation.
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Affiliation(s)
- Susan E. McCann
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (S.Y.); (W.D.); (D.E.)
- Correspondence: ; Tel.: +1-716-845-8842
| | - Meredith A.J. Hullar
- Cancer Prevention Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (M.A.J.H.); (J.W.L.)
| | - David L. Tritchler
- Department of Biostatistics, University at Buffalo, Buffalo, NY 14214, USA;
| | - Eduardo Cortes-Gomez
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (E.C.-G.); (L.Y.)
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (S.Y.); (W.D.); (D.E.)
| | - Warren Davis
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (S.Y.); (W.D.); (D.E.)
| | - Tracey O’Connor
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA;
| | - Deborah Erwin
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (S.Y.); (W.D.); (D.E.)
| | - Lilian U. Thompson
- Department of Nutritional Sciences, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Li Yan
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA; (E.C.-G.); (L.Y.)
| | - Johanna W. Lampe
- Cancer Prevention Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (M.A.J.H.); (J.W.L.)
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15
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Hullar MAJ, Jenkins IC, Randolph TW, Curtis KR, Monroe KR, Ernst T, Shepherd JA, Stram DO, Cheng I, Kristal BS, Wilkens LR, Franke A, Le Marchand L, Lim U, Lampe JW. Associations of the gut microbiome with hepatic adiposity in the Multiethnic Cohort Adiposity Phenotype Study. Gut Microbes 2021; 13:1965463. [PMID: 34491886 PMCID: PMC8425768 DOI: 10.1080/19490976.2021.1965463] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/09/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a risk factor for liver cancer and prevalence varies by ethnicity. Along with genetic and lifestyle factors, the gut microbiome (GM) may contribute to NAFLD and its progression to advanced liver disease. Our cross-sectional analysis assessed the association of the GM with hepatic adiposity among African American, Japanese American, White, Latino, and Native Hawaiian participants in the Multiethnic Cohort. We used MRI to measure liver fat and determine nonalcoholic fatty liver disease (NAFLD) status (n = 511 cases) in 1,544 participants, aged 60-77 years, with 12-53% overall adiposity (BMI of 17.8-46.2 kg/m2). The GM was measured by 16S rRNA gene sequencing and, on a subset, by metagenomic sequencing. Alpha diversity was lower overall with NAFLD and in certain ethnicities (African Americans, Whites, and Latinos). In models regressing genus on NAFLD status, 62 of 149 genera (40%) exhibited a significant interaction between NAFLD and ethnicity stratified analysis found 69 genera significantly associated with NAFLD in at least one ethnic group. No single genus was significantly associated with NAFLD across all ethnicities. In contrast, the same bacterial metabolic pathways were over-represented in participants with NAFLD regardless of ethnicity. Imputed secondary bile acid and carbohydrate pathways were associated with NAFLD, the latter of which was corroborated by metagenomics, although different genera in different ethnicities were associated with these pathways. Overall, we found that NAFLD was associated with altered bacterial composition and metabolism, and that bacterial endotoxin, assessed by plasma lipopolysaccharide binding protein (LBP), may mediate liver fat-associated systemic inflammation in a manner that seems to vary by ethnicity.
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Affiliation(s)
- Meredith A. J. Hullar
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
| | - Isaac C. Jenkins
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
| | - Timothy W. Randolph
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
| | - Keith R. Curtis
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
| | - Kristine R. Monroe
- Preventive Medicine, Keck School Of Medicine, University Of Southern California, Los Angeles, California, U.S.A
| | - Thomas Ernst
- John A. Burns School Of Medicine, University Of Hawaii, Honolulu, Hawaii, U.S.A
| | - John A. Shepherd
- University Of Hawaii Cancer Center, University Of Hawaii, Honolulu, Hawaii, U.S.A
| | - Daniel O. Stram
- Keck School Of Medicine, University Of Southern California, Los Angeles, California, U.S.A
| | - Iona Cheng
- School Of Medicine, University Of California San Francisco, San Francisco, California, U.S.A
| | - Bruce S. Kristal
- Department Of Medicine, Brigham And Women’s Hospital And Harvard Medical School, Boston, Massachusetts, U.S.A
| | - Lynne R. Wilkens
- University Of Hawaii Cancer Center, University Of Hawaii, Honolulu, Hawaii, U.S.A
| | - Adrian Franke
- University Of Hawaii Cancer Center, University Of Hawaii, Honolulu, Hawaii, U.S.A
| | - Loic Le Marchand
- University Of Hawaii Cancer Center, University Of Hawaii, Honolulu, Hawaii, U.S.A
| | - Unhee Lim
- University Of Hawaii Cancer Center, University Of Hawaii, Honolulu, Hawaii, U.S.A
| | - Johanna W. Lampe
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, U.S.A
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16
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Gicquelais RE, Bohnert ASB, Thomas L, Foxman B. Opioid agonist and antagonist use and the gut microbiota: associations among people in addiction treatment. Sci Rep 2020; 10:19471. [PMID: 33173098 PMCID: PMC7655955 DOI: 10.1038/s41598-020-76570-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/28/2020] [Indexed: 12/11/2022] Open
Abstract
Murine models suggest that opioids alter the gut microbiota, which may impact opioid tolerance and psychopathology. We examined how gut microbiota characteristics related to use of opioid agonists and antagonists among people receiving outpatient addiction treatment. Patients (n = 46) collected stool samples and were grouped by use of opioid agonists (heroin, prescription opioids), antagonists (naltrexone), agonist-antagonist combinations (buprenorphine-naloxone), or neither agonists nor antagonists within the month before enrollment. We sequenced the V4 region of the 16S rRNA gene using Illumina MiSeq to examine how alpha diversity, enterotypes, and relative abundance of bacterial genera varied by opioid agonist and antagonist exposures. Compared to 31 participants who used neither agonists nor antagonists, 5 participants who used opioid agonists (without antagonists) had lower microbiota diversity, Bacteroides enterotypes, and lower relative abundance of Roseburia, a butyrate producing genus, and Bilophila, a bile acid metabolizing genus. There were no differences in gut microbiota features between those using agonist + antagonists (n = 4), antagonists only (n = 6), and neither agonists nor antagonists. Similar to murine morphine exposure models, opioid agonist use was associated with lower microbiota diversity. Lower abundance of Roseburia and Bilophila may relate to the gut inflammation/permeability and dysregulated bile acid metabolism observed in opioid-exposed mice.
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Affiliation(s)
- Rachel E Gicquelais
- University of Wisconsin-Madison School of Nursing, 701 Highland Avenue, Madison, WI, 53705, USA.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe St, Baltimore, MD, 21205, USA.
