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Mills S, Ross RP. Colliding and interacting microbiomes and microbial communities - consequences for human health. Environ Microbiol 2021; 23:7341-7354. [PMID: 34390616 DOI: 10.1111/1462-2920.15722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/09/2021] [Accepted: 08/12/2021] [Indexed: 11/26/2022]
Abstract
Living 'things' coexist with microorganisms, known as the microbiota/microbiome that provides essential physiological functions to its host. Despite this reliance, the microbiome is malleable and can be altered by several factors including birth-mode, age, antibiotics, nutrition, and disease. In this minireview, we consider how other microbiomes and microbial communities impact the host microbiome and the host through the concept of microbiome collisions (initial exposures) and interactions. Interactions include changes in host microbiome composition and functionality and/or host responses. Understanding the impact of other microbiomes and microbial communities on the microbiome and host are important considering the decline in human microbiota diversity in the developed world - paralleled by the surge of non-communicable, inflammatory-based diseases. Thus, surrounding ourselves with rich and diverse beneficial microbiomes and microbial communities to collide and interact with should help to diminish the loss in microbial diversity and protect from certain diseases. In the same vein, our microbiomes not only influence our health but potentially the health of those close to us. We also consider strategies for enhanced host microbiome collisions and interactions through the surrounding environment that ensure increased microbiome diversity and functionality contributing to enhanced symbiotic return to the host in terms of health benefit.
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Affiliation(s)
- Susan Mills
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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52
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Nel Van Zyl K, Whitelaw AC, Hesseling AC, Seddon JA, Demers AM, Newton-Foot M. Association between clinical and environmental factors and the gut microbiota profiles in young South African children. Sci Rep 2021; 11:15895. [PMID: 34354176 PMCID: PMC8342602 DOI: 10.1038/s41598-021-95409-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/23/2021] [Indexed: 02/08/2023] Open
Abstract
Differences in the microbiota in populations over age and geographical locations complicate cross-study comparisons, and it is therefore essential to describe the baseline or control microbiota in each population. This includes the determination of the influence of demographic, clinical and environmental factors on the microbiota in a setting, and elucidates possible bias introduced by these factors, prior to further investigations. Little is known about the microbiota of children in South Africa after infancy. We provide a detailed description of the gut microbiota profiles of children from urban Cape Town and describe the influences of various clinical and environmental factors in different age groups during the first 5 years of life. Prevotella was the most common genus identified in the participants, and after infancy, the gut bacteria were dominated by Firmicutes and Bacteroidetes. In this setting, children exposed to antibiotics and indoor cooking fires were at the most risk for dysbiosis, showing significant losses in gut bacterial diversity.
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Affiliation(s)
- Kristien Nel Van Zyl
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Stellenbosch, South Africa.
| | - Andrew C Whitelaw
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Stellenbosch, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
- African Microbiome Institute, Stellenbosch University, Stellenbosch, South Africa
| | - Anneke C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
| | - James A Seddon
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Anne-Marie Demers
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
| | - Mae Newton-Foot
- Division of Medical Microbiology, Department of Pathology, Stellenbosch University, Stellenbosch, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
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53
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Abstract
Characterizing the gut microbiome in the healthy population is the first step in elucidating its associations with host health conditions. Populations with different diet patterns, lifestyles, and genetic backgrounds harbor different gut microbes. In this study, we characterized the gut microbiome of 890 healthy Koreans using 16S rRNA sequencing. The Korean population harbored a relatively large fraction of the Prevotella enterotype and presented a distinctive gut microbiome, compared to that in the populations of other countries. Additionally, we determined the clusters of cooccurring microbes that were quantitatively correlated with each other. We found that microbe composition of the gut was strongly associated with age. We identified that the abundance of members of Bacteroidia and Clostridia differed with the host dietary patterns, body mass index, and stool frequency. The gut microbiome data obtained in this study would be an important resource for future studies addressing microbial contributions in health and disease. IMPORTANCE Comparing the gut microbiomes of healthy controls and disease patients showed that the composition of the gut microbiome is associated with various host health conditions. The gut microbiome in healthy Western populations is well characterized, while that of non-Western populations, with different diet patterns, lifestyles, and genetic backgrounds, is not clearly defined. In this study, we characterized the microbiome of 890 healthy Korean individuals using 16S rRNA sequencing and found that Koreans have a gut microbiome different from that in the individuals of neighboring countries. The members of Bacteroidetes and Firmicutes cooccurred and were quantitatively associated with each other. Additionally, we found that the gut microbial composition is strongly associated with the host’s age. The microbiome data presented here represent the gut microbiome of a healthy Korean population and could be used to unveil gut microbiome-associated host conditions in this population.
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54
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Gao Y, Nanan R, Macia L, Tan J, Sominsky L, Quinn TP, O'Hely M, Ponsonby AL, Tang ML, Collier F, Strickland DH, Dhar P, Brix S, Phipps S, Sly PD, Ranganathan S, Stokholm J, Kristiansen K, Gray L, Vuillermin P. The maternal gut microbiome during pregnancy and offspring allergy and asthma. J Allergy Clin Immunol 2021; 148:669-678. [PMID: 34310928 DOI: 10.1016/j.jaci.2021.07.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/19/2021] [Accepted: 07/19/2021] [Indexed: 10/20/2022]
Abstract
Environmental exposures during pregnancy that alter both the maternal gut microbiome and the infant's risk of allergic disease and asthma include a traditional farm environment and consumption of unpasteurized cow's milk, antibiotic use, dietary fiber and psychosocial stress. Multiple mechanisms acting in concert may underpin these associations and prime the infant to acquire immune competence and homeostasis following exposure to the extrauterine environment. Cellular and metabolic products of the maternal gut microbiome can promote the expression of microbial pattern recognition receptors, as well as thymic and bone marrow hematopoiesis relevant to regulatory immunity. At birth, transmission of maternally derived bacteria likely leverages this in utero programming to accelerate postnatal transition from a Th2 to Th1 and Th17 dominant immune phenotypes and maturation of regulatory immune mechanisms, which in turn reduce the child's risk of allergic disease and asthma. Although our understanding of these phenomena is rapidly evolving, the field is relatively nascent, and we are yet to translate existing knowledge into interventions that substantially reduce disease risk in humans. Here we review evidence that the maternal gut microbiome impacts the offspring's risk of allergic disease and asthma, discuss challenges and future directions for the field, and propose the hypothesis that maternal carriage of Prevotella copri during pregnancy decreases the offspring's risk of allergic disease via production of succinate which in turn promotes bone marrow myelopoiesis of dendritic cell precursors in the fetus.
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Affiliation(s)
- Yuan Gao
- Institute for Physical and Mental Health and Clinical Transformation, Deakin University, Geelong, Australia; Child Health Research Unit, Barwon Health, Geelong, Australia; Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Ralph Nanan
- The Charles Perkins Center, the University of Sydney, Sydney, Australia
| | - Laurence Macia
- The Charles Perkins Center, the University of Sydney, Sydney, Australia; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Jian Tan
- The Charles Perkins Center, the University of Sydney, Sydney, Australia; School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Luba Sominsky
- Institute for Physical and Mental Health and Clinical Transformation, Deakin University, Geelong, Australia; Child Health Research Unit, Barwon Health, Geelong, Australia
| | - Thomas P Quinn
- Applied Artificial Intelligence Institute, Deakin University, Geelong, Australia
| | - Martin O'Hely
- Institute for Physical and Mental Health and Clinical Transformation, Deakin University, Geelong, Australia; Murdoch Children's Research Institute, Melbourne, Australia
| | - Anne-Louise Ponsonby
- The Florey Institute, Melbourne, Australia; Murdoch Children's Research Institute, Melbourne, Australia; University of Melbourne, Melbourne, Australia
| | - Mimi Lk Tang
- Murdoch Children's Research Institute, Melbourne, Australia; University of Melbourne, Melbourne, Australia; Royal Children's Hospital, Melbourne, Australia
| | - Fiona Collier
- Institute for Physical and Mental Health and Clinical Transformation, Deakin University, Geelong, Australia
| | | | - Poshmaal Dhar
- Institute for Physical and Mental Health and Clinical Transformation, Deakin University, Geelong, Australia
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Simon Phipps
- QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia; School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Queensland, Australia; Australian Infectious Diseases Research Centre, The University of Queensland, Queensland, Australia
| | - Peter D Sly
- Australian Infectious Diseases Research Centre, The University of Queensland, Queensland, Australia; Children's Health and Environment Program, Child Health Research Centre, The University of Queensland, Australia
| | - Sarath Ranganathan
- Murdoch Children's Research Institute, Melbourne, Australia; University of Melbourne, Melbourne, Australia; Royal Children's Hospital, Melbourne, Australia
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, 2820 Copenhagen, Denmark; Department of Pediatrics, Slagelse Hospital, 4200 Slagelse, Denmark
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen, China; China National Genebank, Shenzhen, China; Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lawrence Gray
- Institute for Physical and Mental Health and Clinical Transformation, Deakin University, Geelong, Australia; Child Health Research Unit, Barwon Health, Geelong, Australia.
| | - Peter Vuillermin
- Institute for Physical and Mental Health and Clinical Transformation, Deakin University, Geelong, Australia; Child Health Research Unit, Barwon Health, Geelong, Australia.
