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Annunziato A, Vacca M, Cristofori F, Dargenio VN, Celano G, Francavilla R, De Angelis M. Celiac Disease: The Importance of Studying the Duodenal Mucosa-Associated Microbiota. Nutrients 2024; 16:1649. [PMID: 38892582 PMCID: PMC11174386 DOI: 10.3390/nu16111649] [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: 05/02/2024] [Revised: 05/24/2024] [Accepted: 05/24/2024] [Indexed: 06/21/2024] Open
Abstract
There is increasing evidence indicating that changes in both the composition and functionality of the intestinal microbiome are closely associated with the development of several chronic inflammatory diseases, with celiac disease (CeD) being particularly noteworthy. Thanks to the advent of culture-independent methodologies, the ability to identify and quantify the diverse microbial communities residing within the human body has been significantly improved. However, in the context of CeD, a notable challenge lies in characterizing the specific microbiota present on the mucosal surfaces of the intestine, rather than relying solely on fecal samples, which may not fully represent the relevant microbial populations. Currently, our comprehension of the composition and functional importance of mucosa-associated microbiota (MAM) in CeD remains an ongoing field of research because the limited number of available studies have reported few and sometimes contradictory results. MAM plays a crucial role in the development and progression of CeD, potentially acting as both a trigger and modulator of the immune response within the intestinal mucosa, given its proximity to the epithelial cells and direct interaction. According to this background, this review aims to consolidate the existing literature specifically focused on MAM in CeD. By elucidating the complex interplay between the host immune system and the gut microbiota, we aim to pave the way for new interventions based on novel therapeutic targets and diagnostic biomarkers for MAM in CeD.
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Affiliation(s)
- Alessandro Annunziato
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (A.A.); (G.C.); (M.D.A.)
| | - Mirco Vacca
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (A.A.); (G.C.); (M.D.A.)
| | - Fernanda Cristofori
- Interdisciplinary Department of Medicine, Pediatric Section, Children’s Hospital ‘Giovanni XXIII’, University of Bari Aldo Moro, 70126 Bari, Italy; (F.C.); (V.N.D.); (R.F.)
| | - Vanessa Nadia Dargenio
- Interdisciplinary Department of Medicine, Pediatric Section, Children’s Hospital ‘Giovanni XXIII’, University of Bari Aldo Moro, 70126 Bari, Italy; (F.C.); (V.N.D.); (R.F.)
| | - Giuseppe Celano
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (A.A.); (G.C.); (M.D.A.)
| | - Ruggiero Francavilla
- Interdisciplinary Department of Medicine, Pediatric Section, Children’s Hospital ‘Giovanni XXIII’, University of Bari Aldo Moro, 70126 Bari, Italy; (F.C.); (V.N.D.); (R.F.)
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Via Amendola 165/a, 70126 Bari, Italy; (A.A.); (G.C.); (M.D.A.)
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Duncanson K, Williams G, Hoedt EC, Collins CE, Keely S, Talley NJ. Diet-microbiota associations in gastrointestinal research: a systematic review. Gut Microbes 2024; 16:2350785. [PMID: 38725230 PMCID: PMC11093048 DOI: 10.1080/19490976.2024.2350785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Interactions between diet and gastrointestinal microbiota influence health status and outcomes. Evaluating these relationships requires accurate quantification of dietary variables relevant to microbial metabolism, however current dietary assessment methods focus on dietary components relevant to human digestion only. The aim of this study was to synthesize research on foods and nutrients that influence human gut microbiota and thereby identify knowledge gaps to inform dietary assessment advancements toward better understanding of diet-microbiota interactions. Thirty-eight systematic reviews and 106 primary studies reported on human diet-microbiota associations. Dietary factors altering colonic microbiota included dietary patterns, macronutrients, micronutrients, bioactive compounds, and food additives. Reported diet-microbiota associations were dominated by routinely analyzed nutrients, which are absorbed from the small intestine but analyzed for correlation to stool microbiota. Dietary derived microbiota-relevant nutrients are more challenging to quantify and underrepresented in included studies. This evidence synthesis highlights advancements needed, including opportunities for expansion of food composition databases to include microbiota-relevant data, particularly for human intervention studies. These advances in dietary assessment methodology will facilitate translation of microbiota-specific nutrition therapy to practice.
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Affiliation(s)
- Kerith Duncanson
- NHMRC Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Medicine & Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia
| | - Georgina Williams
- NHMRC Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Medicine & Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia
| | - Emily C. Hoedt
- NHMRC Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia
| | - Clare E. Collins
- Immune Health Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Medicine & Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia
| | - Simon Keely
- NHMRC Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Biomedical Sciences & Pharmacy, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia
| | - Nicholas J. Talley
- NHMRC Centre of Research Excellence in Digestive Health, University of Newcastle, Newcastle, NSW, Australia
- Immune Health Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- School of Medicine & Public Health, College of Health, Medicine and Wellbeing, University of Newcastle, Newcastle, NSW, Australia
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Kato-Kogoe N, Kamiya K, Sakaguchi S, Omori M, Komori E, Kudo A, Nakamura S, Nakano T, Ueno T, Tamaki J, Hoshiga M. Salivary Microbiota Associated with Peripheral Microvascular Endothelial Dysfunction. J Atheroscler Thromb 2022. [PMID: 36130883 DOI: 10.5551/jat.63681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
AIMS Oral health is associated with atherosclerotic cardiovascular disease (ACVD). We previously identified the salivary microbiota characteristics of patients with ACVD. However, whether salivary microbiota is characteristic under impaired vascular endothelial function before ACVD onset remains unclear. Therefore, we aimed to evaluate the characteristics of salivary microbiota associated with peripheral microvascular endothelial dysfunction. METHODS We collected saliva samples from 172 community-dwelling elderly individuals without a history of ACVD and performed 16S rRNA metagenomic analysis. We assessed the peripheral microvascular endothelial function using reactive hyperemia index (RHI) and compared the salivary microbiota in the groups with normal (RHI ≥ 2.10), borderline, and abnormal (RHI <1.67) peripheral endothelial function. Furthermore, we applied machine learning techniques to evaluate whether salivary microbiota could discriminate between individuals with normal and abnormal endothelial function. RESULTS The number of operational taxonomic units (OTUs) was higher in the abnormal group than in the normal group (p=0.037), and differences were found in the overall salivary microbiota structure (unweighted UniFrac distances, p=0.038). The linear discriminant analysis (LDA) effect size (LEfSe) algorithm revealed several significantly differentially abundant bacterial genera between the two groups. An Extra Trees classifier model was built to discriminate between groups with normal and abnormal vascular endothelial function based on the microbial composition at the genus level (AUC=0.810). CONCLUSIONS The salivary microbiota in individuals with endothelial dysfunction was distinct from that in individuals with normal endothelial function, indicating that the salivary microbiota may be related to endothelial function.