- Department of Epidemiology, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
- Department of Psychiatry, University of Michigan Medical School, 2800 Plymouth Rd, Ann Arbor, MI, 48109, USA.
| | - Amy S B Bohnert
- Department of Psychiatry, University of Michigan Medical School, 2800 Plymouth Rd, Ann Arbor, MI, 48109, USA
- VA Center for Clinical Management Research, 2800 Plymouth Rd, Ann Arbor, MI, 48109, USA
- Department of Anesthesiology, University of Michigan Medical School, Ann Arbor, 48109, USA
| | - Laura Thomas
- Department of Psychiatry, University of Michigan Medical School, 2800 Plymouth Rd, Ann Arbor, MI, 48109, USA
- VA Center for Clinical Management Research, 2800 Plymouth Rd, Ann Arbor, MI, 48109, USA
| | - Betsy Foxman
- Department of Epidemiology, University of Michigan Medical School, 1415 Washington Heights, Ann Arbor, MI, 48109, USA.
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17
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Sutherland VL, McQueen CA, Mendrick D, Gulezian D, Cerniglia C, Foley S, Forry S, Khare S, Liang X, Manautou JE, Tweedie D, Young H, Alekseyenko AV, Burns F, Dietert R, Wilson A, Chen C. The Gut Microbiome and Xenobiotics: Identifying Knowledge Gaps. Toxicol Sci 2020; 176:1-10. [PMID: 32658296 PMCID: PMC7850111 DOI: 10.1093/toxsci/kfaa060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
There is an increasing awareness that the gut microbiome plays a critical role in human health and disease, but mechanistic insights are often lacking. In June 2018, the Health and Environmental Sciences Institute (HESI) held a workshop, "The Gut Microbiome: Markers of Human Health, Drug Efficacy and Xenobiotic Toxicity" (https://hesiglobal.org/event/the-gut-microbiome-workshop) to identify data gaps in determining how gut microbiome alterations may affect human health. Speakers and stakeholders from academia, government, and industry addressed multiple topics including the current science on the gut microbiome, endogenous and exogenous metabolites, biomarkers, and model systems. The workshop presentations and breakout group discussions formed the basis for identifying data gaps and research needs. Two critical issues that emerged were defining the microbial composition and function related to health and developing standards for models, methods and analysis in order to increase the ability to compare and replicate studies. A series of key recommendations were formulated to focus efforts to further understand host-microbiome interactions and the consequences of exposure to xenobiotics as well as identifying biomarkers of microbiome-associated disease and toxicity.
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Affiliation(s)
- Vicki L Sutherland
- National Toxicology Program, National Institute of Environmental Health Sciences, Durham, North Carolina 27709
| | - Charlene A McQueen
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, Arizona 85721
| | - Donna Mendrick
- National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, MD 20993
| | | | - Carl Cerniglia
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07033
| | - Steven Foley
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07033
| | - Sam Forry
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Sangeeta Khare
- National Center for Toxicological Research, US Food and Drug Administration, Silver Spring, MD 20993
| | - Xue Liang
- Merck Exploratory Science Center, Merck & Co., Inc., Cambridge, Massachusetts 02141
| | - Jose E Manautou
- Department of Pharmaceutics, University of Connecticut, Storrs, Connecticut 06269
| | - Donald Tweedie
- Department of Pharmacokinetics, Pharmacodynamics and Drug Metabolism, Merck & Co., Inc., Kenilworth, New Jersey 07033
| | - Howard Young
- Laboratory of Cancer Immunometabolism, Center for Cancer Research, NCI Frederick, Frederick, Maryland 21702
| | - Alexander V Alekseyenko
- Program for Human Microbiome Research, Biomedical Informatics Center, Department of Public Health Sciences, Department of Oral Health Sciences, Department of Healthcare Leadership & Management, Medical University of South Carolina, Charleston, South Carolina 29425
| | | | - Rod Dietert
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York 14850
| | - Alan Wilson
- Department of Drug Metabolism, Pharmacokinetics, Toxicology and Pathology, Lexicon Pharmaceuticals, Houston, Texas 77381
| | - Connie Chen
- Health and Environmental Sciences Institute, Washington, District of Columbia 20005
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18
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Toker J, Arora R, Wargo JA. The Microbiome in Immuno-oncology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1244:325-334. [PMID: 32301026 DOI: 10.1007/978-3-030-41008-7_19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The field of cancer therapy has been revolutionized through the use of immunotherapy, and treatment with these therapies now spans from early to late stage, and even into prevention. However, there are still a significant proportion of patients who do not derive long-term benefit from monotherapy and even combined therapy regimens, and novel approaches are needed to enhance therapeutic responses. Additionally, ideal biomarkers of response to immunotherapy are lacking and are critically needed. An emerging area of interest in immuno-oncology (IO) is the microbiome, which refers to the collection of microbes (and their genomes) that inhabit an individual and live in symbiosis. There is now evidence that these microbes (particularly those within the gut) impact host physiology and can impact responses to immunotherapy. The field of microbiome research in immuno-oncology is quickly emerging, with the potential use of the microbiome (in the gut as well as in the tumor) as a biomarker for response to IO as well as a therapeutic target. Notably, the microbiome may even have a role in toxicity to therapy. The state of the science in microbiome and IO are discussed and caveats and future directions are outlined to provide insights as we move forward as a field.
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Affiliation(s)
- Joseph Toker
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Reetakshi Arora
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jennifer A Wargo
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. .,Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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19
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Fu BC, Hullar MAJ, Randolph TW, Franke AA, Monroe KR, Cheng I, Wilkens LR, Shepherd JA, Madeleine MM, Le Marchand L, Lim U, Lampe JW. Associations of plasma trimethylamine N-oxide, choline, carnitine, and betaine with inflammatory and cardiometabolic risk biomarkers and the fecal microbiome in the Multiethnic Cohort Adiposity Phenotype Study. Am J Clin Nutr 2020; 111:1226-1234. [PMID: 32055828 PMCID: PMC7266689 DOI: 10.1093/ajcn/nqaa015] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/22/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Trimethylamine N-oxide (TMAO), a compound derived from diet and metabolism by the gut microbiome, has been associated with several chronic diseases, although the mechanisms of action are not well understood and few human studies have investigated microbes involved in its production. OBJECTIVES Our study aims were 1) to investigate associations of TMAO and its precursors (choline, carnitine, and betaine) with inflammatory and cardiometabolic risk biomarkers; and 2) to identify fecal microbiome profiles associated with TMAO. METHODS We conducted a cross-sectional analysis using data collected from 1653 participants (826 men and 827 women, aged 60-77 y) in the Multiethnic Cohort Study. Plasma concentrations of TMAO and its precursors were measured by LC-tandem MS. We also analyzed fasting blood for markers of inflammation, glucose and insulin, cholesterol, and triglycerides (TGs), and further measured blood pressure. Fecal microbiome composition was evaluated by sequencing the 16S ribosomal RNA gene V1-V3 region. Associations of TMAO and its precursors with disease risk biomarkers were assessed by multivariable linear regression, whereas associations between TMAO and the fecal microbiome were assessed by permutational multivariate ANOVA and hurdle regression models using the negative binomial distribution. RESULTS Median (IQR) concentration of plasma TMAO was 3.05 μmol/L (2.10-4.60 μmol/L). Higher concentrations of TMAO and carnitine, and lower concentrations of betaine, were associated with greater insulin resistance (all P < 0.02). Choline was associated with higher systolic blood pressure, TGs, lipopolysaccharide-binding protein, and lower HDL cholesterol (P ranging from <0.001 to 0.03), reflecting an adverse cardiometabolic risk profile. TMAO was associated with abundance of 13 genera (false discovery rate < 0.05), including Prevotella, Mitsuokella, Fusobacterium, Desulfovibrio, and bacteria belonging to the families Ruminococcaceae and Lachnospiraceae, as well as the methanogen Methanobrevibacter smithii. CONCLUSIONS Plasma TMAO concentrations were associated with a number of trimethylamine-producing bacterial taxa, and, along with its precursors, may contribute to inflammatory and cardiometabolic risk pathways.