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55
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Cui M, Trimigno A, Aru V, Rasmussen MA, Khakimov B, Engelsen SB. Influence of Age, Sex, and Diet on the Human Fecal Metabolome Investigated by 1H NMR Spectroscopy. J Proteome Res 2021; 20:3642-3653. [PMID: 34048241 DOI: 10.1021/acs.jproteome.1c00220] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The human fecal metabolome is increasingly studied to explore the impact of diet and lifestyle on health and the gut microbiome. However, systematic differences and confounding factors related to age, sex, and diet remain largely unknown. In this study, absolute concentrations of fecal metabolites from 205 healthy Danes (105 males and 100 females, 49 ± 31 years old) were quantified using 1H NMR spectroscopy and the newly developed SigMa software. The largest systemic variation was found to be highly related to age. Fecal concentrations of short-chain fatty acids (SCFA) were higher in the 18 years old group, while amino acids (AA) were higher in the elderly. Sex-related metabolic differences were weak but significant and mainly related to changes in SCFA. The concentrations of butyric, valeric, propionic, and isovaleric acids were found to be higher in males compared to females. Sex differences were associated with a stronger, possibly masking, effect from differential intake of macronutrients. Dietary fat intake decreased levels of SCFA and AA of both sexes, while carbohydrate intake showed weak correlations with valeric and isovaleric acids in females. This study highlights some possible demographic confounders linked to diet, disease, lifestyle, and microbiota that have to be taken into account when analyzing fecal metabolome data.
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Affiliation(s)
- Mengni Cui
- Chemometrics and Analytical Technology Section Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Alessia Trimigno
- Chemometrics and Analytical Technology Section Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Violetta Aru
- Chemometrics and Analytical Technology Section Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Morten A Rasmussen
- Chemometrics and Analytical Technology Section Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark.,COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen 2820, Denmark
| | - Bekzod Khakimov
- Chemometrics and Analytical Technology Section Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
| | - Søren Balling Engelsen
- Chemometrics and Analytical Technology Section Department of Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg C, Denmark
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56
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Ailioaie LM, Litscher G. Probiotics, Photobiomodulation, and Disease Management: Controversies and Challenges. Int J Mol Sci 2021; 22:ijms22094942. [PMID: 34066560 PMCID: PMC8124384 DOI: 10.3390/ijms22094942] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/26/2021] [Accepted: 04/29/2021] [Indexed: 02/06/2023] Open
Abstract
In recent decades, researchers around the world have been studying intensively how micro-organisms that are present inside living organisms could affect the main processes of life, namely health and pathological conditions of mind or body. They discovered a relationship between the whole microbial colonization and the initiation and development of different medical disorders. Besides already known probiotics, novel products such as postbiotics and paraprobiotics have been developed in recent years to create new non-viable micro-organisms or bacterial-free extracts, which can provide benefits to the host with additional bioactivity to probiotics, but without the risk of side effects. The best alternatives in the use of probiotics and postbiotics to maintain the health of the intestinal microbiota and to prevent the attachment of pathogens to children and adults are highlighted and discussed as controversies and challenges. Updated knowledge of the molecular and cellular mechanisms involved in the balance between microbiota and immune system for the introspection on the gut-lung-brain axis could reveal the latest benefits and perspectives of applied photobiomics for health. Multiple interconditioning between photobiomodulation (PBM), probiotics, and the human microbiota, their effects on the human body, and their implications for the management of viral infectious diseases is essential. Coupled complex PBM and probiotic interventions can control the microbiome, improve the activity of the immune system, and save the lives of people with immune imbalances. There is an urgent need to seek and develop innovative treatments to successfully interact with the microbiota and the human immune system in the coronavirus crisis. In the near future, photobiomics and metabolomics should be applied innovatively in the SARS-CoV-2 crisis (to study and design new therapies for COVID-19 immediately), to discover how bacteria can help us through adequate energy biostimulation to combat this pandemic, so that we can find the key to the hidden code of communication between RNA viruses, bacteria, and our body.
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Affiliation(s)
- Laura Marinela Ailioaie
- Department of Medical Physics, Alexandru Ioan Cuza University, 11 Carol I Boulevard, 700506 Iasi, Romania;
- Ultramedical & Laser Clinic, 83 Arcu Street, 700135 Iasi, Romania
| | - Gerhard Litscher
- Research Unit of Biomedical Engineering in Anesthesia and Intensive Care Medicine, Research Unit for Complementary and Integrative Laser Medicine, and Traditional Chinese Medicine (TCM) Research Center Graz, Medical University of Graz, Auenbruggerplatz 39, 8036 Graz, Austria
- Correspondence: ; Tel.: +43-316-385-83907
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57
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Affiliation(s)
- Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Amar Sarkar
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Aspen T Reese
- Division of Biological Sciences, Section of Ecology, Behavior, and Evolution, University of California, San Diego, La Jolla, CA, USA.
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58
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Yang J, Wu J, Li Y, Zhang Y, Cho WC, Ju X, van Schothorst EM, Zheng Y. Gut bacteria formation and influencing factors. FEMS Microbiol Ecol 2021; 97:6168382. [PMID: 33705527 DOI: 10.1093/femsec/fiab043] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/09/2021] [Indexed: 12/11/2022] Open
Abstract
The gut microbiota plays an important role in human health. In modern life, with the improvement of living conditions, the intake of high-sugar and high-fat diets as well as the large-scale use of antibacterial drugs have an extensive impact on the gut microbiota, even leading to gut microbiota-orchestrating disorders. This review discusses the effects of various factors, including geographic location, age, diet, antibacterial drugs, psychological situation and exercise on gut bacteria, which helps us profoundly to understand the significance of gut bacteria to human health and to find effective solutions to prevent or treat related diseases.
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Affiliation(s)
- Jing Yang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Chengguan District, Lanzhou 730046, China
| | - Jin'en Wu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Chengguan District, Lanzhou 730046, China
| | - Yating Li
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Chengguan District, Lanzhou 730046, China
| | - Yong'e Zhang
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Chengguan District, Lanzhou 730046, China
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, 30 Gascoigne Road, Hong Kong SAR 999077, China
| | - Xianghong Ju
- Department of Veterinary Medicine, College of Agriculture, Guangdong Ocean University, 1 Haida Road, Mazhang District, 524088, China
| | - Evert M van Schothorst
- Human and Animal Physiology, Wageningen University, De Elst 1, Wageningen 6708WD, The Netherlands
| | - Yadong Zheng
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, CAAS, 1 Xujiaping, Chengguan District, Lanzhou 730046, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, 88 Daxuenan Road, Yangzhou 225009, China
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59
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Soto-Girón MJ, Peña-Gonzalez A, Hatt JK, Montero L, Páez M, Ortega E, Smith S, Cevallos W, Trueba G, Konstantinidis KT, Levy K. Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador. Am J Trop Med Hyg 2021; 104:2275-2285. [PMID: 33872206 DOI: 10.4269/ajtmh.20-0831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Previous studies have reported lower fecal bacterial diversity in urban populations compared with those living in rural settings. However, most of these studies compare geographically distant populations from different countries and even continents. The extent of differences in the gut microbiome in adjacent rural versus urban populations, and the role of such differences, if any, during enteric infections remain poorly understood. To provide new insights into these issues, we sampled the gut microbiome of young children with and without acute diarrheal disease (ADD) living in rural and urban areas in northern Ecuador. Shotgun metagenomic analyses of non-ADD samples revealed small but significant differences in the abundance of microbial taxa, including a greater abundance of Prevotella and a lower abundance of Bacteroides and Alistipes in rural populations. Greater and more significant shifts in taxon abundance, metabolic pathway abundance, and diversity were observed between ADD and non-ADD status when comparing urban to rural sites (Welch's t-test, P < 0.05). Collectively our data show substantial functional, diversity, and taxonomic shifts in the gut microbiome of urban populations with, ADD supporting the idea that the microbiome of rural populations may be more resilient to ADD episodes.