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Affiliation(s)
- Nahoko Kato-Kogoe
- Department of Dentistry and Oral Surgery, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Kuniyasu Kamiya
- Department of Hygiene and Public Health, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Michi Omori
- Department of Dentistry and Oral Surgery, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Eri Komori
- Department of Dentistry and Oral Surgery, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Asako Kudo
- Department of Hygiene and Public Health, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Takaaki Ueno
- Department of Dentistry and Oral Surgery, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Junko Tamaki
- Department of Hygiene and Public Health, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Masaoki Hoshiga
- Department of Cardiology, Faculty of Medicine, Osaka Medical and Pharmaceutical University
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Marruganti C, Traversi J, Gaeta C, Ferrari Cagidiaco E, Parrini S, Discepoli N, Grandini S. Adherence to mediterranean diet, physical activity level and severity of periodontitis. Results from a University-based cross-sectional study. J Periodontol 2022; 93:1218-1232. [PMID: 35119695 PMCID: PMC9544461 DOI: 10.1002/jper.21-0643] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 11/06/2022]
Abstract
AIM to evaluate the association between adherence to Mediterranean Diet (MD) and Physical Activity (PA) level with the periodontal status of a University-based cohort of individuals. MATERIALS AND METHODS 235 individuals were included in the study. MD adherence and PA level were registered through validated questionnaires, together with a full periodontal examination. Crude and adjusted Odds ratios (ORs) [95% Confidence Interval] were calculated to evaluate the association between MD adherence, PA level and periodontitis severity. A final logistic multivariate regression model was built to evaluate the impact of the combination between low MD adherence and low PA level on the prevalence of stage III/IV periodontitis. RESULTS The adjusted ORs for stage III/IV periodontitis were 1.65[0.84-3.28;p = .42] for low PA and 5.63[3.21-9.84;p = .00] for low MD adherence. The final logistic multivariate regression model resulted in OR = 10.23[4.01,26.09;p = .00] of having stage III/IV periodontitis in individuals with low MD adherence and low PA. CONCLUSIONS Individuals conducing a lifestyle characterized by the combination of low MD adherence and lack of regular exercise had 10 times the odds to have severe forms of periodontitis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Crystal Marruganti
- Unit of Periodontology, Endodontology and Restorative dentistry, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Jacopo Traversi
- Unit of Periodontology, Endodontology and Restorative dentistry, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Carlo Gaeta
- Unit of Periodontology, Endodontology and Restorative dentistry, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | - Stefano Parrini
- Unit of Oral Surgery, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Nicola Discepoli
- Unit of Periodontology, Endodontology and Restorative dentistry, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Simone Grandini
- Unit of Periodontology, Endodontology and Restorative dentistry, Department of Medical Biotechnologies, University of Siena, Siena, Italy
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Blum J, Silva M, Byrne SJ, Butler CA, Adams GG, Reynolds EC, Dashper SG. Temporal development of the infant oral microbiome. Crit Rev Microbiol 2022; 48:730-742. [PMID: 35015598 DOI: 10.1080/1040841x.2021.2025042] [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: 12/21/2022]
Abstract
The human oral microbiome is becoming recognized as playing roles in health and disease well beyond the oral cavity over the lifetime of the individual. The oral microbiome is hypothesized to result from specific colonization events followed by a reproducible and ordered development of complex bacterial communities. Colonization events, proliferation, succession and subsequent community development are dependent on a range of host and environmental factors, most notably the neonate diet. It is now becoming apparent that early childhood and prenatal influences can have long term effects on the development of human oral microbiomes. In this review, the temporal development of the infant human oral microbiome is examined, with the effects of prenatal and postnatal influences and the roles of specific bacteria. Dietary and environmental factors, especially breastfeeding, have a significant influence on the development of the infant oral microbiome. The evidence available regarding the roles and functions of early colonizing bacteria is still limited, and gaps in knowledge where further research is needed to elucidate these specific roles in relation to health and disease still exist.
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Affiliation(s)
- Jordan Blum
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
| | - Mihiri Silva
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
| | - Samantha J Byrne
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
| | - Catherine A Butler
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
| | - Geoffrey G Adams
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
| | - Eric C Reynolds
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
| | - Stuart G Dashper
- Centre for Oral Health Research, Melbourne Dental School, University of Melbourne, Carlton, Australia
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Laswi I, Shafiq A, Al-Ali D, Burney Z, Pillai K, Salameh M, Mhaimeed N, Zakaria D, Chaari A, Yousri NA, Bendriss G. A Comparative Pilot Study of Bacterial and Fungal Dysbiosis in Neurodevelopmental Disorders and Gastrointestinal Disorders: Commonalities, Specificities and Correlations with Lifestyle. Microorganisms 2021; 9:741. [PMID: 33918112 PMCID: PMC8065742 DOI: 10.3390/microorganisms9040741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/15/2023] Open
Abstract
Gastrointestinal disorders (GIDs) are a common comorbidity in patients with neurodevelopmental disorders (NDDs), while anxiety-like behaviors are common among patients with gastrointestinal diseases. It is still unclear as to which microbes differentiate these two groups. This pilot study aims at proposing an answer by exploring both the bacteriome and the mycobiome in a cohort of 55 volunteers with NDD, GID or controls, while accounting for additional variables that are not commonly included such as probiotic intake and diet. Recruited participants answered a questionnaire and provided a stool sample using the Fisherbrand collection kit. Bacterial and fungal DNA was extracted using the Qiagen Stool minikit. Sequencing (16sRNA and ITS) and phylogenetic analyses were performed using the PE300 Illumina Miseq v3 sequencing. Statistical analysis was performed using the R package. Results showed a significant decrease in bacterial alpha diversity in both NDD and GID, but an increased fungal alpha diversity in NDD. Data pointed at a significant bacterial dysbiosis between the three groups, but the mycobiome dysbiosis is more pronounced in NDD than in GID. Fungi seem to be more affected by probiotics, diet and antibiotic exposure and are proposed to be the main key player in differentiation between NDD and GID dybiosis.
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Affiliation(s)
- Ibrahim Laswi
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Ameena Shafiq
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Dana Al-Ali
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Zain Burney
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Krishnadev Pillai
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Mohammad Salameh
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Nada Mhaimeed
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Dalia Zakaria
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Ali Chaari
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
| | - Noha A. Yousri
- Research Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar;
- Computers and System Engineering, Alexandria University, Alexandria 21526, Egypt
| | - Ghizlane Bendriss
- Premedical Education Department, Weill Cornell Medicine Qatar, Doha 24144, Qatar; (I.L.); (A.S.); (D.A.-A.); (Z.B.); (K.P.); (M.S.); (N.M.); (D.Z.); (A.C.)