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Affiliation(s)
- Benjamin C Fu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA,Department of Epidemiology, University of Washington, Seattle, WA, USA,Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Meredith A J Hullar
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Timothy W Randolph
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Adrian A Franke
- Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Kristine R Monroe
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - John A Shepherd
- Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Margaret M Madeleine
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Unhee Lim
- Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Johanna W Lampe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA,Department of Epidemiology, University of Washington, Seattle, WA, USA,Address correspondence to JWL (e-mail: )
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20
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Antosca K, Hoen AG, Palys T, Hilliard M, Morrison HG, Coker M, Madan J, Karagas MR. Reliability of stool microbiome methods for DNA yields and sequencing among infants and young children. Microbiologyopen 2020; 9:e1018. [PMID: 32166902 PMCID: PMC7221451 DOI: 10.1002/mbo3.1018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/04/2020] [Accepted: 02/11/2020] [Indexed: 12/15/2022] Open
Abstract
With the emergence of large‐scale epidemiologic human microbiome studies, there is a need to understand the reproducibility of microbial DNA sequencing and the impact of specimen collection and processing methods on measures of microbial community composition and structure, with reproducibility studies in infants and young children particularly lacking. Here, we examined batch‐to‐batch variability and reliability of collection, handling, and processing protocols, testing replicate stool samples from infants and young children using Illumina MiSeq sequencing of the bacterial 16S rRNA gene V4‐V5 hypervariable region, evaluating 33 conditions with different protocols and extraction methods. We detected no evidence of batch effects in replicate DNA samples or extractions from the same stool sample. Variability in DNA yield and alpha diversity was observed between the different collection, handling, and processing protocols. However, across all protocols, subject variability was the dominant contributor to microbiome structure, with comparatively little impact of the protocol used. While collection method and DNA extraction kit may affect DNA yield, and correspondingly alpha diversity, our findings suggest that characterization of the structure and composition of the fecal microbiome of infants and young children are reliably measurable by standardized collection, handling, and processing protocols and DNA extraction methods within an individual longitudinal study.
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Affiliation(s)
- Katherine Antosca
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.,Department of Microbiology and Immunology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Anne G Hoen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.,Center for Molecular Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.,Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Lebanon, NH, USA
| | - Thomas Palys
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.,Center for Molecular Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA
| | - Margaret Hilliard
- Department of Food Science, University of Massachusetts, Amherst, MA, USA
| | - Hilary G Morrison
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA
| | - Modupe Coker
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Juliette Madan
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.,Center for Molecular Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.,Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Lebanon, NH, USA.,Division of Neonatology, Department of Pediatrics, Children's Hospital at Dartmouth, Lebanon, NH, USA
| | - Margaret R Karagas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.,Center for Molecular Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.,Children's Environmental Health and Disease Prevention Research Center at Dartmouth, Lebanon, NH, USA
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21
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Pan S, Hullar MAJ, Lai LA, Peng H, May DH, Noble WS, Raftery D, Navarro SL, Neuhouser ML, Lampe PD, Lampe JW, Chen R. Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach. Microorganisms 2020; 8:E379. [PMID: 32156071 PMCID: PMC7143255 DOI: 10.3390/microorganisms8030379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/02/2020] [Accepted: 03/04/2020] [Indexed: 12/11/2022] Open
Abstract
Although the gut microbiome has been associated with dietary patterns linked to health, microbial metabolism is not well characterized. This ancillary study was a proof of principle analysis for a novel application of metaproteomics to study microbial protein expression in a controlled dietary intervention. We measured the response of the microbiome to diet in a randomized crossover dietary intervention of a whole-grain, low glycemic load diet (WG) and a refined-grain, high glycemic load diet (RG). Total proteins in stools from 9 participants at the end of each diet period (n = 18) were analyzed by LC MS/MS and proteins were identified using the Human Microbiome Project (HMP) human gut microbiome database and UniProt human protein databases. T-tests, controlling for false discovery rate (FDR) <10%, were used to compare the Gene Ontology (GO) biological processes and bacterial enzymes between the two interventions. Using shotgun proteomics, more than 53,000 unique peptides were identified including microbial (89%) and human peptides (11%). Forty-eight bacterial enzymes were statistically different between the diets, including those implicated in SCFA production and degradation of fatty acids. Enzymes associated with degradation of human mucin were significantly enriched in the RG diet. These results illustrate that the metaproteomic approach is a valuable tool to study the microbial metabolism of diets that may influence host health.
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Affiliation(s)
- Sheng Pan
- Institute of Molecular Medicine, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (S.P.); (H.P.)
| | - Meredith A. J. Hullar
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA; (D.R.); (S.L.N.); (M.L.N.); (P.D.L.); (J.W.L.)
| | - Lisa A. Lai
- Department of Medicine, University of Washington, Seattle, WA 98105, USA;
| | - Hong Peng
- Institute of Molecular Medicine, the University of Texas Health Science Center at Houston, Houston, TX 77030, USA; (S.P.); (H.P.)
| | - Damon H. May
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA; (D.H.M.)
| | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA; (D.H.M.)
| | - Daniel Raftery
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA; (D.R.); (S.L.N.); (M.L.N.); (P.D.L.); (J.W.L.)
- Department of Anesthesiology and Pain Medicine, Northwest Metabolomics Research Center, University of Washington, Seattle, WA 98109 USA
| | - Sandi L. Navarro
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA; (D.R.); (S.L.N.); (M.L.N.); (P.D.L.); (J.W.L.)
| | - Marian L. Neuhouser
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA; (D.R.); (S.L.N.); (M.L.N.); (P.D.L.); (J.W.L.)
| | - Paul D. Lampe
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA; (D.R.); (S.L.N.); (M.L.N.); (P.D.L.); (J.W.L.)
| | - Johanna W. Lampe
- Fred Hutchinson Cancer Research Center, Division of Public Health Sciences, Seattle, WA 98109, USA; (D.R.); (S.L.N.); (M.L.N.); (P.D.L.); (J.W.L.)