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Affiliation(s)
- Maria J Soto-Girón
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Angela Peña-Gonzalez
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Janet K Hatt
- 2School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Lorena Montero
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Maritza Páez
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Estefania Ortega
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Shanon Smith
- 4School of Public Health, University of Washington, Seattle, Washington
| | - William Cevallos
- 5Centro de Biomedicina, Universidad Central del Ecuador, Quito, Ecuador
| | - Gabriel Trueba
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Konstantinos T Konstantinidis
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,2School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Karen Levy
- 4School of Public Health, University of Washington, Seattle, Washington
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60
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Rampelli S, Fabbrini M, Candela M, Biagi E, Brigidi P, Turroni S. G2S: A New Deep Learning Tool for Predicting Stool Microbiome Structure From Oral Microbiome Data. Front Genet 2021; 12:644516. [PMID: 33897763 PMCID: PMC8062976 DOI: 10.3389/fgene.2021.644516] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/09/2021] [Indexed: 12/15/2022] Open
Abstract
Deep learning methodologies have revolutionized prediction in many fields and show the potential to do the same in microbial metagenomics. However, deep learning is still unexplored in the field of microbiology, with only a few software designed to work with microbiome data. Within the meta-community theory, we foresee new perspectives for the development and application of deep learning algorithms in the field of the human microbiome. In this context, we developed G2S, a bioinformatic tool for taxonomic prediction of the human fecal microbiome directly from the oral microbiome data of the same individual. The tool uses a deep convolutional neural network trained on paired oral and fecal samples from populations across the globe, which allows inferring the stool microbiome at the family level more accurately than other available approaches. The tool can be used in retrospective studies, where fecal sampling was not performed, and especially in the field of paleomicrobiology, as a unique opportunity to recover data related to ancient gut microbiome configurations. G2S was validated on already characterized oral and fecal sample pairs, and then applied to ancient microbiome data from dental calculi, to derive putative intestinal components in medieval subjects.
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Affiliation(s)
- Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marco Fabbrini
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.,Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Elena Biagi
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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61
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Janiak MC, Montague MJ, Villamil CI, Stock MK, Trujillo AE, DePasquale AN, Orkin JD, Bauman Surratt SE, Gonzalez O, Platt ML, Martínez MI, Antón SC, Dominguez-Bello MG, Melin AD, Higham JP. Age and sex-associated variation in the multi-site microbiome of an entire social group of free-ranging rhesus macaques. MICROBIOME 2021; 9:68. [PMID: 33752735 PMCID: PMC7986251 DOI: 10.1186/s40168-021-01009-w] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/02/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND An individual's microbiome changes over the course of its lifetime, especially during infancy, and again in old age. Confounding factors such as diet and healthcare make it difficult to disentangle the interactions between age, health, and microbial changes in humans. Animal models present an excellent opportunity to study age- and sex-linked variation in the microbiome, but captivity is known to influence animal microbial abundance and composition, while studies of free-ranging animals are typically limited to studies of the fecal microbiome using samples collected non-invasively. Here, we analyze a large dataset of oral, rectal, and genital swabs collected from 105 free-ranging rhesus macaques (Macaca mulatta, aged 1 month-26 years), comprising one entire social group, from the island of Cayo Santiago, Puerto Rico. We sequenced 16S V4 rRNA amplicons for all samples. RESULTS Infant gut microbial communities had significantly higher relative abundances of Bifidobacterium and Bacteroides and lower abundances of Ruminococcus, Fibrobacter, and Treponema compared to older age groups, consistent with a diet high in milk rather than solid foods. The genital microbiome varied widely between males and females in beta-diversity, taxonomic composition, and predicted functional profiles. Interestingly, only penile, but not vaginal, microbiomes exhibited distinct age-related changes in microbial beta-diversity, taxonomic composition, and predicted functions. Oral microbiome composition was associated with age, and was most distinctive between infants and other age classes. CONCLUSIONS Across all three body regions, with notable exceptions in the penile microbiome, while infants were distinctly different from other age groups, microbiomes of adults were relatively invariant, even in advanced age. While vaginal microbiomes were exceptionally stable, penile microbiomes were quite variable, especially at the onset of reproductive age. Relative invariance among adults, including elderly individuals, is contrary to findings in humans and mice. We discuss potential explanations for this observation, including that age-related microbiome variation seen in humans may be related to changes in diet and lifestyle. Video abstract.
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Affiliation(s)
- Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada.
- Alberta Children's Hospital Research Institute, Alberta, Canada.
- Department of Anthropology, New York University, New York, USA.
- School of Science, Engineering and Environment, University of Salford, Salford, UK.
| | - Michael J Montague
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Catalina I Villamil
- School of Chiropractic, Universidad Central del Caribe, Bayamón, Puerto Rico
| | - Michala K Stock
- Department of Sociology and Anthropology, Metropolitan State University of Denver, Denver, CO, USA
| | - Amber E Trujillo
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Allegra N DePasquale
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
| | - Joseph D Orkin
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | | | - Olga Gonzalez
- Disease Intervention and Prevention, Southwest National Primate Research Center, San Antonio, TX, USA
| | - Michael L Platt
- Department of Neuroscience, University of Pennsylvania, Philadelphia, PA, USA
| | - Melween I Martínez
- Caribbean Primate Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Susan C Antón
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
| | - Maria Gloria Dominguez-Bello
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
- Department of Anthropology, Rutgers University, New Brunswick, NJ, USA
| | - Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, Alberta, Canada
- Alberta Children's Hospital Research Institute, Alberta, Canada
- Department of Medical Genetics, University of Calgary, Alberta, Canada
| | - James P Higham
- Department of Anthropology, New York University, New York, USA
- New York Consortium in Evolutionary Primatology, New York, NY, USA
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Mehta O, Inbaraj LR, Astbury S, Grove JI, Norman G, Aithal GP, Valdes AM, Vijay A. Gut Microbial Profile Is Associated With Residential Settings and Not Nutritional Status in Adults in Karnataka, India. Front Nutr 2021; 8:595756. [PMID: 33708787 PMCID: PMC7940358 DOI: 10.3389/fnut.2021.595756] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Undernutrition is a leading contributor to disease and disability in people of all ages. Several studies have reported significant association between nutritional status and gut microbiome composition but other factors such as demographic settings may also influence the adult microbiome. The relationship between undernourishment and gut microbiome in adults has not been described to date. In this study, we compared the gut microbiome in fecal samples of 48 individuals, from two demographic settings (rural and urban slum) in Karnataka, India using 16S rRNA sequencing. Nutritional status was assessed based on BMI, with a BMI of < 18.5 kg/m2 classified as undernourished, and a BMI in the range 18.5–25 kg/m2 as nourished. We analyzed 25 individuals from rural settings (12 undernourished and 13 nourished) and 23 individuals from urban slum settings (11 undernourished and 12 nourished). We found no significant difference in overall gut microbial diversity (Shannon and Unweighted UniFrac) between undernourished and nourished individuals in either geographical settings, however, microbial taxa at the phylum level (i.e., Firmicutes and Proteobacteria) and beta diversity (unweighted UniFrac) differed significantly between the rural and urban slum settings. By predicting microbial function from 16S data profiling we found significant differences in metabolic pathways present in the gut microbiota from people residing in different settings; specifically, those related to carbohydrate and lipid metabolism. The weighted sum of the KEGG Orthologs associated with carbohydrate metabolism (Spearman's correlation coefficient, ρ = −0.707, p < 0.001), lipid metabolism (Spearman's correlation coefficient, ρ = −0.330, p < 0.022) and biosynthesis of secondary metabolites (Spearman's correlation coefficient, ρ = −0.507, p < 0.001) were decreased in the urban slum group compared to the rural group. In conclusion, we report that the geographical location of residence is associated with differences in gut microbiome composition in adults. We found no significant differences in microbiome composition between nourished and undernourished adults from urban slum or rural settings in India.
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Affiliation(s)
- Ojasvi Mehta
- Nottingham Digestive Diseases Center, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,National Institute of Health Research (NIHR) Nottingham Biomedical Research Center, Nottingham University Hospitals National Health Service (NHS) Trust and University of Nottingham, Nottingham, United Kingdom
| | | | - Stuart Astbury
- Nottingham Digestive Diseases Center, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,National Institute of Health Research (NIHR) Nottingham Biomedical Research Center, Nottingham University Hospitals National Health Service (NHS) Trust and University of Nottingham, Nottingham, United Kingdom
| | - Jane I Grove
- Nottingham Digestive Diseases Center, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,National Institute of Health Research (NIHR) Nottingham Biomedical Research Center, Nottingham University Hospitals National Health Service (NHS) Trust and University of Nottingham, Nottingham, United Kingdom
| | - Gift Norman
- Department of Community Health, Bangalore Baptist Hospital, Bangalore, India
| | - Guruprasad P Aithal
- Nottingham Digestive Diseases Center, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,National Institute of Health Research (NIHR) Nottingham Biomedical Research Center, Nottingham University Hospitals National Health Service (NHS) Trust and University of Nottingham, Nottingham, United Kingdom
| | - Ana M Valdes
- National Institute of Health Research (NIHR) Nottingham Biomedical Research Center, Nottingham University Hospitals National Health Service (NHS) Trust and University of Nottingham, Nottingham, United Kingdom.,Division of Rheumatology, Orthopedics and Dermatology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Amrita Vijay
- Nottingham Digestive Diseases Center, School of Medicine, University of Nottingham, Nottingham, United Kingdom.,National Institute of Health Research (NIHR) Nottingham Biomedical Research Center, Nottingham University Hospitals National Health Service (NHS) Trust and University of Nottingham, Nottingham, United Kingdom.,Division of Rheumatology, Orthopedics and Dermatology, School of Medicine, University of Nottingham, Nottingham, United Kingdom
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63
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An overview of the level of dietary support in the gut microbiota at different stages of life: A systematic review. Clin Nutr ESPEN 2021; 42:41-52. [PMID: 33745615 DOI: 10.1016/j.clnesp.2021.01.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS The gut microbiome is an essential factor for the health of the host. Several factors may alter the gut's microbiota composition, including genetic factors, lifestyle, aging, and dietary intervention. This process can be an essential element in the prevention and treatment of diseases associated with microbiome dysfunction through appropriate dietary interventions. Based on this context, a systematic review was carried out in order to assess the effect of dietary intervention on the profile of the gut microbiota throughout different stages of life. METHODS The systematic review was conducted following the Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA), with the eligibility criteria following the principle of PICOS. The literature search was carried out in 2019 throughout PubMed/MEDLINE, Scopus, and Science Direct. Thus, 1237 studies were selected, and 40 articles were included by criteria. RESULTS According to the level of evidence of Centre for Evidence-Based Medicine (OCEBM), 21 studies reached the level of evidence B1, 15 articles were classified with B2, and four articles with B3. No dietary intervention was applied at all stages of life, nor with similar proportions of intervention. No dietary intervention was applied at all stages of life, nor with similar proportions of intervention. On the other hand, dietary interventions alter the intestinal microbiota in different pathological realities. CONCLUSIONS Different dietary interventions change the microbiome composition at all stages of life in healthy and pathological individuals. However, more clinical studies are needed to identify the specifics of each stage in response to interventions.