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7
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Salami B, Fernandez-Sanchez H, Fouche C, Evans C, Sibeko L, Tulli M, Bulaong A, Kwankye SO, Ani-Amponsah M, Okeke-Ihejirika P, Gommaa H, Agbemenu K, Ndikom CM, Richter S. A Scoping Review of the Health of African Immigrant and Refugee Children. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18073514. [PMID: 33800663 PMCID: PMC8038070 DOI: 10.3390/ijerph18073514] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/02/2022]
Abstract
Migration is a growing phenomenon around the world, including within the African continent. Many migrants, especially African children, face challenges related to health and social inclusion and can face increased health risks. A systematic scoping review of available literature on the health of African migrant children across the globe was conducted to offer insight into these health risks. The review was conducted over a 15-month period from January 2019 to April 2020, yielding 6602 articles once duplicates were removed. This search included electronic databases, reference lists of articles reviewed, and searches of libraries of relevant organisations. A total of 187 studies met the inclusion criteria, of which 159 were quantitative, 22 were qualitative, and 6 used mixed methods. The findings reveal decreased health in this population in areas of nutrition, infectious diseases, mental health, birth outcomes, sexual and reproductive health, physical and developmental health, parasitic infections, oral health, respiratory health, preventative health, endocrine disorders, health care services, and haematological conditions. The findings offer insights into factors influencing the health of African immigrant and refugee children. Further studies, especially qualitative studies, are needed to determine barriers to service access after migration and to investigate other underexplored and overlooked health concerns of African migrant children, including pneumonia and child maltreatment.
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Affiliation(s)
- Bukola Salami
- Faculty of Nursing, University of Alberta, 11405 87 Avenue, Edmonton, AB T6G 0Z7, Canada; (H.F.-S.); (M.T.); (A.B.); (S.R.)
- Correspondence:
| | - Higinio Fernandez-Sanchez
- Faculty of Nursing, University of Alberta, 11405 87 Avenue, Edmonton, AB T6G 0Z7, Canada; (H.F.-S.); (M.T.); (A.B.); (S.R.)
| | - Christa Fouche
- Faculty of Education and Social Work, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand;
| | - Catrin Evans
- School of Health Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK;
| | - Lindiwe Sibeko
- Department of Nutrition, School of Public Health and Health Sciences, University of Massachusetts, 204 Chenoweth Laboratory, Amherst, MA 01003-9282, USA;
| | - Mia Tulli
- Faculty of Nursing, University of Alberta, 11405 87 Avenue, Edmonton, AB T6G 0Z7, Canada; (H.F.-S.); (M.T.); (A.B.); (S.R.)
| | - Ashley Bulaong
- Faculty of Nursing, University of Alberta, 11405 87 Avenue, Edmonton, AB T6G 0Z7, Canada; (H.F.-S.); (M.T.); (A.B.); (S.R.)
| | - Stephen Owusu Kwankye
- Regional Institute for Population Studies, University of Ghana, P.O. Box LG 96, Legon, Accra GA184, Ghana;
| | - Mary Ani-Amponsah
- School of Nursing, University of Ghana, P.O. Box LG 43, Legon, Accra GA184, Ghana;
| | | | - Hayat Gommaa
- Department of Nursing Science, Ahmadu Bello University, Sokoto Road, PMB 06, Zaria 810107, Nigeria;
| | - Kafuli Agbemenu
- School of Nursing, The State University of New York (SUNY), University at Buffalo, 3435 Main Street, Buffalo, NY 14214, USA;
| | | | - Solina Richter
- Faculty of Nursing, University of Alberta, 11405 87 Avenue, Edmonton, AB T6G 0Z7, Canada; (H.F.-S.); (M.T.); (A.B.); (S.R.)
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Poddighe D, Kushugulova A. Salivary Microbiome in Pediatric and Adult Celiac Disease. Front Cell Infect Microbiol 2021; 11:625162. [PMID: 33680992 PMCID: PMC7927425 DOI: 10.3389/fcimb.2021.625162] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/06/2021] [Indexed: 12/15/2022] Open
Abstract
The human salivary microbiota includes hundreds of bacterial species. Alterations in gut microbiota have been explored in Celiac Disease (CD), but fewer studies investigated the characteristics of salivary microbiome in these patients, despite the potential implications in its pathogenesis. Indeed, some recent studies suggested that the partial digestion of gluten proteins by some bacteria may affect the array of gluten peptides reaching the gut and the way by which those are presented to the intestinal immune system. The available clinical studies investigating the salivary microbiota in children and adults, are insufficient to make any reliable conclusion, even though some bacterial species/phyla differences have been reported between celiac patients and controls. However, the salivary microbiome could correlate better with the duodenal microbiota, than the fecal one. Therefore, further clinical studies on salivary microbiome by different and independent research groups and including different populations, are advisable in order to explore the usefulness of the salivary microbiome analysis and understand some aspects of CD pathogenesis with potential clinical and practical implications.
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Affiliation(s)
- Dimitri Poddighe
- Department of Medicine, Nazarbayev University School of Medicine (NUSOM), Nur-Sultan, Kazakhstan.,Department of Pediatrics, National Research Center for Mother and Child Health, University Medical Center, Nur-Sultan, Kazakhstan
| | - Almagul Kushugulova
- Laboratory of Human Microbiome and Longevity, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
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9
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Zaura E, Pappalardo VY, Buijs MJ, Volgenant CMC, Brandt BW. Optimizing the quality of clinical studies on oral microbiome: A practical guide for planning, performing, and reporting. Periodontol 2000 2021; 85:210-236. [PMID: 33226702 PMCID: PMC7756869 DOI: 10.1111/prd.12359] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
With this review, we aim to increase the quality standards for clinical studies with microbiome as an output parameter. We critically address the existing body of evidence for good quality practices in oral microbiome studies based on 16S rRNA gene amplicon sequencing. First, we discuss the usefulness of microbiome profile analyses. Is a microbiome study actually the best approach for answering the research question? This is followed by addressing the criteria for the most appropriate study design, sample size, and the necessary data (study metadata) that should be collected. Next, we evaluate the available evidence for best practices in sample collection, transport, storage, and DNA isolation. Finally, an overview of possible sequencing options (eg, 16S rRNA gene hypervariable regions, sequencing platforms), processing and data interpretation approaches, as well as requirements for meaningful data storage, sharing, and reporting are provided.