| | - Ru Chen
- Division of Gastroenterology and Hepatology, Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
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22
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Byrd DA, Sinha R, Hoffman KL, Chen J, Hua X, Shi J, Chia N, Petrosino J, Vogtmann E. Comparison of Methods To Collect Fecal Samples for Microbiome Studies Using Whole-Genome Shotgun Metagenomic Sequencing. mSphere 2020; 5:e00827-19. [PMID: 32250964 PMCID: PMC7045388 DOI: 10.1128/msphere.00827-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/12/2020] [Indexed: 12/16/2022] Open
Abstract
Few previous studies have assessed stability and "gold-standard" concordance of fecal sample collection methods for whole-genome shotgun metagenomic sequencing (WGSS), an increasingly popular method for studying the gut microbiome. We used WGSS data to investigate ambient temperature stability and putative gold-standard concordance of microbial profiles in fecal samples collected and stored using fecal occult blood test (FOBT) cards, fecal immunochemical test (FIT) tubes, 95% ethanol, or RNAlater. Among 15 Mayo Clinic employees, for each collection method, we calculated intraclass correlation coefficients (ICCs) to estimate stability of fecal microbial profiles after storage for 4 days at ambient temperature and concordance with immediately frozen, no-solution samples (i.e., the putative gold standard). ICCs were estimated for multiple metrics, including relative abundances of select phyla, species, KEGG k-genes (representing any coding sequence that had >70% identity and >70% query coverage with respect to a known KEGG ortholog), KEGG modules, and KEGG pathways; species and k-gene alpha diversity; and Bray-Curtis and Jaccard species beta diversity. ICCs for microbial profile stability were excellent (≥90%) for fecal samples collected via most of the collection methods, except those preserved in 95% ethanol. Concordance with the immediately frozen, no-solution samples varied for all collection methods, but the number of observed species and the beta diversity metrics tended to have higher concordance than other metrics. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT cards, FIT tubes, and RNAlater are acceptable choices for fecal sample collection methods in future WGSS studies.IMPORTANCE A major direction for future microbiome research is implementation of fecal sample collections in large-scale, prospective epidemiologic studies. Studying microbiome-disease associations likely requires microbial data to be pooled from multiple studies. Our findings suggest collection methods that are most optimal to be used standardly across future WGSS microbiome studies.
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Affiliation(s)
- Doratha A Byrd
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kristi L Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Jun Chen
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Xing Hua
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, USA
- Biomedical Engineering and Physiology, Mayo Clinic, Rochester, Minnesota, USA
| | - Joseph Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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23
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Berzero G, Psimaras D, Weiss N, Sokol H, Alentorn A. Gut microbiome alterations in anti-NMDA receptor encephalitis: caveats for result interpretation. Ann Clin Transl Neurol 2019; 7:153-154. [PMID: 31880105 PMCID: PMC6952320 DOI: 10.1002/acn3.50970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 11/05/2019] [Indexed: 11/29/2022] Open
Affiliation(s)
- Giulia Berzero
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, service de Neurologie 2-Mazarin, Paris, France.,Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,PhD program in Biomedical Sciences, University of Pavia, Pavia, Italy.,Neuroncology Unit, IRCCS Mondino Foundation, Pavia, Italy
| | - Dimitri Psimaras
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, service de Neurologie 2-Mazarin, Paris, France.,Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France.,Centre de Compétence des Syndromes Neurologiques Paraneoplasiques et Encéphalites Autoimmunes, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Nicolas Weiss
- Sorbonne Université, Brain Liver Pitié-Salpêtrière (BLIPS) Study Group, INSERM UMR_S 938, Centre de recherche Saint-Antoine, Maladies métaboliques, biliaires et fibro-inflammatoire du foie, Institute of Cardiometabolism and Nutrition (ICAN), Assistance Publique - Hôpitaux de Paris, AP-HP.Sorbonne Université, Hôpital Pitié-Salpêtrière, Département de Neurologie, Unité de médecine intensive réanimation neurologique, Paris, France
| | - Harry Sokol
- Sorbonne Université, Inserm, Centre de Recherche Saint-Antoine, CRSA, AP-HP, Hôpital Saint Antoine, Service de Gastroenterologie, F-75012, Paris, France.,INRA, UMR1319 Micalis, AgroParisTech, Jouy-en-Josas, France
| | - Agusti Alentorn
- AP-HP, Groupe Hospitalier Pitié-Salpêtrière, service de Neurologie 2-Mazarin, Paris, France.,Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau et de la Moelle épinière, ICM, Paris, France
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24
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Navarro SL, Levy L, Curtis KR, Lampe JW, Hullar MA. Modulation of Gut Microbiota by Glucosamine and Chondroitin in a Randomized, Double-Blind Pilot Trial in Humans. Microorganisms 2019; 7:microorganisms7120610. [PMID: 31771179 PMCID: PMC6956221 DOI: 10.3390/microorganisms7120610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/16/2019] [Accepted: 11/22/2019] [Indexed: 12/18/2022] Open
Abstract
Glucosamine and chondroitin (G&C), typically taken for joint pain, are among the most frequently used specialty supplements by US adults. More recently, G&C have been associated with lower incidence of colorectal cancer in human observational studies and reduced severity of experimentally-induced ulcerative colitis in rodents. However, little is known about their effects on colon-related physiology. G&C are poorly absorbed and therefore metabolized by gut microbiota. G&C have been associated with changes in microbial structure, which may alter host response. We conducted a randomized, double-blind, placebo-controlled crossover trial in ten healthy adults to evaluate the effects of a common dose of G&C compared to placebo for 14 days on gut microbial community structure, measured by 16S rRNA gene sequencing. Linear mixed models were used to evaluate the effect of G&C compared to placebo on fecal microbial alpha and beta diversity, seven phyla, and 137 genera. Nine genera were significantly different between interventions (False Discovery Rate < 0.05). Abundances of four Lachnospiraceae genera, two Prevotellaceae genera, and Desulfovibrio were increased after G&C compared to placebo, while Bifidobacterium and a member of the Christensenellaceae family were decreased. Our results suggest that G&C affect the composition of the gut microbiome which may have implications for therapeutic efficacy.
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Affiliation(s)
- Sandi L. Navarro
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (J.W.L.)
- Correspondence: ; Tel.: +1-206-667-6583
| | - Lisa Levy
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (J.W.L.)
| | - Keith R. Curtis
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (J.W.L.)
| | - Johanna W. Lampe
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (J.W.L.)
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Meredith A.J. Hullar
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; (L.L.); (K.R.C.); (J.W.L.)