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64
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Rampelli S, Turroni S, Mallol C, Hernandez C, Galván B, Sistiaga A, Biagi E, Astolfi A, Brigidi P, Benazzi S, Lewis CM, Warinner C, Hofman CA, Schnorr SL, Candela M. Components of a Neanderthal gut microbiome recovered from fecal sediments from El Salt. Commun Biol 2021; 4:169. [PMID: 33547403 PMCID: PMC7864912 DOI: 10.1038/s42003-021-01689-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 01/05/2021] [Indexed: 12/19/2022] Open
Abstract
A comprehensive view of our evolutionary history cannot ignore the ancestral features of our gut microbiota. To provide some glimpse into the past, we searched for human gut microbiome components in ancient DNA from 14 archeological sediments spanning four stratigraphic units of El Salt Middle Paleolithic site (Spain), including layers of unit X, which has yielded well-preserved Neanderthal occupation deposits dating around 50 kya. According to our findings, bacterial genera belonging to families known to be part of the modern human gut microbiome are abundantly represented only across unit X samples, showing that well-known beneficial gut commensals, such as Blautia, Dorea, Roseburia, Ruminococcus, Faecalibacterium and Bifidobacterium already populated the intestinal microbiome of Homo since as far back as the last common ancestor between humans and Neanderthals.
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Affiliation(s)
- Simone Rampelli
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy
| | - Carolina Mallol
- Department of Geography and History, University of La Laguna, Campus de Guajara, La Laguna, Tenerife, Spain.,Archaeological Micromorphology and Biomarker Research Lab, University of La Laguna, Avenida Astrofísico Francisco Sánchez 2, La Laguna, Tenerife, Spain.,ICArEHB - Interdisciplinary Center for Archaeology and the Evolution of Human Behaviour, Universidade do Algarve, Campus de Gambelas, Edificio 1, Faro, Portugal
| | - Cristo Hernandez
- Department of Geography and History, University of La Laguna, Campus de Guajara, La Laguna, Tenerife, Spain
| | - Bertila Galván
- Department of Geography and History, University of La Laguna, Campus de Guajara, La Laguna, Tenerife, Spain
| | - Ainara Sistiaga
- Earth, Atmospheric and Planetary Sciences Department, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA, USA.,GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Oester Voldgade 5-7, Copenhagen, Denmark
| | - Elena Biagi
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy
| | - Annalisa Astolfi
- "Giorgio Prodi" Cancer Research Center, University of Bologna, Via Massarenti 11, Bologna, Italy.,Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Via Fossato di Mortara 70, Ferrara, Italy
| | - Patrizia Brigidi
- Department of Medical and Surgical Sciences, University of Bologna, Via Massarenti 9, Bologna, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani 1, Ravenna, Italy.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, Germany
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, 455W Lindsey St, Norman, OK, USA
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, 455W Lindsey St, Norman, OK, USA.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, Jena, Germany
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, USA.,Department of Anthropology, University of Oklahoma, 455W Lindsey St, Norman, OK, USA
| | - Stephanie L Schnorr
- Konrad Lorenz Institute for Evolution and Cognition Research, Martinstraße 12, Klosterneuburg, Austria. .,Department of Anthropology, University of Nevada, 4505S. Maryland Pkwy, Las Vegas, NV, USA.
| | - Marco Candela
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, Bologna, Italy.
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65
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Abstract
Both the gut microbiome and innate immunity are known to differ across biogeographically diverse human populations. The gut microbiome has been shown to directly influence systemic immunity in animal models. The gut microbiome is a well-recognized modulator of host immunity, and its compositions differ between geographically separated human populations. Systemic innate immune responses to microbial derivatives also differ between geographically distinct human populations. However, the potential role of the microbiome in mediating geographically varied immune responses is unexplored. We here applied 16S amplicon sequencing to profile the stool microbiome and, in parallel, measured whole-blood innate immune cytokine responses to several pattern recognition receptor (PRR) agonists among 2-year-old children across biogeographically diverse settings. Microbiomes differed mainly between high- and low-resource environments and were not strongly associated with other demographic factors. We found strong correlations between responses to Toll-like receptor 2 (TLR2) and relative abundances of Bacteroides and Prevotella populations, shared among Canadian and Ecuadorean children. Additional correlations between responses to TLR2 and bacterial populations were specific to individual geographic cohorts. As a proof of concept, we gavaged germfree mice with human donor stools and found murine splenocyte responses to TLR stimulation were consistent with responses of the corresponding human donor populations. This study identified differences in immune responses correlating to gut microbiomes across biogeographically diverse settings and evaluated biological plausibility using a mouse model. This insight paves the way to guide optimization of population-specific interventions aimed to improve child health outcomes.
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66
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Berlow M, Phillips JN, Derryberry EP. Effects of Urbanization and Landscape on Gut Microbiomes in White-Crowned Sparrows. MICROBIAL ECOLOGY 2021; 81:253-266. [PMID: 32803364 DOI: 10.1007/s00248-020-01569-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/28/2020] [Indexed: 06/11/2023]
Abstract
Habitats are changing rapidly around the globe and urbanization is one of the primary drivers. Urbanization changes food availability, environmental stressors, and the prevalence of disease for many species. These changes can lead to divergence in phenotypic traits, including behavioral, physiological, and morphological features between urban and rural populations. Recent research highlights that urbanization is also changing the gut microbial communities found in a diverse group of host species. These changes have not been uniform, leaving uncertainty as to how urban habitats are shaping gut microbial communities. To better understand these effects, we investigated the gut bacterial communities of White-Crowned Sparrow (Zonotrichia leucophrys) populations along an urbanization gradient in the San Francisco Bay area. We examined how gut bacterial communities vary with the local environment and host morphological characteristics. We found direct effects of environmental factors, including urban noise levels and territory land cover, as well as indirect effects through body size and condition, on alpha and beta diversity of gut microbial communities. We also found that urban and rural birds' microbiomes differed in which variables predicted their diversity, with urban communities driven by host morphology, and rural communities driven by environmental factors. Elucidating these effects provides a better understanding of how urbanization affects wild avian physiology.
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Affiliation(s)
- Mae Berlow
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA.
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA.
| | - Jennifer N Phillips
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA, 93407, USA
| | - Elizabeth P Derryberry
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
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67
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Biological transformation of chlorophyll-rich spinach (Spinacia oleracea L.) extracts under in vitro gastrointestinal digestion and colonic fermentation. Food Res Int 2020; 139:109941. [PMID: 33509495 DOI: 10.1016/j.foodres.2020.109941] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 01/04/2023]
Abstract
Chlorophyll can be obtained from a variety of green vegetables. In this study, chlorophyll-rich spinach (Spinacia oleracea L.) extracts were subjected to early-life and adult-life gastrointestinal digestion and colonic fermentation in a murine model in vitro to investigate the biological transformation of the chlorophyll. Chlorophylls a and b were the main compounds present in the extracts. Furthermore, some other compounds were also confirmed, such as 151-hydroxy-lactone chlorophyll a, 132-hydroxy chlorophyll a, and 151-hydroxy-lactone chlorophyll b. Chlorophylls favored pheophytinization and oxidative reactions under in vitro early-life and adult-life gastrointestinal digestion, leading to the formation of pheophytin a, pheophytin b, 132-hydroxy pheophytin a, and 151-hydroxy-lactone pheophytin a. 16S rRNA gene sequencing conveyed that pheophytins modulated the gut microbiota composition during in vitro colonic fermentation. Notably, Blautia in the gut microbiota of 3-week-old mice (early life) and unclassified Lachnospiraceae in 8-week-old mice (adult life) were advantageous for transforming the pheophytins to pheophorbide a, pheophorbide b, 151-hydroxy-lactone pheophorbide a, and 132-hydroxy pheophorbide a, thereby demonstrating the loss of the phytol chain in the pheophytins. Meanwhile, total short-chain fatty acids, as well as acetic, propionic, and butyric acids, were increased by the process of microbial fermentation in the presence of pheophytins. Our study provides fundamental insight into the contribution of diverse gut microbiota functions toward the biological transformation of pheophytins.