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Affiliation(s)
- Egija Zaura
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
| | - Vincent Y. Pappalardo
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
| | - Mark J. Buijs
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
| | - Catherine M. C. Volgenant
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
| | - Bernd W. Brandt
- Department of Preventive DentistryAcademic Centre for Dentistry Amsterdam (ACTA)Vrije Universiteit Amsterdam and University of AmsterdamAmsterdamthe Netherlands
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10
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Koslovsky MD, Hoffman KL, Daniel CR, Vannucci M. A Bayesian model of microbiome data for simultaneous identification of covariate associations and prediction of phenotypic outcomes. Ann Appl Stat 2020. [DOI: 10.1214/20-aoas1354] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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A Mediterranean Diet Intervention Reduces the Levels of Salivary Periodontopathogenic Bacteria in Overweight and Obese Subjects. Appl Environ Microbiol 2020; 86:AEM.00777-20. [PMID: 32276980 DOI: 10.1128/aem.00777-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 04/08/2020] [Indexed: 12/12/2022] Open
Abstract
The human oral cavity is a complex ecosystem, and the alterations in salivary microbial communities are associated with both oral and nonoral diseases. The Mediterranean diet (MD) is a healthy dietary pattern useful for both prevention and treatment of several diseases. To further explore the effects of the MD on human health, in this study, we investigated the changes in the salivary microbial communities in overweight/obese subjects after an individually tailored MD-based nutritional intervention. Healthy overweight and obese subjects were randomized between two intervention groups. The MD group (Med-D group) increased their MD adherence during 8 weeks of intervention while the control diet (control-D) group did not change their dietary habits. The salivary microbiota was assessed at baseline and after 4 and 8 weeks of intervention. Despite no observed changes in the overall salivary microbiota composition, we found a significant decrease in the relative abundances of species-level operational taxonomic units annotated as Porphyromonas gingivalis, Prevotella intermedia, and Treponema denticola in the Med-D group compared to that in the control-D group after 8 weeks of intervention, which are known to be associated with periodontal disease. Such variations were significantly linked to dietary variables such as MD adherence rates and intakes of animal versus vegetable proteins. In addition, increased levels of Streptococcus cristatus were observed in the Med-D group, which has been reported as an antagonistic taxon inhibiting P. gingivalis gene expression. Our findings suggest that an MD-based nutritional intervention may be implicated in reducing periodontal bacteria, and an MD may be a dietary strategy supportive of oral homeostasis.IMPORTANCE Changes in dietary behavior with increased adherence to a Mediterranean diet can determine a reduction of periodontopathogenic bacterial abundances in the saliva of overweight subjects with cardiometabolic risk due to an unhealthy lifestyle, without any change in individual energy intake, nutrient intake, and physical activity.
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A Two-Sample Mendelian Randomization Analysis Investigates Associations Between Gut Microbiota and Celiac Disease. Nutrients 2020; 12:nu12051420. [PMID: 32423041 PMCID: PMC7284592 DOI: 10.3390/nu12051420] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 12/20/2022] Open
Abstract
Celiac disease (CeD) is a complex immune-mediated inflammatory condition triggered by the ingestion of gluten in genetically predisposed individuals. Literature suggests that alterations in gut microbiota composition and function precede the onset of CeD. Considering that microbiota is partly determined by host genetics, we speculated that the genetic makeup of CeD patients could elicit disease development through alterations in the intestinal microbiota. To evaluate potential causal relationships between gut microbiota and CeD, we performed a two-sample Mendelian randomization analysis (2SMR). Exposure data were obtained from the raw results of a previous genome-wide association study (GWAS) of gut microbiota and outcome data from summary statistics of CeD GWAS and Immunochip studies. We identified a number of putative associations between gut microbiota single nucleotide polymorphisms (SNPs) associated with CeD. Regarding bacterial composition, most of the associated SNPs were related to Firmicutes phylum, whose relative abundance has been previously reported to be altered in CeD patients. In terms of functional units, we linked a number of SNPs to several bacterial metabolic pathways that seemed to be related to CeD. Overall, this study represented the first 2SMR approach to elucidate the relationship between microbiome and CeD.
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Viljakainen J, Raju SC, Viljakainen H, Figueiredo RADO, Roos E, Weiderpass E, Rounge TB. Meal Regularity Plays a Role in Shaping the Saliva Microbiota. Front Microbiol 2020; 11:757. [PMID: 32390990 PMCID: PMC7194025 DOI: 10.3389/fmicb.2020.00757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/30/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Diet may influence health directly or indirectly via the human microbiota, emphasizing the need to unravel these complex relationships for future health benefits. Associations between eating habits and gut microbiota have been shown, but less is known about the association between eating habits and saliva microbiota. OBJECTIVE The aim of this study was to investigate if eating habits and meal patterns are associated with the saliva microbiota. METHODS In total, 842 adolescents, aged 11-14 years, from the Finnish Health in Teens (Fin-HIT) study cohort were included in this study. Eating habits and breakfast and dinner patterns were derived from a web-based questionnaire answered in school. Three major eating habit groups were identified: fruit and vegetable avoiders (FV avoiders), healthy and unhealthy. Microbiota profiles were produced from 16S rRNA gene (V3-V4) sequencing of DNA from the saliva samples. Statistical models were adjusted for gender, age, parental language, body mass index (BMI) categories, and sequencing depth. RESULTS Regular breakfast eaters had a higher alpha diversity (Shannon index with mean (standard error of means) 2.27 (0.03) vs. 2.22 (0.03), p = 0.06, inverse Simpson's index with 6.27 (0.17) vs. 5.80 (0.02), p = 0.01), and slight differences in bacterial composition (PERMANOVA: p = 0.001) compared with irregular breakfast eaters. A similar trend in alpha diversity was observed between regular and irregular dinner eaters (Shannon index with 2.27 (0.03) vs. 2.22 (0.03), p = 0.054, inverse Simpson's index with 6.23 (0.17) vs. 6.04 (0.22), p = 0.28), while no difference was found in composition (PERMANOVA: p = 0.08). No differences were identified between eating habit groups and saliva microbiota diversity (Shannon index p = 0.77, inverse Simpson's index p = 0.94) or composition (PERMANOVA: p = 0.13). FV avoiders, irregular breakfast eaters and irregular dinner eaters had high abundances of Prevotella. CONCLUSION Regularity of eating, especially breakfast eating, was associated with more diverse saliva microbiota and different composition compared with irregular eaters. However, the dissimilarities in composition were small between regular and irregular breakfast eaters. Our results suggest that Prevotella abundances in saliva were common in FV avoiders and meal skippers. However, the clinical implications of these findings need to be evaluated in future studies.