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25
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Byrd DA, Chen J, Vogtmann E, Hullings A, Song SJ, Amir A, Kibriya MG, Ahsan H, Chen Y, Nelson H, Knight R, Shi J, Chia N, Sinha R. Reproducibility, stability, and accuracy of microbial profiles by fecal sample collection method in three distinct populations. PLoS One 2019; 14:e0224757. [PMID: 31738775 PMCID: PMC6860998 DOI: 10.1371/journal.pone.0224757] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/20/2019] [Indexed: 12/30/2022] Open
Abstract
The gut microbiome likely plays a role in the etiology of multiple health conditions, especially those affecting the gastrointestinal tract. Little consensus exists as to the best, standard methods to collect fecal samples for future microbiome analysis. We evaluated three distinct populations (N = 132 participants) using 16S rRNA gene amplicon sequencing data to investigate the reproducibility, stability, and accuracy of microbial profiles in fecal samples collected and stored via fecal occult blood test (FOBT) or Flinders Technology Associates (FTA) cards, fecal immunochemical tests (FIT) tubes, 70% and 95% ethanol, RNAlater, or with no solution. For each collection method, based on relative abundance of select phyla and genera, two alpha diversity metrics, and four beta diversity metrics, we calculated intraclass correlation coefficients (ICCs) to estimate reproducibility and stability, and Spearman correlation coefficients (SCCs) to estimate accuracy of the fecal microbial profile. Comparing duplicate samples, reproducibility ICCs for all collection methods were excellent (ICCs ≥75%). After 4–7 days at ambient temperature, ICCs for microbial profile stability were excellent (≥75%) for most collection methods, except those collected via no-solution and 70% ethanol. SCCs comparing each collection method to immediately-frozen no-solution samples ranged from fair to excellent for most methods; however, accuracy of genus-level relative abundances differed by collection method. Our findings, taken together with previous studies and feasibility considerations, indicated that FOBT/FTA cards, FIT tubes, 95% ethanol, and RNAlater are excellent choices for fecal sample collection methods in future microbiome studies. Furthermore, establishing standard collection methods across studies is highly desirable.
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Affiliation(s)
- Doratha A. Byrd
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Jun Chen
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Autumn Hullings
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Se Jin Song
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Amnon Amir
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
| | - Muhammad G. Kibriya
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - Habibul Ahsan
- Department of Public Health Sciences, University of Chicago, Chicago, Illinois, United States of America
| | - Yu Chen
- New York School of Medicine, New York, New York, United States of America
| | - Heidi Nelson
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, United States of America
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, California, United States of America
| | - Jianxin Shi
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
- Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
- Department of Surgery, Mayo Clinic, Rochester, Minnesota, United States of America
- Biomedical Engineering and Physiology, Mayo College, Rochester, Minnesota, United States of America
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
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26
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Videnska P, Smerkova K, Zwinsova B, Popovici V, Micenkova L, Sedlar K, Budinska E. Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform. Sci Rep 2019; 9:13837. [PMID: 31554833 PMCID: PMC6761292 DOI: 10.1038/s41598-019-49520-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 08/22/2019] [Indexed: 12/30/2022] Open
Abstract
Many studies correlate changes in human gut microbiome with the onset of various diseases, mostly by 16S rRNA gene sequencing. Setting up the optimal sampling and DNA isolation procedures is crucial for robustness and reproducibility of the results. We performed a systematic comparison of several sampling and DNA isolation kits, quantified their effect on bacterial gDNA quality and the bacterial composition estimates at all taxonomic levels. Sixteen volunteers tested three sampling kits. All samples were consequently processed by two DNA isolation kits. We found that the choice of both stool sampling and DNA isolation kits have an effect on bacterial composition with respect to Gram-positivity, however the isolation kit had a stronger effect than the sampling kit. The proportion of bacteria affected by isolation and sampling kits was larger at higher taxa levels compared to lower taxa levels. The PowerLyzer PowerSoil DNA Isolation Kit outperformed the QIAamp DNA Stool Mini Kit mainly due to better lysis of Gram-positive bacteria while keeping the values of all the other assessed parameters within a reasonable range. The presented effects need to be taken into account when comparing results across multiple studies or computing ratios between Gram-positive and Gram-negative bacteria.
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Affiliation(s)
- Petra Videnska
- RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Kristyna Smerkova
- RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Barbora Zwinsova
- RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Vlad Popovici
- RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lenka Micenkova
- RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Karel Sedlar
- Department of Biomedical Engineering, Brno University of Technology, Technicka 12, Brno, Czech Republic
| | - Eva Budinska
- RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
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27
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Maskarinec G, Hullar MAJ, Monroe KR, Shepherd JA, Hunt J, Randolph TW, Wilkens LR, Boushey CJ, Le Marchand L, Lim U, Lampe JW. Fecal Microbial Diversity and Structure Are Associated with Diet Quality in the Multiethnic Cohort Adiposity Phenotype Study. J Nutr 2019; 149:1575-1584. [PMID: 31187868 PMCID: PMC6862930 DOI: 10.1093/jn/nxz065] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/07/2019] [Accepted: 03/18/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Variation in gut microbial community structure is partly attributed to variations in diet. A priori dietary indexes capture diet quality and have been associated with chronic disease risk. OBJECTIVES The aim of this study was to examine the association of diet quality, as assessed by the Healthy Eating Index, Alternative Healthy Eating Index-2010, alternate Mediterranean Diet, and the Dietary Approaches to Stop Hypertension Trial, with measures of fecal microbial community structure assessed in the Adiposity Phenotype Study (APS), an ethnically diverse study population with varied food intakes. METHODS Multiethnic Cohort Study members completed a validated quantitative food frequency questionnaire (QFFQ) at cohort entry (1993-1996) and, for the APS subset, at clinic visit (2013-2015), when they also provided a stool sample. DNA was extracted from stool, and the V1-V3 region of the 16S rRNA gene was amplified and sequenced. Dietary index scores were computed based on the QFFQ and an extensive nutritional database. Using linear regression adjusted for relevant covariates, we estimated associations of dietary quality with microbiome measures and computed adjusted mean values of microbial measures by tertiles of dietary index scores. RESULTS The 858 men and 877 women of white, Japanese American, Latino, Native Hawaiian, and African American ancestry had a mean age of 69.2 years at stool collection. Alpha diversity according to the Shannon index increased by 1-2% across tertiles of all 4 diet indexes measured at clinic visit. The mean relative abundance of the phylum Actinobacteria was 13-19% lower with higher diet quality across all 4 indexes (difference between tertile 3 and tertile 1 divided by tertile 1). Of the 104 bacterial genera tested, 21 (primarily from the phylum Firmicutes) were positively associated with at least 1 index after Bonferroni adjustment. CONCLUSION Diet quality was strongly associated with fecal microbial alpha diversity and beta diversity and several genera previously associated with human health.
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Affiliation(s)
| | - Meredith A J Hullar
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Kristine R Monroe
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA
| | | | - Jeani Hunt
- School of Public Health, University of Washington, Seattle, WA
| | - Timothy W Randolph
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | - Unhee Lim
- University of Hawaii Cancer Center, Honolulu, HI
| | - Johanna W Lampe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- School of Public Health, University of Washington, Seattle, WA
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28
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Abstract
The interaction between drug use, the microbiome, and the host is complex and multidimensional. Drugs and the microbiota may be risk factors or protective factors for disease. These interactions may explain interpersonal variations in drug efficacy and toxicity, but also interpersonal variations in microbiota composition and functioning, and potential (long-term) side effects from drugs.
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Affiliation(s)
- Nele Brusselaers
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Visionsgatan 4, Stockholm 17177, Sweden; Science for Life Laboratory, Tomtebodavägen 23a, Stockholm 171 65, Sweden.