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68
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Reese AT, Phillips SR, Owens LA, Venable EM, Langergraber KE, Machanda ZP, Mitani JC, Muller MN, Watts DP, Wrangham RW, Goldberg TL, Emery Thompson M, Carmody RN. Age Patterning in Wild Chimpanzee Gut Microbiota Diversity Reveals Differences from Humans in Early Life. Curr Biol 2020; 31:613-620.e3. [PMID: 33232664 DOI: 10.1016/j.cub.2020.10.075] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/24/2020] [Accepted: 10/26/2020] [Indexed: 01/26/2023]
Abstract
Survival in primates is facilitated by commensal gut microbes that ferment otherwise indigestible plant matter, resist colonization by pathogens, and train the developing immune system.1,2 However, humans are unique among primates in that we consume highly digestible foods, wean early, mature slowly, and exhibit high lifelong investments in maintenance.3-6 These adaptations suggest that lifetime trajectories of human-microbial relationships could differ from those of our closest living relatives. Here, we profile the gut microbiota of 166 wild chimpanzees aged 8 months to 67 years in the Kibale National Park, Uganda and compare the patterns of gut microbial maturation to those previously observed in humans. We found that chimpanzee gut microbial alpha-diversity, composition, density, interindividual variation, and within-individual change over time varied significantly with age. Notably, gut microbial signatures in infants <2 years old were distinct across all five metrics. Infant chimpanzee guts were enriched in some of the same taxa prevalent in infant humans (e.g., Bifidobacterium, Streptococcus, and Bacteroides), and chimpanzee gut microbial communities, like those of humans, exhibited higher interindividual variation in infancy versus later in life. However, in direct contrast to human infants, chimpanzee infants harbored surprisingly high-diversity rather than low-diversity gut bacterial communities compared with older conspecifics. These data indicate differential trajectories of gut microbiota development in humans and chimpanzees that are consistent with interspecific differences in lactation, diet, and immune function. Probing the phenotypic consequences of differential early-life gut microbial diversity in chimpanzees and other primates will illuminate the life history impacts of the hominid-microbiome partnership.
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Affiliation(s)
- Aspen T Reese
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Society of Fellows, Harvard University, Cambridge, MA, USA
| | - Sarah R Phillips
- Department of Anthropology, University of New Mexico, Albuquerque, NM, USA
| | - Leah A Owens
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Emily M Venable
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA; Ngogo Chimpanzee Project, Waltham, MA, USA; Institute of Human Origins, Tempe, AZ, USA
| | - Zarin P Machanda
- Department of Anthropology, Tufts University, Medford, MA, USA; Kibale Chimpanzee Project, Fort Portal, Uganda
| | - John C Mitani
- Ngogo Chimpanzee Project, Waltham, MA, USA; Department of Anthropology, University of Michigan, Ann Arbor, MI, USA
| | - Martin N Muller
- Department of Anthropology, University of New Mexico, Albuquerque, NM, USA; Kibale Chimpanzee Project, Fort Portal, Uganda
| | - David P Watts
- Ngogo Chimpanzee Project, Waltham, MA, USA; Department of Anthropology, Yale University, New Haven, CT, USA
| | - Richard W Wrangham
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Kibale Chimpanzee Project, Fort Portal, Uganda
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA; Global Health Institute, University of Wisconsin-Madison, Madison, WI, USA; Department of Zoology, Makerere University, Kampala, Uganda
| | - Melissa Emery Thompson
- Department of Anthropology, University of New Mexico, Albuquerque, NM, USA; Kibale Chimpanzee Project, Fort Portal, Uganda
| | - Rachel N Carmody
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
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69
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Mukherjee A, Lordan C, Ross RP, Cotter PD. Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health. Gut Microbes 2020; 12:1802866. [PMID: 32835590 PMCID: PMC7524325 DOI: 10.1080/19490976.2020.1802866] [Citation(s) in RCA: 211] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/10/2020] [Accepted: 07/22/2020] [Indexed: 02/06/2023] Open
Abstract
Over the last two decades our understanding of the gut microbiota and its contribution to health and disease has been transformed. Among a new 'generation' of potentially beneficial microbes to have been recognized are members of the genus Eubacterium, who form a part of the core human gut microbiome. The genus consists of phylogenetically, and quite frequently phenotypically, diverse species, making Eubacterium a taxonomically unique and challenging genus. Several members of the genus produce butyrate, which plays a critical role in energy homeostasis, colonic motility, immunomodulation and suppression of inflammation in the gut. Eubacterium spp. also carry out bile acid and cholesterol transformations in the gut, thereby contributing to their homeostasis. Gut dysbiosis and a consequently modified representation of Eubacterium spp. in the gut, have been linked with various human disease states. This review provides an overview of Eubacterium species from a phylogenetic perspective, describes how they alter with diet and age and summarizes its association with the human gut and various health conditions.
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Affiliation(s)
- Arghya Mukherjee
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
| | - Cathy Lordan
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - R. Paul Ross
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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70
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Han M, Yang K, Yang P, Zhong C, Chen C, Wang S, Lu Q, Ning K. Stratification of athletes' gut microbiota: the multifaceted hubs associated with dietary factors, physical characteristics and performance. Gut Microbes 2020; 12:1-18. [PMID: 33289609 PMCID: PMC7734118 DOI: 10.1080/19490976.2020.1842991] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Gut microbial communities of athletes differ from that of sedentary persons in both diversity and the presence of certain taxa. However, it is unclear to what degree elite athletes and non-elite athletes harbor different gut microbial community patterns and if we can effectively monitor the potential of athletes based on microbiota. A team of professional female rowing athletes in China was recruited and 306 fecal samples were collected from 19 individuals, which were separated into three cohorts: adult elite athlete's (AE), youth elite athlete's (YE), and youth non-elite athlete's (YN). The differences in gut microbiome among different cohorts were compared, and their associations with dietary factors, physical characteristics, and athletic performance were investigated. The microbial diversities of elite athletes were higher than those of youth non-elite athletes. The taxonomical, functional, and phenotypic compositions of AE, YE and YN were significantly different. Additionally, three enterotypes with clear separation were identified in athlete's fecal samples, with majority of elite athletes stratified into enterotype 3. And this enterotype-dependent gut microbiome is strongly associated with athlete performances. These differences in athlete gut microbiota lead to establishment of a random forest classifier based on taxonomical and functional biomarkers, capable of differentiating elite athletes and non-elite athletes with high accuracy. Finally, these versatilities of athlete microbial communities of athletes were found to be associated with dietary factors and physical characteristics, which can in concert explain 41% of the variability in gut microbiome.
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Affiliation(s)
- Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China,School of Life Sciences, Anhui Medical University, Hefei, Anhui, China,CONTACT Kang Ning
| | - Kun Yang
- Exercise Immunology Center, Wuhan Sports University, Wuhan, Hubei, China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chaofang Zhong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chaoyun Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Song Wang
- Exercise Immunology Center, Wuhan Sports University, Wuhan, Hubei, China,Song Wang Exercise Immunology Center, Wuhan Sports University, Wuhan, Hubei430079, China
| | - Qunwei Lu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China,Qunwei Lu Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei430074, China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China,CONTACT Kang Ning
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71
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Bickler SW, Prieto JM, Cauvi DM, De Cos V, Nasamran C, Ameh E, Amin S, Nicholson S, Din H, Mocumbi AO, Noormahomed EV, Tellez-Isaias G, Fisch KM, De Maio A. Differential expression of nuclear genes encoding mitochondrial proteins from urban and rural populations in Morocco. Cell Stress Chaperones 2020; 25:847-856. [PMID: 32319023 PMCID: PMC7591688 DOI: 10.1007/s12192-020-01108-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 11/25/2022] Open
Abstract
Urbanization in low-income countries represents an important inflection point in the epidemiology of disease, with rural populations experiencing high rates of chronic and recurrent infections and urban populations displaying a profile of noncommunicable diseases. To investigate if urbanization alters the expression of genes encoding mitochondrial proteins, we queried gene microarray data from rural and urban populations living in Morocco (GSE17065). The R Bioconductor packages edgeR and limma were used to identify genes with different expression. The experimental design was modeled upon location and sex. Nuclear genes encoding mitochondrial proteins were identified from the MitoCarta2.0 database. Of the 1158 genes listed in the MitoCarta2.0 database, 847 genes (73%) were available for analysis in the Moroccan dataset. The urban-rural comparison with the greatest environmental differences showed that 76.5% of the MitoCarta2.0 genes were differentially expressed, with 97% of the genes having an increased expression in the urban area. Enrichment analysis revealed 367 significantly enriched pathways (adjusted p value < 0.05), with oxidative phosphorylation, insulin secretion and glucose regulations (adj.p values = 6.93E-16) being the top three. Four significantly perturbed KEGG disease pathways were associated with urbanization-three degenerative neurological diseases (Huntington's, Alzheimer's, and Parkinson's diseases) and herpes simplex infection (false discover rate corrected p value (PGFdr) < 0.2). Mitochondrial RNA metabolic processing and translational elongation were the biological processes that had the greatest enrichment (enrichment ratios 14.0 and 14.8, respectively, FDR < 0.5). Our study links urbanization in Morocco with changes in the expression of the nuclear genes encoding mitochondrial proteins.