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Affiliation(s)
- Jannina Viljakainen
- Folkhälsan Research Center, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sajan C. Raju
- Folkhälsan Research Center, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Heli Viljakainen
- Folkhälsan Research Center, Helsinki, Finland
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | | | - Eva Roos
- Folkhälsan Research Center, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Food and Nutrition, University of Helsinki, Helsinki, Finland
| | - Elisabete Weiderpass
- International Agency for Research on Cancer – World Health Organization, Lyon, France
| | - Trine B. Rounge
- Folkhälsan Research Center, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Research, Cancer Registry of Norway, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
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De Angelis M, Garruti G, Minervini F, Bonfrate L, Portincasa P, Gobbetti M. The Food-gut Human Axis: The Effects of Diet on Gut Microbiota and Metabolome. Curr Med Chem 2019; 26:3567-3583. [PMID: 28462705 DOI: 10.2174/0929867324666170428103848] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 02/08/2023]
Abstract
Gut microbiota, the largest symbiont community hosted in human organism, is emerging as a pivotal player in the relationship between dietary habits and health. Oral and, especially, intestinal microbes metabolize dietary components, affecting human health by producing harmful or beneficial metabolites, which are involved in the incidence and progression of several intestinal related and non-related diseases. Habitual diet (Western, Agrarian and Mediterranean omnivore diets, vegetarian, vegan and gluten-free diets) drives the composition of the gut microbiota and metabolome. Within the dietary components, polymers (mainly fibers, proteins, fat and polyphenols) that are not hydrolyzed by human enzymes seem to be the main leads of the metabolic pathways of gut microbiota, which in turn directly influence the human metabolome. Specific relationships between diet and microbes, microbes and metabolites, microbes and immune functions and microbes and/or their metabolites and some human diseases are being established. Dietary treatments with fibers are the most effective to benefit the metabolome profile, by improving the synthesis of short chain fatty acids and decreasing the level of molecules, such as p-cresyl sulfate, indoxyl sulfate and trimethylamine N-oxide, involved in disease state. Based on the axis diet-microbiota-health, this review aims at describing the most recent knowledge oriented towards a profitable use of diet to provide benefits to human health, both directly and indirectly, through the activity of gut microbiota.
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Affiliation(s)
- Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Gabriella Garruti
- Department of Emergency and Organ Transplants, Section of Endocrinology, Andrology and Metabolic Diseases, University of Bari Medical School, Bari, Italy
| | - Fabio Minervini
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy
| | - Leonilde Bonfrate
- Department of Soil, Plant and Food Science, University of Bari Aldo Moro, Bari, Italy.,Clinica Medica "A. Murri", Department of Biomedical Sciences and Human Oncology, University of Bari Medical School, Bari, Italy
| | - Piero Portincasa
- Clinica Medica "A. Murri", Department of Biomedical Sciences and Human Oncology, University of Bari Medical School, Bari, Italy
| | - Marco Gobbetti
- Faculty of Science and Technology, Free University of Bozen, Bolzano, Italy
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Sandell MA, Collado MC. Genetic variation in the TAS2R38 taste receptor contributes to the oral microbiota in North and South European locations: a pilot study. GENES AND NUTRITION 2018. [DOI: 10.1186/s12263-018-0617-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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16
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Garcia-Mazcorro JF, Rivera-Gutierrez X, Cobos-Quevedo ODJ, Grube-Pagola P, Meixueiro-Daza A, Hernandez-Flores K, Cabrera-Jorge FJ, Vivanco-Cid H, Dowd SE, Remes-Troche JM. First Insights into the Gut Microbiota of Mexican Patients with Celiac Disease and Non-Celiac Gluten Sensitivity. Nutrients 2018; 10:E1641. [PMID: 30400238 PMCID: PMC6266755 DOI: 10.3390/nu10111641] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 10/20/2018] [Accepted: 10/31/2018] [Indexed: 12/13/2022] Open
Abstract
Gluten-related disorders (GRDs) are common chronic enteropathies and increasing evidence suggests an involvement of the gut microbiota. We examined the gut microbiota in Mexican people afflicted with GRDs. Ultra-high-throughput 16S marker sequencing was used to deeply describe the duodenal and fecal microbiota of patients with celiac disease (CD, n = 6), non-celiac gluten sensitivity (NCGS, n = 12), and healthy subjects (n = 12) from our local area. Additionally, we also investigated the changes in gut microbiota after four weeks on a gluten-free diet (GFD) in a subset of patients from whom paired samples were available. Despite a high inter-individual variability, significant differences in various microbial populations were identified. The linear discriminant analysis (LDA) effect size (LEfSe) method revealed that the genus Actinobacillus and the family Ruminococcaceae were higher in the duodenal and fecal microbiota of NCGS patients, respectively, while Novispirillum was higher in the duodenum of CD patients (p < 0.05, LDA score > 3.5). Interestingly, paired samples from NCGS patients showed a significant difference in duodenal Pseudomonas between the baseline period (median: 1.3%; min/max: 0.47⁻6.8%) and the period after four weeks on GFD (14.8%; 2.3⁻38.5%, p < 0.01, Wilcoxon signed-rank test). These results encourage more research on GRDs in México.
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Affiliation(s)
- Jose F Garcia-Mazcorro
- Instituto de Investigaciones Medico Biológicas, Universidad Veracruzana, Calle Agustín de Iturbide, Salvador Díaz Mirón, 91700 Veracruz, México.
| | - Xaira Rivera-Gutierrez
- Instituto de Investigaciones Medico Biológicas, Universidad Veracruzana, Calle Agustín de Iturbide, Salvador Díaz Mirón, 91700 Veracruz, México.
| | - Orestes De Jesus Cobos-Quevedo
- Instituto de Investigaciones Medico Biológicas, Universidad Veracruzana, Calle Agustín de Iturbide, Salvador Díaz Mirón, 91700 Veracruz, México.
| | - Peter Grube-Pagola
- Instituto de Investigaciones Medico Biológicas, Universidad Veracruzana, Calle Agustín de Iturbide, Salvador Díaz Mirón, 91700 Veracruz, México.
| | - Arturo Meixueiro-Daza
- Instituto de Investigaciones Medico Biológicas, Universidad Veracruzana, Calle Agustín de Iturbide, Salvador Díaz Mirón, 91700 Veracruz, México.
| | - Karina Hernandez-Flores
- Instituto de Investigaciones Medico Biológicas, Universidad Veracruzana, Calle Agustín de Iturbide, Salvador Díaz Mirón, 91700 Veracruz, México.
| | - Francisco J Cabrera-Jorge
- Instituto de Investigaciones Medico Biológicas, Universidad Veracruzana, Calle Agustín de Iturbide, Salvador Díaz Mirón, 91700 Veracruz, México.
| | - Hector Vivanco-Cid
- Instituto de Investigaciones Medico Biológicas, Universidad Veracruzana, Calle Agustín de Iturbide, Salvador Díaz Mirón, 91700 Veracruz, México.
| | - Scot E Dowd
- Molecular Research LP, 503 Clovis Rd, Shallowater, TX 79363, USA.
| | - Jose M Remes-Troche
- Laboratorio de Fisiología Digestiva y Motilidad Gastrointestinal, Instituto de Investigaciones Medico Biológicas, Universidad Veracruzana, Calle Agustín de Iturbide, Salvador Díaz Mirón, 91700 Veracruz, México.