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29
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Stanislawski MA, Dabelea D, Lange LA, Wagner BD, Lozupone CA. Gut microbiota phenotypes of obesity. NPJ Biofilms Microbiomes 2019; 5:18. [PMID: 31285833 PMCID: PMC6603011 DOI: 10.1038/s41522-019-0091-8] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 06/06/2019] [Indexed: 12/28/2022] Open
Abstract
Obesity is a disease with a complex etiology and variable prevalence across different populations. While several studies have reported gut microbiota composition differences associated with obesity in humans, there has been a lack of consistency in the nature of the reported changes; it has been difficult to determine whether methodological differences between studies, underlying differences in the populations studied, or other factors are responsible for this discordance. Here we use 16 S rRNA data from previously published studies to explore how the gut microbiota-obesity relationship varies across heterogeneous Western populations, focusing mainly on the relationship between (1) alpha diversity and (2) Prevotella relative abundance with BMI. We provide evidence that the relationship between lower alpha diversity and higher BMI may be most consistent in non-Hispanic white (NHW) populations and/or those with high socioeconomic status, while the relationship between higher Prevotella relative abundance and BMI may be stronger among black and Hispanic populations. We further examine how diet may impact these relationships. This work suggests that gut microbiota phenotypes of obesity may differ with race/ethnicity or its correlates, such as dietary components or socioeconomic status. However, microbiome cohorts are often too small to study complex interaction effects and non-white individuals are greatly underrepresented, creating substantial challenges to understanding population-level patterns in the microbiome-obesity relationship. Further study of how population heterogeneity influences the relationship between the gut microbiota and obesity is warranted.
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Affiliation(s)
- Maggie A. Stanislawski
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO USA
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO USA
| | - Dana Dabelea
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO USA
- Lifecourse Epidemiology of Adiposity and Diabetes (LEAD) Center, Aurora, CO USA
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO USA
| | - Leslie A. Lange
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO USA
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO USA
| | - Brandie D. Wagner
- Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO USA
| | - Catherine A. Lozupone
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO USA
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30
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Cogdill AP, Gaudreau PO, Arora R, Gopalakrishnan V, Wargo JA. The Impact of Intratumoral and Gastrointestinal Microbiota on Systemic Cancer Therapy. Trends Immunol 2019; 39:900-920. [PMID: 30392721 DOI: 10.1016/j.it.2018.09.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 01/04/2023]
Abstract
The human microbiome is a complex aggregate of microorganisms, and their genomes exert a number of influences crucial to the metabolic, immunologic, hormonal, and homeostatic function of the host. Recent work, both in preclinical mouse models and human studies, has shed light on the impact of gut and tumor microbiota on responses to systemic anticancer therapeutics. In light of this, strategies to target the microbiome to improve therapeutic responses are underway, including efforts to target gut and intratumoral microbes. Here, we discuss mechanisms by which microbiota may impact systemic and antitumor immunity, in addition to outstanding questions in the field. A deeper understanding of these is critical as we devise putative strategies to target the microbiome.
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Affiliation(s)
- Alexandria P Cogdill
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Pierre Olivier Gaudreau
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Reetakshi Arora
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Vancheswaran Gopalakrishnan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; These authors contributed equally to this work
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA; These authors contributed equally to this work.
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31
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Vangay P, Johnson AJ, Ward TL, Al-Ghalith GA, Shields-Cutler RR, Hillmann BM, Lucas SK, Beura LK, Thompson EA, Till LM, Batres R, Paw B, Pergament SL, Saenyakul P, Xiong M, Kim AD, Kim G, Masopust D, Martens EC, Angkurawaranon C, McGready R, Kashyap PC, Culhane-Pera KA, Knights D. US Immigration Westernizes the Human Gut Microbiome. Cell 2018; 175:962-972.e10. [PMID: 30388453 PMCID: PMC6498444 DOI: 10.1016/j.cell.2018.10.029] [Citation(s) in RCA: 445] [Impact Index Per Article: 74.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 09/10/2018] [Accepted: 10/12/2018] [Indexed: 12/26/2022]
Abstract
Many US immigrant populations develop metabolic diseases post immigration, but the causes are not well understood. Although the microbiome plays a role in metabolic disease, there have been no studies measuring the effects of US immigration on the gut microbiome. We collected stool, dietary recalls, and anthropometrics from 514 Hmong and Karen individuals living in Thailand and the United States, including first- and second-generation immigrants and 19 Karen individuals sampled before and after immigration, as well as from 36 US-born European American individuals. Using 16S and deep shotgun metagenomic DNA sequencing, we found that migration from a non-Western country to the United States is associated with immediate loss of gut microbiome diversity and function in which US-associated strains and functions displace native strains and functions. These effects increase with duration of US residence and are compounded by obesity and across generations.
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Affiliation(s)
- Pajau Vangay
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA
| | - Abigail J Johnson
- Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tonya L Ward
- Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gabriel A Al-Ghalith
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Benjamin M Hillmann
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sarah K Lucas
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lalit K Beura
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Emily A Thompson
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Lisa M Till
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55902, USA
| | - Rodolfo Batres
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Bwei Paw
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Shannon L Pergament
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Pimpanitta Saenyakul
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Mary Xiong
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Austin D Kim
- Department of Mathematics, Statistics, and Computer Science, Macalester College, St. Paul, MN 55105, USA
| | - Grant Kim
- College of Biological Sciences, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Masopust
- Center for Immunology, Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Eric C Martens
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chaisiri Angkurawaranon
- Department of Family Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Rose McGready
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot 63110, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7BN, UK
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN 55902, USA
| | - Kathleen A Culhane-Pera
- Somali, Latino, and Hmong Partnership for Health and Wellness, West Side Community Health Services, St. Paul, MN 55106, USA
| | - Dan Knights
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA; Biotechnology Institute, University of Minnesota, Minneapolis, MN 55455, USA; Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN 55455, USA.
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32
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Fu BC, Randolph TW, Lim U, Monroe KR, Cheng I, Wilkens LR, Le Marchand L, Lampe JW, Hullar MAJ. Temporal Variability and Stability of the Fecal Microbiome: The Multiethnic Cohort Study. Cancer Epidemiol Biomarkers Prev 2018; 28:154-162. [PMID: 30206059 DOI: 10.1158/1055-9965.epi-18-0348] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/15/2018] [Accepted: 09/05/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Measurement reliability and biological stability need to be considered when developing sampling protocols for population-based fecal microbiome studies. METHODS Stool samples were collected biannually over a 2-year period and sequenced for the V1-V3 region of the 16S rRNA gene in 50 participants from the Multiethnic Cohort Study. We evaluated the temporal stability of the fecal microbiome on a community level with permutational multivariate analysis of variance (PERMANOVA), as well as on taxa and diversity measures with intraclass correlation coefficients. RESULTS Interindividual differences were the predominant source of fecal microbiome variation, and variation within individual was driven more by changing abundances than by the complete loss or introduction of taxa. Phyla and diversity measures were reliable over the 2 years. Most genera were stable over time, although those with low abundances tended to be more dynamic. Reliability was lower among participants who used antibiotics, with the greatest difference seen in samples taken within 1 month of reported use. CONCLUSIONS The fecal microbiome as a whole is stable over a 2-year period, although certain taxa may exhibit more temporal variability. IMPACT When designing large epidemiologic studies, a single sample is sufficient to capture the majority of the variation in the fecal microbiome from 16S rRNA gene sequencing, while multiple samples may be needed for rare or less-abundant taxa.