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Affiliation(s)
- Stephen W. Bickler
- Division of Pediatric Surgery, Rady Children’s Hospital—University of California San Diego, 3030 Children’s Way, San Diego, CA 92123 USA
- Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Center for Investigations of Health and Education Disparities, University of California San Diego, La Jolla, CA 92093 USA
| | - James M. Prieto
- Department of Surgery, Naval Medical Center San Diego, San Diego, CA USA
| | - David M. Cauvi
- Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Center for Investigations of Health and Education Disparities, University of California San Diego, La Jolla, CA 92093 USA
| | - Victor De Cos
- Division of Pediatric Surgery, Rady Children’s Hospital—University of California San Diego, 3030 Children’s Way, San Diego, CA 92123 USA
| | - Chanond Nasamran
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093 USA
| | - Emmanuel Ameh
- Department of Pediatric Surgery, National Hospital, Abuja, Nigeria
| | - Said Amin
- Department of Histopathology, National Hospital, Abuja, Nigeria
| | - Sneha Nicholson
- Division of Pediatric Surgery, Rady Children’s Hospital—University of California San Diego, 3030 Children’s Way, San Diego, CA 92123 USA
| | - Hena Din
- Division of Pediatric Surgery, Rady Children’s Hospital—University of California San Diego, 3030 Children’s Way, San Diego, CA 92123 USA
| | - Ana Olga Mocumbi
- Instituto Nacional de Saúde, Maputo, Mozambique
- Department of Microbiology, Faculty of Medicine, Universidade Eduardo Mondlane (UEM), Maputo, Mozambique
| | | | | | - Kathleen M. Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA 92093 USA
| | - Antonio De Maio
- Department of Surgery, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
- Center for Investigations of Health and Education Disparities, University of California San Diego, La Jolla, CA 92093 USA
- Department of Neurosciences, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
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72
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Oduaran OH, Tamburini FB, Sahibdeen V, Brewster R, Gómez-Olivé FX, Kahn K, Norris SA, Tollman SM, Twine R, Wade AN, Wagner RG, Lombard Z, Bhatt AS, Hazelhurst S. Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition. BMC Microbiol 2020; 20:330. [PMID: 33129264 PMCID: PMC7603784 DOI: 10.1186/s12866-020-02017-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 10/19/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition. Yet, little is known about the gut microbiome composition of most communities in the very diverse African continent. South Africa comprises a richly diverse ethnolinguistic population that is experiencing an ongoing epidemiological transition and concurrent spike in the prevalence of obesity, largely attributed to a shift towards more Westernized diets and increasingly inactive lifestyle practices. To characterize the microbiome of African adults living in more mainstream lifestyle settings and investigate associations between the microbiome and obesity, we conducted a pilot study, designed collaboratively with community leaders, in two South African cohorts representative of urban and transitioning rural populations. As the rate of overweight and obesity is particularly high in women, we collected single time-point stool samples from 170 HIV-negative women (51 at Soweto; 119 at Bushbuckridge), performed 16S rRNA gene sequencing on these samples and compared the data to concurrently collected anthropometric data. RESULTS We found the overall gut microbiome of our cohorts to be reflective of their ongoing epidemiological transition. Specifically, we find that geographical location was more important for sample clustering than lean/obese status and observed a relatively higher abundance of the Melainabacteria, Vampirovibrio, a predatory bacterium, in Bushbuckridge. Also, Prevotella, despite its generally high prevalence in the cohorts, showed an association with obesity. In comparisons with benchmarked datasets representative of non-Western populations, relatively higher abundance values were observed in our dataset for Barnesiella (log2fold change (FC) = 4.5), Alistipes (log2FC = 3.9), Bacteroides (log2FC = 4.2), Parabacteroides (log2FC = 3.1) and Treponema (log2FC = 1.6), with the exception of Prevotella (log2FC = - 4.7). CONCLUSIONS Altogether, this work identifies putative microbial features associated with host health in a historically understudied community undergoing an epidemiological transition. Furthermore, we note the crucial role of community engagement to the success of a study in an African setting, the importance of more population-specific studies to inform targeted interventions as well as present a basic foundation for future research.
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Affiliation(s)
- O. H. Oduaran
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - F. B. Tamburini
- Department of Genetics, Stanford University, Stanford, CA USA
| | - V. Sahibdeen
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - R. Brewster
- School of Medicine, Stanford University, Stanford, CA USA
| | - F. X. Gómez-Olivé
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- INDEPTH Network, East Legon, Accra, Ghana
| | - K. Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- INDEPTH Network, East Legon, Accra, Ghana
| | - S. A. Norris
- SAMRC Developmental Pathways for Health Research Unit, Department of Paediatrics, University of the Witwatersrand, Johannesburg, South Africa
- School of Human Development and Health, University of Southampton, Southampton, UK
| | - S. M. Tollman
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- INDEPTH Network, East Legon, Accra, Ghana
| | - R. Twine
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. N. Wade
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - R. G. Wagner
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- INDEPTH Network, East Legon, Accra, Ghana
| | - Z. Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - A. S. Bhatt
- Department of Genetics, Stanford University, Stanford, CA USA
- School of Medicine, Stanford University, Stanford, CA USA
- Department of Medicine (Hematology), Stanford University, Stanford, CA USA
| | - S. Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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73
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Gut Microbiome in Children from Indigenous and Urban Communities in México: Different Subsistence Models, Different Microbiomes. Microorganisms 2020; 8:microorganisms8101592. [PMID: 33081076 PMCID: PMC7602701 DOI: 10.3390/microorganisms8101592] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/31/2020] [Accepted: 09/03/2020] [Indexed: 12/12/2022] Open
Abstract
The human gut microbiome is an important component that defines host health. Childhood is a particularly important period for the establishment and development of gut microbiota (GM). We sequenced the 16S rRNA gene from fecal samples of children between 5 and 10 years old, in two Mexican communities with contrasting lifestyles, i.e., “Westernized” (México City, n = 13) and “non-Westernized” (Me’phaa indigenous group, n = 29), in order to characterize and compare their GM. The main differences between these two communities were in bacteria associated with different types of diets (high animal protein and refined sugars vs. high fiber food, respectively). In addition, the GM of Me’phaa children showed higher total diversity and the presence of exclusive phyla, such as Deinococcus-Thermus, Chloroflexi, Elusimicrobia, Acidobacteria, and Fibrobacteres. In contrast, the children from México City showed less diversity and the presence of Saccharibacteria phylum, which was associated with the degradation of sugar compounds and was not present in the samples from Me’phaa children. This comparison provided further knowledge of the selective pressures affecting microbial ecosystemic composition over the course of human evolution and the potential consequences of pathophysiological states correlated with Westernization lifestyles.
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74
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Schnorr SL. The soil in our microbial DNA informs about environmental interfaces across host and subsistence modalities. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190577. [PMID: 33012224 DOI: 10.1098/rstb.2019.0577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
In this study, I use microbiome datasets from global soil samples and diverse hosts to learn whether soil microbial taxa are found in host microbiomes, and whether these observations fit the narrative that environmental interaction influences human microbiomes. A major motivation for conducting host-associated microbiome research is to contribute towards understanding how the environment may influence host physiology. The microbial molecular network is considered a key vector by which environmental traits may be transmitted to the host. Research on human evolution seeks evidence that can inform about the living experiences of human ancestors. This objective is substantially enhanced by recent work on ancient biomolecules from preserved microbial tissues, such as dental calculus, faecal sediments and whole coprolites. A challenge yet is to distinguish authentic biomolecules from environmental contaminants deposited contemporaneously, primarily from soil. However, we do not have sound expectations about the soil microbial elements arriving to host-associated microbiomes in a modern context. One assumption in human microbiome research is that proximity to the natural environment should affect biodiversity or impart genetic elements. I present evidence supporting the assumption that environmental soil taxa are found among host-associated gut taxa, which can recapitulate the surrounding host habitat ecotype. Soil taxa found in gut microbiomes relate to a set of universal 'core' taxa for all soil ecotypes, demonstrating that widespread host organisms may experience a consistent pattern of external environmental cues, perhaps critical for development. Observed differentiation of soil feature diversity, abundance and composition among human communities, great apes and invertebrate hosts also indicates that lifestyle patterns are inferable from an environmental signal that is retrievable from gut microbiome amplicon data. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Stephanie L Schnorr
- Department of Anthropology, University of Nevada, Las Vegas, NV, USA.,Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria
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75
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Sprockett DD, Martin M, Costello EK, Burns AR, Holmes SP, Gurven MD, Relman DA. Microbiota assembly, structure, and dynamics among Tsimane horticulturalists of the Bolivian Amazon. Nat Commun 2020; 11:3772. [PMID: 32728114 PMCID: PMC7391733 DOI: 10.1038/s41467-020-17541-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 07/03/2020] [Indexed: 01/16/2023] Open
Abstract
Selective and neutral forces shape human microbiota assembly in early life. The Tsimane are an indigenous Bolivian population with infant care-associated behaviors predicted to increase mother-infant microbial dispersal. Here, we characterize microbial community assembly in 47 infant-mother pairs from six Tsimane villages, using 16S rRNA gene amplicon sequencing of longitudinal stool and tongue swab samples. We find that infant consumption of dairy products, vegetables, and chicha (a fermented drink inoculated with oral microbes) is associated with stool microbiota composition. In stool and tongue samples, microbes shared between mothers and infants are more abundant than non-shared microbes. Using a neutral model of community assembly, we find that neutral processes alone explain the prevalence of 79% of infant-colonizing microbes, but explain microbial prevalence less well in adults from river villages with more regular access to markets. Our results underscore the importance of neutral forces during microbiota assembly. Changing lifestyle factors may alter traditional modes of microbiota assembly by decreasing the role of neutral processes. Selective and neutral forces shape human microbiota assembly in early life. Here, Sprockett et al. study microbial community assembly in 47 infant-mother pairs from the Tsimane, an indigenous Bolivian population, highlighting the importance of neutral forces during microbiota assembly.