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Chander AM, Yadav H, Jain S, Bhadada SK, Dhawan DK. Cross-Talk Between Gluten, Intestinal Microbiota and Intestinal Mucosa in Celiac Disease: Recent Advances and Basis of Autoimmunity. Front Microbiol 2018; 9:2597. [PMID: 30443241 PMCID: PMC6221985 DOI: 10.3389/fmicb.2018.02597] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/11/2018] [Indexed: 12/17/2022] Open
Abstract
Celiac disease (CD) is an autoimmune disorder of the small intestine, caused by gluten induced inflammation in some individuals susceptible to genetic and environmental influences. To date, pathophysiology of CD in relation to intestinal microbiota is not known well. This review relies on contribution of intestinal microbiome and oral microbiome in pathogenesis of CD based on their interactions with gluten, thereby highlighting the role of upper gastrointestinal microbiota. It has been hypothesized that CD might be triggered by additive effects of immunotoxic gluten peptides and intestinal dysbiosis (microbial imbalance) in the people with or without genetic susceptibilities, where antibiotics may be deriving dysbiotic agents. In contrast to the intestinal dysbiosis, genetic factors even seem secondary in disease outcome thus suggesting the importance of interaction between microbes and dietary factors in immune regulation at intestinal mucosa. Moreover, association of imbalanced counts of some commensal microbes in intestine of CD patients suggests the scope for probiotic therapies. Lactobacilli and specific intestinal and oral bacteria are potent source of gluten degrading enzymes (glutenases) that may contribute to commercialization of a novel glutenase therapy. In this review, we shall discuss advantages and disadvantages of food based therapies along with probiotic therapies where probiotic therapies are expected to emerge as the safest biotherapies among other in-process therapies. In addition, this review emphasizes on differential targets of probiotics that make them suitable to manage CD as along with glutenase activity, they also exhibit immunomodulatory and intestinal microbiome modulatory properties.
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Affiliation(s)
- Atul Munish Chander
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.,Department of Biophysics, Panjab University, Chandigarh, India
| | - Hariom Yadav
- Center for Diabetes, Obesity and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Shalini Jain
- Center for Diabetes, Obesity and Metabolism, Wake Forest School of Medicine, Winston-Salem, NC, United States
| | - Sanjay Kumar Bhadada
- Department of Endocrinology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Pulikkan J, Maji A, Dhakan DB, Saxena R, Mohan B, Anto MM, Agarwal N, Grace T, Sharma VK. Gut Microbial Dysbiosis in Indian Children with Autism Spectrum Disorders. MICROBIAL ECOLOGY 2018; 76:1102-1114. [PMID: 29564487 DOI: 10.1007/s00248-018-1176-2] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/06/2018] [Indexed: 05/02/2023]
Abstract
Autism spectrum disorder (ASD) is a term associated with a group of neurodevelopmental disorders. The etiology of ASD is not yet completely understood; however, a disorder in the gut-brain axis is emerging as a prominent factor leading to autism. To identify the taxonomic composition and markers associated with ASD, we compared the fecal microbiota of 30 ASD children diagnosed using Childhood Autism Rating Scale (CARS) score, DSM-5 approved AIIMS-modified INCLEN Diagnostic Tool for Autism Spectrum Disorder (INDT-ASD), and Indian Scale for Assessment of Autism (ISAA) tool, with family-matched 24 healthy children from Indian population using next-generation sequencing (NGS) of 16S rRNA gene amplicon. Our study showed prominent dysbiosis in the gut microbiome of ASD children, with higher relative abundances of families Lactobacillaceae, Bifidobacteraceae, and Veillonellaceae, whereas the gut microbiome of healthy children was dominated by the family Prevotellaceae. Comparative meta-analysis with a publicly available dataset from the US population consisting of 20 ASD and 20 healthy control samples from children of similar age, revealed a significantly high abundance of genus Lactobacillus in ASD children from both the populations. The results reveal the microbial dysbiosis and an association of selected Lactobacillus species with the gut microbiome of ASD children.
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Affiliation(s)
- Joby Pulikkan
- Department of Genomic Science, Central University of Kerala, Kasaragod, India
| | - Abhijit Maji
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Darshan Bharat Dhakan
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Rituja Saxena
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
| | - Binoop Mohan
- Department of Genomic Science, Central University of Kerala, Kasaragod, India
| | - Milu Maria Anto
- Department of Psychology, Prajyoti Niketan College, Pudukad, Kerala, India
| | - Neeti Agarwal
- Department of Paediatrics and Neurology, Mahaveer Institute of Medical Science, Bhopal, India
| | - Tony Grace
- Department of Genomic Science, Central University of Kerala, Kasaragod, India.
- Division of Biology, Kansas State University, Manhattan, KS, USA.
| | - Vineet K Sharma
- Metagenomics and Systems Biology Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India.
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Garcia-Mazcorro JF, Noratto G, Remes-Troche JM. The Effect of Gluten-Free Diet on Health and the Gut Microbiota Cannot Be Extrapolated from One Population to Others. Nutrients 2018; 10:E1421. [PMID: 30287726 PMCID: PMC6212913 DOI: 10.3390/nu10101421] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/25/2018] [Accepted: 10/01/2018] [Indexed: 02/07/2023] Open
Abstract
Gluten-related disorders (GRD) affect millions of people worldwide and have been related to the composition and metabolism of the gut microbiota. These disorders present differently in each patient and the only treatment available is a strict life-long gluten-free diet (GFD). Several studies have investigated the effect of a GFD on the gut microbiota of patients afflicted with GRD as well as healthy people. The purpose of this review is to persuade the biomedical community to think that, while useful, the results from the effect of GFD on health and the gut microbiota cannot be extrapolated from one population to others. This argument is primarily based on the highly individualized pattern of gut microbial composition and metabolic activity in each person, the variability of the gut microbiota over time and the plethora of factors associated with this variation. In addition, there is wide variation in the composition, economic viability, and possible deleterious effects to health among different GFD, both within and among countries. Overall, this paper encourages the conception of more collaborative efforts to study local populations in an effort to reach biologically and medically useful conclusions that truly contribute to improve health in patients afflicted with GRD.
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Affiliation(s)
- Jose F Garcia-Mazcorro
- Instituto de Investigaciones Medico Biológicas, Universidad Veracruzana, Calle Agustín de Iturbide, Salvador Díaz Mirón, Veracruz 91700, Mexico.
| | - Giuliana Noratto
- Department of Nutrition and Food Science, Texas A&M University, 2253 TAMU, College Station, TX 77843, USA.
| | - Jose M Remes-Troche
- Instituto de Investigaciones Medico Biológicas, Universidad Veracruzana, Calle Agustín de Iturbide, Salvador Díaz Mirón, Veracruz 91700, Mexico.