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Affiliation(s)
- Benjamin C Fu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Timothy W Randolph
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Unhee Lim
- Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Kristine R Monroe
- Department of Preventive Medicine, University of Southern California, Los Angeles, California
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, Hawaii
| | - Johanna W Lampe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Meredith A J Hullar
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
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33
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Hullar MAJ, Lampe JW, Torok-Storb BJ, Harkey MA. The canine gut microbiome is associated with higher risk of gastric dilatation-volvulus and high risk genetic variants of the immune system. PLoS One 2018; 13:e0197686. [PMID: 29889838 PMCID: PMC5995382 DOI: 10.1371/journal.pone.0197686] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 05/07/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Large and giant dog breeds have a high risk for gastric dilatation-volvulus (GDV) which is an acute, life-threatening condition. Previous work by our group identified a strong risk of GDV linked to specific alleles in innate and adaptive immune genes. We hypothesize that variation in the genes of the immune system act through modulation of the gut microbiome, or through autoimmune mechanisms, or both, to predispose dogs to this condition. Here, we investigate whether differences in the canine fecal microbiome are associated with GDV and are linked to previously identified risk alleles. METHODOLOGY/PRINCIPLE FINDINGS Fecal samples from healthy Great Danes (n = 38), and dogs with at least one occurrence of GDV (n = 37) were collected and analyzed by paired-end sequencing of the 16S rRNA gene. Dietary intake and temperament were estimated from a study-specific dietary and temperament questionnaire. Dogs with GDV had significantly more diverse fecal microbiomes than healthy control dogs. Alpha diversity was significantly increased in dogs with GDV, as well as dogs with at least one risk allele for DRB1 and TRL5. We found no significant association of dietary intake and GDV. Dogs with GDV showed a significant expansion of the rare lineage Actinobacteria (p = 0.004), as well as a significantly greater abundance of Firmicutes (p = 0.004) and a significantly lower abundance of Bacteroidetes (p<0.004). There was a significant difference in the abundance of 10 genera but after correction for multiple comparisons, none were significant. Bacterial phyla were significantly different between controls and dogs with GDV and at least one risk allele for DRB1 and TRL5. Actinobacteria were significantly higher in dogs with GDV and with one risk allele for DRB1 and TLR5 but not DLA88 genes. Furthermore, Collinsella was significantly increased in dogs with at least one risk allele for DRB1 and TLR5. Logistic regression showed that a model which included Actinobacteria, at least one risk allele,and temperament, explained 29% of the variation in risk of GDV in Great Danes. CONCLUSIONS The microbiome in GDV was altered by an expansion of a minor lineage and was associated with specific alleles of both innate and adaptive immunity genes. These associations are consistent with our hypothesis that immune genes may play a role in predisposition to GDV by altering the gut microbiome. Further research will be required to directly test the causal relationships of immune genes, the gut microbiome and GDV.
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Affiliation(s)
- Meredith A. J. Hullar
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Johanna W. Lampe
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Beverly J. Torok-Storb
- Department of Transplantation Biology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Michael A. Harkey
- Department of Transplantation Biology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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34
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Sinha R, Abu-Ali G, Vogtmann E, Fodor AA, Ren B, Amir A, Schwager E, Crabtree J, Ma S, Abnet CC, Knight R, White O, Huttenhower C. Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium. Nat Biotechnol 2017; 35:1077-1086. [PMID: 28967885 DOI: 10.1038/nbt.3981] [Citation(s) in RCA: 299] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 09/11/2017] [Indexed: 12/14/2022]
Abstract
In order for human microbiome studies to translate into actionable outcomes for health, meta-analysis of reproducible data from population-scale cohorts is needed. Achieving sufficient reproducibility in microbiome research has proven challenging. We report a baseline investigation of variability in taxonomic profiling for the Microbiome Quality Control (MBQC) project baseline study (MBQC-base). Blinded specimen sets from human stool, chemostats, and artificial microbial communities were sequenced by 15 laboratories and analyzed using nine bioinformatics protocols. Variability depended most on biospecimen type and origin, followed by DNA extraction, sample handling environment, and bioinformatics. Analysis of artificial community specimens revealed differences in extraction efficiency and bioinformatic classification. These results may guide researchers in experimental design choices for gut microbiome studies.
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Affiliation(s)
- Rashmi Sinha
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Galeb Abu-Ali
- Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Emily Vogtmann
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Anthony A Fodor
- Bioinformatics and Genomics, University of North Carolina, Charlotte, Charlotte, North Carolina, USA
| | - Boyu Ren
- Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Amnon Amir
- Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Emma Schwager
- Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Siyuan Ma
- Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Christian C Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Rob Knight
- Pediatrics, University of California, San Diego, La Jolla, California, USA.,Computer Science and Engineering and Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Owen White
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Curtis Huttenhower
- Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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35
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Mehta RS, Nishihara R, Cao Y, Song M, Mima K, Qian ZR, Nowak JA, Kosumi K, Hamada T, Masugi Y, Bullman S, Drew DA, Kostic AD, Fung TT, Garrett WS, Huttenhower C, Wu K, Meyerhardt JA, Zhang X, Willett WC, Giovannucci EL, Fuchs CS, Chan AT, Ogino S. Association of Dietary Patterns With Risk of Colorectal Cancer Subtypes Classified by Fusobacterium nucleatum in Tumor Tissue. JAMA Oncol 2017; 3:921-927. [PMID: 28125762 PMCID: PMC5502000 DOI: 10.1001/jamaoncol.2016.6374] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
IMPORTANCE Fusobacterium nucleatum appears to play a role in colorectal carcinogenesis through suppression of the hosts' immune response to tumor. Evidence also suggests that diet influences intestinal F nucleatum. However, the role of F nucleatum in mediating the relationship between diet and the risk of colorectal cancer is unknown. OBJECTIVE To test the hypothesis that the associations of prudent diets (rich in whole grains and dietary fiber) and Western diets (rich in red and processed meat, refined grains, and desserts) with colorectal cancer risk may differ according to the presence of F nucleatum in tumor tissue. DESIGN, SETTING, AND PARTICIPANTS A prospective cohort study was conducted using data from the Nurses' Health Study (June 1, 1980, to June 1, 2012) and the Health Professionals Follow-up Study (June 1, 1986, to June 1, 2012) on a total of 121 700 US female nurses and 51 529 US male health professionals aged 30 to 55 years and 40 to 75 years, respectively (both predominantly white individuals), at enrollment. Data analysis was performed from March 15, 2015, to August 10, 2016. EXPOSURES Prudent and Western diets. MAIN OUTCOMES AND MEASURES Incidence of colorectal carcinoma subclassified by F nucleatum status in tumor tissue, determined by quantitative polymerase chain reaction. RESULTS Of the 173 229 individuals considered for the study, 137 217 were included in the analysis, 47 449 were male (34.6%), and mean (SD) baseline age for men was 54.0 (9.8) years and for women, 46.3 (7.2) years. A total of 1019 incident colon and rectal cancer cases with available F nucleatum data were documented over 26 to 32 years of follow-up, encompassing 3 643 562 person-years. The association of prudent diet with colorectal cancer significantly differed by tissue F nucleatum status (P = .01 for heterogeneity); prudent diet score was associated with a lower risk of F nucleatum-positive cancers (P = .003 for trend; multivariable hazard ratio of 0.43; 95% CI, 0.25-0.72, for the highest vs the lowest prudent score quartile) but not with F nucleatum-negative cancers (P = .47 for trend, the corresponding multivariable hazard ratio of 0.95; 95% CI, 0.77-1.17). There was no significant heterogeneity between the subgroups in relation to Western dietary pattern scores. CONCLUSIONS AND RELEVANCE Prudent diets rich in whole grains and dietary fiber are associated with a lower risk for F nucleatum-positive colorectal cancer but not F nucleatum-negative cancer, supporting a potential role for intestinal microbiota in mediating the association between diet and colorectal neoplasms.