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Affiliation(s)
- Daniel D Sprockett
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Melanie Martin
- Department of Anthropology, University of Washington, Seattle, WA, 98195, USA.,Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Elizabeth K Costello
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Adam R Burns
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Susan P Holmes
- Department of Statistics, Stanford University, Stanford, CA, 94305, USA
| | - Michael D Gurven
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, 93106, USA.,Broom Center for Demography, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - David A Relman
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Infectious Diseases Section, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, 94304, USA.
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76
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Bajinka O, Tan Y, Abdelhalim KA, Özdemir G, Qiu X. Extrinsic factors influencing gut microbes, the immediate consequences and restoring eubiosis. AMB Express 2020; 10:130. [PMID: 32710186 PMCID: PMC7381537 DOI: 10.1186/s13568-020-01066-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 07/18/2020] [Indexed: 02/07/2023] Open
Abstract
From the emerging studies, the more diverse the microbial population in the gut, the healthier the gut. Health benefits are associated with the functional characteristics of these diverse microbial genes. Extrinsic factors causing dysbiosis are extensively studied however, linking the varying degree of consequences to the respective factors and therapeutic possibilities are not explored at length. This review aims to examine from previous studies and put forward the types of dysbiosis, the immediate consequences and the scientific approaches to restore disrupted microbiota. Dietary supplements are found to be one of the factors contributing profoundly to the alteration of gut microbiota. While diet rich in fibre and fermented food established a diverse microbiome and produce vital metabolites, high fat, animal proteins and high caloric carbohydrate are as well relative to dysbiosis among infants, adult or diseases individuals. The intermittent fasting, feeding methods, the pH and water quality are among the factors associated with dysbiosis. Prebiotics and Probiotics maintain and restore gut homeostasis. Antibiotic-induced dysbiosis are relatively on the spectrum of activity, the pharmacokinetics properties, the dose taken during the treatment route of administration and the duration of drug therapy. The higher the altitude, the lesser the diversity. Extreme temperatures as well are related to reduced microbial activity and metabolism. Delivery through caserium-section deprived the newborn from restoring valuable vaginal bacterial species and the baby will instead assumed intestinal microbiota-like. While exercise and oxidative stress contribute even though moderately, fecal microbial transfer (FMT) also influence gut microbiota.
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77
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Golloso-Gubat MJ, Ducarmon QR, Tan RCA, Zwittink RD, Kuijper EJ, Nacis JS, Santos NLC. Gut Microbiota and Dietary Intake of Normal-Weight and Overweight Filipino Children. Microorganisms 2020; 8:microorganisms8071015. [PMID: 32650516 PMCID: PMC7409305 DOI: 10.3390/microorganisms8071015] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 12/11/2022] Open
Abstract
Diet and body mass index (BMI) have been shown to affect the gut microbiota of children, but studies are largely performed in developed countries. Here, we conducted a cross-sectional investigation on the differences in the bacterial gut microbiota between normal-weight and overweight urban Filipino children, and determined the relationship between their energy, macronutrient and dietary fiber intakes, and their gut microbiota composition and diversity. Forty-three children (normal-weight, n = 32; overweight, n = 11) participated in the study. Energy and fiber intakes were collected using a semi-quantitative Food Frequency Questionnaire (FFQ). The gut microbiota was profiled using 16S rRNA gene amplicon sequencing of the V3–V4 region. The diet of the children was a mixture of traditional and Western patterns. There were no significant differences in energy, macronutrients and energy-adjusted fiber intakes between the normal-weight and overweight groups, but there were significantly more children meeting the recommended fiber intake in the overweight group. Alpha and beta bacterial diversities did not significantly differ between weight groups. Relative abundance of Bifidobacterium, Turicibacter and Clostridiaceae 1 were higher in the normal-weight than overweight children, and Lachnospira was higher in overweight children.
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Affiliation(s)
- Maria Julia Golloso-Gubat
- Department of Science and Technology-Food and Nutrition Research Institute, Taguig City 1631, Philippines; (R.C.A.T.); (J.S.N.); (N.L.C.S.)
- Correspondence: ; Tel.: +632-8837-2071 (ext. 2299)
| | - Quinten R. Ducarmon
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (Q.R.D.); (R.D.Z.); (E.J.K.)
| | - Robby Carlo A. Tan
- Department of Science and Technology-Food and Nutrition Research Institute, Taguig City 1631, Philippines; (R.C.A.T.); (J.S.N.); (N.L.C.S.)
| | - Romy D. Zwittink
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (Q.R.D.); (R.D.Z.); (E.J.K.)
| | - Ed J. Kuijper
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands; (Q.R.D.); (R.D.Z.); (E.J.K.)
| | - Jacus S. Nacis
- Department of Science and Technology-Food and Nutrition Research Institute, Taguig City 1631, Philippines; (R.C.A.T.); (J.S.N.); (N.L.C.S.)
| | - Noelle Lyn C. Santos
- Department of Science and Technology-Food and Nutrition Research Institute, Taguig City 1631, Philippines; (R.C.A.T.); (J.S.N.); (N.L.C.S.)
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78
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Luz PLD, Haas EA, Favarato D. Intestinal Microbiota and Cardiovascular Diseases. INTERNATIONAL JOURNAL OF CARDIOVASCULAR SCIENCES 2020. [DOI: 10.36660/ijcs.20200043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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79
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Moran-Ramos S, Lopez-Contreras BE, Villarruel-Vazquez R, Ocampo-Medina E, Macias-Kauffer L, Martinez-Medina JN, Villamil-Ramirez H, León-Mimila P, Del Rio-Navarro BE, Ibarra-Gonzalez I, Vela-Amieva M, Gomez-Perez FJ, Velazquez-Cruz R, Salmeron J, Reyes-Castillo Z, Aguilar-Salinas C, Canizales-Quinteros S. Environmental and intrinsic factors shaping gut microbiota composition and diversity and its relation to metabolic health in children and early adolescents: A population-based study. Gut Microbes 2020; 11:900-917. [PMID: 31973685 PMCID: PMC7524342 DOI: 10.1080/19490976.2020.1712985] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Gut microbiota, by influencing multiple metabolic processes in the host, is an important determinant of human health and disease. However, gut dysbiosis associated with metabolic complications shows inconsistent patterns. This is likely driven by factors shaping gut microbial composition that have largely been under-evaluated, at a population level, in school-age children, especially from developing countries. RESULTS Through characterization, by 16S sequencing, of the largest gut microbial population-based school-aged children cohort in Latin America (ORSMEC, N = 926, aged 6-12 y), we identified associations of 14 clinical and environmental covariates (PFDR<0.1), collectively explaining 15.7% of the inter-individual gut microbial variation. Extrinsic factors such as markers of socioeconomic status showed a major influence in the most abundant taxa and in the enterotypes' distribution. Age was positively correlated with higher diversity, but only in normal-weight children (rho = 0.138, P =2 × 10-3). In contrast, this correlation although not significant, was negative in overweight and obese children (rho = -0.125, P = 0.104 and rho = -0.058, P = 0.409, respectively). Finally, co-abundance groups (CAGs) were associated with the presence of metabolic complications. CONCLUSIONS Our study offers evidence that the presence of overweight and obesity could impair the microbial diversity maturation associated with age. Furthermore, it provides novel results toward a better understanding of gut microbiota in the pediatric population that will ultimately help to develop therapeutic approaches to improve metabolic status.