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Skelly E, Kapellas K, Cooper A, Weyrich LS. Consequences of colonialism: A microbial perspective to contemporary Indigenous health. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:423-437. [DOI: 10.1002/ajpa.23637] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 05/31/2018] [Accepted: 06/01/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Emily Skelly
- Australian Centre for Ancient DNA, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Kostas Kapellas
- Australian Research Centre for Population Oral Health, Adelaide Dental School University of Adelaide Adelaide South Australia Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
| | - Laura S. Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences University of Adelaide Adelaide South Australia Australia
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Savo Sardaro ML, Perin LM, Bancalari E, Neviani E, Gatti M. Advancement in LH-PCR methodology for multiple microbial species detections in fermented foods. Food Microbiol 2018; 74:113-119. [PMID: 29706326 DOI: 10.1016/j.fm.2018.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 03/13/2018] [Accepted: 03/15/2018] [Indexed: 12/31/2022]
Abstract
The length-heterogeneity PCR is a low throughput molecular biology methods explored to monitor bacteria populations in different environments. It could be more used in food microbiology analysis, not only for fingerprinting analysis, but it has been hampered until now by a limiting factor which relates to the high percentage of secondary peaks. With the aim to overcome this problem, different experiments were performed focusing on changing PCR parameters in order to obtain more specific amplicon patterns and also to reduce the complexity of community patterns. With this purpose, different annealing temperatures were tested on complex fermented food matrices taken from both animal and vegetable origin and also on the bacteria isolated from the same food source. In particular, the optimal annealing temperature identified for the fermented food samples is 59 °C and the optimal for bacterial strains varied between 63 °C and 65 °C. The approach allowed the modification of the LH-PCR protocol increasing the amplification efficiency and therefore the bacteria species discrimination. These temperatures also allowed the implementation of the previous LH-PCR published database. The modification in the level of accuracy of the LH-PCR technique could also allow an improvement in the relative species quantification by the peak area evaluation.
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Affiliation(s)
- Maria Luisa Savo Sardaro
- University of Parma, Department of Food and Drug, Parco Area delle Scienze 49A, 43124 Parma, Italy; San Raffaele University, Department of Nutrition and Gastronomy, Via Val Cannuta 247, Rome, Italy.
| | - Luana Martins Perin
- Universidade Federal de Viçosa, Departamento de Veterinaria, Campus Universitario, Centro, 36570-900 Viçosa, MG, Brazil
| | - Elena Bancalari
- University of Parma, Department of Food and Drug, Parco Area delle Scienze 49A, 43124 Parma, Italy
| | - Erasmo Neviani
- University of Parma, Department of Food and Drug, Parco Area delle Scienze 49A, 43124 Parma, Italy
| | - Monica Gatti
- University of Parma, Department of Food and Drug, Parco Area delle Scienze 49A, 43124 Parma, Italy
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Selected Probiotic Lactobacilli Have the Capacity To Hydrolyze Gluten Peptides during Simulated Gastrointestinal Digestion. Appl Environ Microbiol 2017; 83:AEM.00376-17. [PMID: 28500039 DOI: 10.1128/aem.00376-17] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 05/02/2017] [Indexed: 12/14/2022] Open
Abstract
The aim of this study was to demonstrate the capacity of probiotic lactobacilli to hydrolyze immunogenic gluten peptides. Eighteen commercial strains of probiotic lactobacilli with highly variable peptidase activity (i.e., aminopeptidase N, iminopeptidase, prolyl endopeptidyl peptidase, tripeptidase, prolidase, prolinase, and dipeptidase), including toward Pro-rich peptides, were tested in this study. Ten probiotic strains were selected on the basis of their specific enzyme activity. When pooled, these 10 strains provided the peptidase portfolio that is required to completely degrade the immunogenic gluten peptides involved in celiac disease (CD). The selected probiotic mixture was able to completely hydrolyze well-known immunogenic epitopes, including the gliadin 33-mer peptide, the peptide spanning residues 57 to 68 of the α9-gliadin (α9-gliadin peptide 57-68), A-gliadin peptide 62-75, and γ-gliadin peptide 62-75. During digestion under simulated gastrointestinal conditions, the pool of 10 selected probiotic lactobacilli strongly hydrolyzed the wheat bread gluten (ca. 18,000 ppm) to less than 10 ppm after 360 min of treatment. As determined by multidimensional chromatography (MDLC) coupled to nanoelectrospray ionization (nano-ESI)-tandem mass spectrometry (MS/MS), no known immunogenic peptides were detected in wheat bread that was digested in the presence of the probiotics. Accordingly, the level of cytokines (interleukin 2 [IL-2], IL-10, and interferon gamma [IFN-γ]) produced by duodenal biopsy specimens from CD patients who consumed wheat bread digested by probiotics was similar to the baseline value (negative control). Probiotics that specifically hydrolyze gluten polypeptides could also be used to hydrolyze immunogenic peptides that contaminate gluten-free products. This could provide a new and safe adjunctive therapy alternative to the gluten-free diet (GFD).IMPORTANCE This study confirmed that probiotic Lactobacillus strains have different enzymatic abilities for hydrolyzing polypeptides, including the Pro-rich epitopes involved in the pathology of CD. Ten lactobacilli with complementary peptidase activities that hydrolyze gluten peptides during simulated gastrointestinal digestion were selected and tested. The results collected showed the potential of probiotic formulas as novel dietary treatments for CD patients.
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Salivary Gluten Degradation and Oral Microbial Profiles in Healthy Individuals and Celiac Disease Patients. Appl Environ Microbiol 2017; 83:AEM.03330-16. [PMID: 28087531 DOI: 10.1128/aem.03330-16] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/09/2017] [Indexed: 12/20/2022] Open
Abstract
Celiac disease (CD) is a chronic immune-mediated enteropathy induced by dietary gluten in genetically predisposed individuals. Saliva harbors the second highest bacterial load of the gastrointestinal (GI) tract after the colon. We hypothesized that enzymes produced by oral bacteria may be involved in gluten processing in the intestine and susceptibility to celiac disease. The aim of this study was to investigate salivary enzymatic activities and oral microbial profiles in healthy subjects versus patients with classical and refractory CD. Stimulated whole saliva was collected from patients with CD in remission (n = 21) and refractory CD (RCD; n = 8) and was compared to healthy controls (HC; n = 20) and subjects with functional GI complaints (n = 12). Salivary gluten-degrading activities were monitored with the tripeptide substrate Z-Tyr-Pro-Gln-pNA and the α-gliadin-derived immunogenic 33-mer peptide. The oral microbiome was profiled by 16S rRNA-based MiSeq analysis. Salivary glutenase activities were higher in CD patients compared to controls, both before and after normalization for protein concentration or bacterial load. The oral microbiomes of CD and RCD patients showed significant differences from that of healthy subjects, e.g., higher salivary levels of lactobacilli (P < 0.05), which may partly explain the observed higher gluten-degrading activities. While the pathophysiological link between the oral and gut microbiomes in CD needs further exploration, the presented data suggest that oral microbe-derived enzyme activities are elevated in subjects with CD, which may impact gluten processing and the presentation of immunogenic gluten epitopes to the immune system in the small intestine.IMPORTANCE Ingested gluten proteins are the triggers of intestinal inflammation in celiac disease (CD). Certain immunogenic gluten domains are resistant to intestinal proteases but can be hydrolyzed by oral microbial enzymes. Very little is known about the endogenous proteolytic processing of gluten proteins in the oral cavity. Given that this occurs prior to gluten reaching the small intestine, such enzymes are likely to contribute to the composition of the gluten digest that ultimately reaches the small intestine and causes CD. We demonstrated that endogenous salivary protease activities are incomplete, likely liberating peptides from larger gluten proteins. The potentially responsible microbes were identified. The study included refractory CD patients, who have been studied less with regard to CD pathogenesis.