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Affiliation(s)
- Raaj S Mehta
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston2Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Reiko Nishihara
- Division of MPE Molecular Pathological Epidemiology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts4Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts5Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge6Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts7Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts8Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts9Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Yin Cao
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston2Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston6Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Mingyang Song
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston2Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston6Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Kosuke Mima
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Zhi Rong Qian
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Jonathan A Nowak
- Division of MPE Molecular Pathological Epidemiology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts4Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Keisuke Kosumi
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Tsuyoshi Hamada
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Yohei Masugi
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Susan Bullman
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - David A Drew
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston2Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston
| | - Aleksandar D Kostic
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge
| | - Teresa T Fung
- Program in Dietetics, Simmons College, Boston, Massachusetts
| | - Wendy S Garrett
- Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge9Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts11Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Kana Wu
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Jeffrey A Meyerhardt
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Xuehong Zhang
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Walter C Willett
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts12Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Edward L Giovannucci
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts7Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts12Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Charles S Fuchs
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts12Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Andrew T Chan
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston2Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston5Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge12Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Shuji Ogino
- Division of MPE Molecular Pathological Epidemiology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts4Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts7Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts9Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts13Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
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Loftfield E, Vogtmann E, Sampson JN, Moore SC, Nelson H, Knight R, Chia N, Sinha R. Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies. Cancer Epidemiol Biomarkers Prev 2016; 25:1483-1490. [PMID: 27543620 PMCID: PMC5093035 DOI: 10.1158/1055-9965.epi-16-0409] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/05/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The gut metabolome may be associated with the incidence and progression of numerous diseases. The composition of the gut metabolome can be captured by measuring metabolite levels in the feces. However, there are little data describing the effect of fecal sample collection methods on metabolomic measures. METHODS We collected fecal samples from 18 volunteers using four methods: no solution, 95% ethanol, fecal occult blood test (FOBT) cards, and fecal immunochemical test (FIT). One set of samples was frozen after collection (day 0), and for 95% ethanol, FOBT, and FIT, a second set was frozen after 96 hours at room temperature. We evaluated (i) technical reproducibility within sample replicates, (ii) stability after 96 hours at room temperature for 95% ethanol, FOBT, and FIT, and (iii) concordance of metabolite measures with the putative "gold standard," day 0 samples without solution. RESULTS Intraclass correlation coefficients (ICC) estimating technical reproducibility were high for replicate samples for each collection method. ICCs estimating stability at room temperature were high for 95% ethanol and FOBT (median ICC > 0.87) but not FIT (median ICC = 0.52). Similarly, Spearman correlation coefficients (rs) estimating metabolite concordance with the "gold standard" were higher for 95% ethanol (median rs = 0.82) and FOBT (median rs = 0.70) than for FIT (median rs = 0.40). CONCLUSIONS Metabolomic measurements appear reproducible and stable in fecal samples collected with 95% ethanol or FOBT. Concordance with the "gold standard" is highest with 95% ethanol and acceptable with FOBT. IMPACT Future epidemiologic studies should collect feces using 95% ethanol or FOBT if interested in studying fecal metabolomics. Cancer Epidemiol Biomarkers Prev; 25(11); 1483-90. ©2016 AACR.
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Affiliation(s)
- Erikka Loftfield
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Emily Vogtmann
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Joshua N Sampson
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven C Moore
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Heidi Nelson
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
| | - Rob Knight
- Health Sciences Research, Mayo Clinic, Rochester, Minnesota
- Department of Pediatrics, University of California San Diego, San Diego, California
| | - Nicholas Chia
- Microbiome Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Surgery, Mayo Clinic, Rochester, Minnesota
- Department of Computer Science and Engineering, University of California San Diego, San Diego, California
| | - Rashmi Sinha
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Dąbrowska K, Witkiewicz W. Correlations of Host Genetics and Gut Microbiome Composition. Front Microbiol 2016; 7:1357. [PMID: 27625642 PMCID: PMC5003823 DOI: 10.3389/fmicb.2016.01357] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/16/2016] [Indexed: 12/12/2022] Open
Abstract
The human gut microbiome has a considerable impact on host health. The long list of microbiome-related health disorders raises the question of what in fact determines microbiome composition. In this review we sought to understand how the host itself impacts the structure of the gut microbiota population, specifically by correlations of host genetics and gut microbiome composition. Host genetic profile has been linked to differences in microbiome composition, thus suggesting that host genetics can shape the gut microbiome of the host. However, cause-consequence mechanisms behind these links are still unclear. A survey of the possible mechanisms allowing host genetics to shape microbiota composition in the gut demonstrated the major role of metabolic functions and the immune system. A considerable impact of other factors, such as diet, may outweigh the effects of host genetic background. More studies are necessary for good understanding of the relations between the host genetic profile, gut microbiome composition, and host health. According to the idea of personalized medicine, patient-tailored management of microbiota content remains a fascinating area for further inquiry.
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Affiliation(s)
- Krystyna Dąbrowska
- Research and Development Center, Regional Specialized HospitalWrocław, Poland; Bacteriophage Laboratory, Institute of Immunology and Experimental Therapy, Polish Academy of SciencesWrocław, Poland
| | - Wojciech Witkiewicz
- Research and Development Center, Regional Specialized Hospital Wrocław, Poland
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Foxman B, Seitz SM, Rothenberg R. Epidemiology and the microbiome. Ann Epidemiol 2016; 26:386-7. [PMID: 27180115 PMCID: PMC10519180 DOI: 10.1016/j.annepidem.2016.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 04/09/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Betsy Foxman
- Department of Epidemiology, University of Michigan, Ann Arbor.
| | | | - Richard Rothenberg
- Division of Epidemiology and Biostatistics, Georgia State University, Atlanta
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