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De Angelis M, Vannini L, Di Cagno R, Cavallo N, Minervini F, Francavilla R, Ercolini D, Gobbetti M. Salivary and fecal microbiota and metabolome of celiac children under gluten-free diet. Int J Food Microbiol 2016; 239:125-132. [PMID: 27452636 DOI: 10.1016/j.ijfoodmicro.2016.07.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 07/10/2016] [Accepted: 07/18/2016] [Indexed: 02/06/2023]
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Putignani L, Dallapiccola B. Foodomics as part of the host-microbiota-exposome interplay. J Proteomics 2016; 147:3-20. [PMID: 27130534 DOI: 10.1016/j.jprot.2016.04.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/10/2016] [Accepted: 04/20/2016] [Indexed: 02/08/2023]
Abstract
UNLABELLED The functional complexity of human gut microbiota and its relationship with host physiology and environmental modulating factors, offers the opportunity to investigate (i) the host and microbiota role in organism-environment relationship; (ii) the individual functional diversity and response to environmental stimuli (exposome); (iii) the host genome and microbiota metagenomes' modifications by diet-mediated epigenomic controls (nutriepigenomics); and (iv) the genotype-phenotype "trajectories" under physiological and disease constraints. Systems biology-based approaches aim at integrating biological data at cellular, tissue and organ organization levels, using computational modeling to interpret diseases' physiopathological mechanisms (i.e., onset and progression). Proteomics improves the existing gene models by profiling molecular phenotypes at protein abundance level, by analyzing post-translational modifications and protein-protein interactions and providing specific pathway information, hence contributing to functional molecular networks. Transcriptomics and metabolomics may determine host ad microbiota changes induced by food ingredients at molecular level, complementing functional genomics and proteomics data. Since foodomics is an -omic wide methodology may feed back all integrative data to foster the omics-based systems medicine field. Hence, coupled to ecological genomics of gut microbial communities, foodomics may highlight health benefits from nutrients, dissecting diet-induced gut microbiota eubiosis mechanisms and significantly contributing to understand and prevent complex disease phenotypes. BIOLOGICAL SIGNIFICANCE Besides transcriptomics and proteomics there is a growing interest in applying metabolic profiling to food science for the development of functional foods. Indeed, one of the biggest challenges of modern nutrition is to propose a healthy diet to populations worldwide, intrinsically respecting the high inter-individual variability, driven by complex host/nutrients/microbiota/environment interactions. Therefore, metabolic profiling can assist at various levels for the development of functional foods, starting from screening for food composition to identification of new biomarkers to trace food intake. This current approach can support diet intervention strategies, epidemiological studies, and controlling of metabolic disorders worldwide spreading, hence ensuring healthy aging. With high-throughput molecular technologies driving foodomics, studying bidirectional interactions of host-microbial co-metabolism, innate immune development, dysfunctional nutrient absorption and processing, complex signaling pathways involved in nutritional metabolism, is now likely. In all cases, as microbiome pipeline efforts continue, it is possible that enhanced standardized protocols can be developed, which may lead to new testable biological and clinical hypotheses. This Review provides a comprehensive update on the current state-of-the-art of the integrated -omics route in food, microbiota and host co-metabolism studies, which may revolutionize the design of new dietary intervention strategies.
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Affiliation(s)
- Lorenza Putignani
- Units of Parasitology and Human Microbiome, Bambino Gesù Children's Hospital and Research Institute, Piazza Sant'Onofrio 4, 00165 Rome, Italy.
| | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children's Hospital and Research Institute, Piazza Sant'Onofrio 4, 00165 Rome, Italy
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Fourie NH, Wang D, Abey SK, Sherwin LB, Joseph PV, Rahim-Williams B, Ferguson EG, Henderson WA. The microbiome of the oral mucosa in irritable bowel syndrome. Gut Microbes 2016; 7:286-301. [PMID: 26963804 PMCID: PMC4988452 DOI: 10.1080/19490976.2016.1162363] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Irritable bowel syndrome (IBS) is a poorly understood disorder characterized by persistent symptoms, including visceral pain. Studies have demonstrated oral microbiome differences in inflammatory bowel diseases suggesting the potential of the oral microbiome in the study of non-oral conditions. In this exploratory study we examine whether differences exist in the oral microbiome of IBS participants and healthy controls, and whether the oral microbiome relates to symptom severity. The oral buccal mucosal microbiome of 38 participants was characterized using PhyloChip microarrays. The severity of visceral pain was assessed by orally administering a gastrointestinal test solution. Participants self-reported their induced visceral pain. Pain severity was highest in IBS participants (P = 0.0002), particularly IBS-overweight participants (P = 0.02), and was robustly correlated to the abundance of 60 OTUs, 4 genera, 5 families and 4 orders of bacteria (r2 > 0.4, P < 0.001). IBS-overweight participants showed decreased richness in the phylum Bacteroidetes (P = 0.007) and the genus Bacillus (P = 0.008). Analysis of β-diversity found significant separation of the IBS-overweight group (P < 0.05). Our oral microbial results are concordant with described fecal and colonic microbiome-IBS and -weight associations. Having IBS and being overweight, rather than IBS-subtypes, was the most important factor in describing the severity of visceral pain and variation in the microbiome. Pain severity was strongly correlated to the abundance of many taxa, suggesting the potential of the oral microbiome in diagnosis and patient phenotyping. The oral microbiome has potential as a source of microbial information in IBS.
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Affiliation(s)
- Nicolaas H. Fourie
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Dan Wang
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Sarah K. Abey
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - LeeAnne B. Sherwin
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Paule V. Joseph
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Bridgett Rahim-Williams
- National Institute on Minority Health and Health Disparities, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Eric G. Ferguson
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
| | - Wendy A. Henderson
- Division of Intramural Research, National Institute of Nursing Research, National Institutes of Health, DHHS, Bethesda, MD, USA
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