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Affiliation(s)
- Sofia Moran-Ramos
- Catedratica, Consejo Nacional De Ciencia Y Tecnología (CONACYT), Mexico City, México,Unidad De Genómica De Poblaciones Aplicada a La Salud, Facultad De Química, UNAM/Instituto Nacional De Medicina Genómica (INMEGEN), Mexico City, México
| | - Blanca E. Lopez-Contreras
- Unidad De Genómica De Poblaciones Aplicada a La Salud, Facultad De Química, UNAM/Instituto Nacional De Medicina Genómica (INMEGEN), Mexico City, México
| | - Ricardo Villarruel-Vazquez
- Unidad De Genómica De Poblaciones Aplicada a La Salud, Facultad De Química, UNAM/Instituto Nacional De Medicina Genómica (INMEGEN), Mexico City, México
| | - Elvira Ocampo-Medina
- Unidad De Genómica De Poblaciones Aplicada a La Salud, Facultad De Química, UNAM/Instituto Nacional De Medicina Genómica (INMEGEN), Mexico City, México
| | - Luis Macias-Kauffer
- Unidad De Genómica De Poblaciones Aplicada a La Salud, Facultad De Química, UNAM/Instituto Nacional De Medicina Genómica (INMEGEN), Mexico City, México
| | - Jennifer N. Martinez-Medina
- Unidad De Genómica De Poblaciones Aplicada a La Salud, Facultad De Química, UNAM/Instituto Nacional De Medicina Genómica (INMEGEN), Mexico City, México
| | - Hugo Villamil-Ramirez
- Unidad De Genómica De Poblaciones Aplicada a La Salud, Facultad De Química, UNAM/Instituto Nacional De Medicina Genómica (INMEGEN), Mexico City, México
| | - Paola León-Mimila
- Unidad De Genómica De Poblaciones Aplicada a La Salud, Facultad De Química, UNAM/Instituto Nacional De Medicina Genómica (INMEGEN), Mexico City, México
| | - Blanca E. Del Rio-Navarro
- Servicio de Alergia e Inmunologia Clinica, Hospital Infantil México Federico Gómez, Mexico City, México
| | - Isabel Ibarra-Gonzalez
- Instituto De Investigaciones Biomédicas, UNAM - Instituto Nacional De Pediatría, Mexico City, México
| | - Marcela Vela-Amieva
- Laboratorio De Errores Innatos Del Metabolismo Y Tamiz, Instituto Nacional De Pediatría, Mexico City, México
| | - Francisco J Gomez-Perez
- Departamento De Endocrinología Y Metabolismo, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Mexico City, México
| | | | - Jorge Salmeron
- Centro de Investigación en Políticas, Población y Salud de la Facultad de Medicina-UNAM, Mexico City, Mexico
| | - Zyanya Reyes-Castillo
- Instituto de Investigaciones en Comportamiento Alimentario y Nutricion (IICAN), Universidad de Guadalajara - Centro Universitario del Sur, Ciudad Guzman, Jalisco, Mexico
| | - Carlos Aguilar-Salinas
- Unidad De Investigación En Enfermedades Metabólicas and Departamento De Endocrinología Y Metabolismo, Instituto Nacional De Ciencias Médicas Y Nutrición Salvador Zubirán, Mexico City, Mexico,Tecnológico De Monterrey, Escuela De Medicina Y Ciencias De La Salud, Monterrey, México
| | - Samuel Canizales-Quinteros
- Unidad De Genómica De Poblaciones Aplicada a La Salud, Facultad De Química, UNAM/Instituto Nacional De Medicina Genómica (INMEGEN), Mexico City, México,CONTACT Samuel Canizales-Quinteros
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Li X, Guo R, Wu X, Liu X, Ai L, Sheng Y, Song Z, Wu Y. Dynamic digestion of tamarind seed polysaccharide: Indigestibility in gastrointestinal simulations and gut microbiota changes in vitro. Carbohydr Polym 2020; 239:116194. [DOI: 10.1016/j.carbpol.2020.116194] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 03/07/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023]
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81
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Fukunaga M, Kuda T, Xia Y, Nakamura S, Takahashi H, Kimura B. Detection and isolation of the typical gut indigenous bacteria from ddY mice fed a casein-beef tallow-based or egg yolk-based diet. J Food Biochem 2020; 44:e13246. [PMID: 32462679 DOI: 10.1111/jfbc.13246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/27/2020] [Accepted: 03/21/2020] [Indexed: 12/16/2022]
Abstract
The effects of whole egg on the cecal microbiome of ddY mice has been reported. To investigate the existence of susceptible indigenous bacteria (SIB) to egg yolks (EY), mice were fed a diet containing either 20% (w/w) milk casein and 17% beef tallow (CT) or 12% milk casein and 27% EY for 14 days, and then, the cecal microbiome was analyzed by 16S rRNA (V4) amplicon sequencing. To isolate the typical species in each diet group, culture-dependent viable bacterial counts were determined on Blood Liver (BL) and Gifu Anaerobic Medium (GAM) agar plates. The amplicon sequencing analysis revealed typical CT-SIB, such as Lachnospiraceae-like bacteria, and EY-SIB, such as Allobaculum-, Lactobacillus murinus-, and Bacteroides vulgatus-like bacteria. Two of the detected SIB species, L. murinus- and B. vulgatus-like bacteria, were successfully isolated from the BL and GAM agar plates and defined using a 16S rDNA BLAST search. PRACTICAL APPLICATIONS: The SIB defined in the CT and EY groups might have some effects on the nutritional and functional chemical compounds in the milk casein, beef tallow, and/or EY. Analysis of its functional properties of the isolates might develop the new and unique probiotic strains.
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Affiliation(s)
- Mayu Fukunaga
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Takashi Kuda
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Yumeng Xia
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Saori Nakamura
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Hajime Takahashi
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Bon Kimura
- Department of Food Science and Technology, Tokyo University of Marine Science and Technology, Tokyo, Japan
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82
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Rubel MA, Abbas A, Taylor LJ, Connell A, Tanes C, Bittinger K, Ndze VN, Fonsah JY, Ngwang E, Essiane A, Fokunang C, Njamnshi AK, Bushman FD, Tishkoff SA. Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians. Genome Biol 2020; 21:122. [PMID: 32450885 PMCID: PMC7249393 DOI: 10.1186/s13059-020-02020-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 04/15/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND African populations provide a unique opportunity to interrogate host-microbe co-evolution and its impact on adaptive phenotypes due to their genomic, phenotypic, and cultural diversity. We integrate gut microbiome 16S rRNA amplicon and shotgun metagenomic sequence data with quantification of pathogen burden and measures of immune parameters for 575 ethnically diverse Africans from Cameroon. Subjects followed pastoralist, agropastoralist, and hunter-gatherer lifestyles and were compared to an urban US population from Philadelphia. RESULTS We observe significant differences in gut microbiome composition across populations that correlate with subsistence strategy and country. After these, the variable most strongly associated with gut microbiome structure in Cameroonians is the presence of gut parasites. Hunter-gatherers have high frequencies of parasites relative to agropastoralists and pastoralists. Ascaris lumbricoides, Necator americanus, Trichuris trichiura, and Strongyloides stercoralis soil-transmitted helminths ("ANTS" parasites) significantly co-occur, and increased frequency of gut parasites correlates with increased gut microbial diversity. Gut microbiome composition predicts ANTS positivity with 80% accuracy. Colonization with ANTS, in turn, is associated with elevated levels of TH1, TH2, and proinflammatory cytokines, indicating an association with multiple immune mechanisms. The unprecedented size of this dataset allowed interrogation of additional questions-for example, we find that Fulani pastoralists, who consume high levels of milk, possess an enrichment of gut bacteria that catabolize galactose, an end product of lactose metabolism, and of bacteria that metabolize lipids. CONCLUSIONS These data document associations of bacterial microbiota and eukaryotic parasites with each other and with host immune responses; each of these is further correlated with subsistence practices.
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Affiliation(s)
- Meagan A. Rubel
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104 USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Present Address: Department of Radiology, Center for Translational Imaging and Precision Medicine, UC San Diego, San Diego, CA USA
| | - Arwa Abbas
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Present Address: Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Louis J. Taylor
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Andrew Connell
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104 USA
| | - Valantine N. Ndze
- Johns Hopkins Cameroon Program, Yaoundé, Cameroon
- Department of Microbiology, Hematology, Parasitology and Infectious Diseases, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Julius Y. Fonsah
- Department of Neurology, Faculty of Medicine and Biomedical Sciences, Yaoundé Central Hospital, Yaoundé, Cameroon
| | - Eric Ngwang
- Department of Anthropology, Faculty of Arts, Letters and Social Sciences, University of Yaoundé I, PO Box 755, Yaoundé, Cameroon
| | | | - Charles Fokunang
- Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Alfred K. Njamnshi
- Department of Neurology, Central Hospital Yaoundé, Yaoundé, Cameroon
- Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
- Brain Research Africa Initiative (BRAIN), Yaoundé, Cameroon
| | - Frederic D. Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
| | - Sarah A. Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104 USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104 USA
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83
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Afolayan A, Adebusoye L, Cadmus E, Ayeni F. Insights into the gut microbiota of Nigerian elderly with type 2 diabetes and non-diabetic elderly persons. Heliyon 2020; 6:e03971. [PMID: 32490229 PMCID: PMC7262409 DOI: 10.1016/j.heliyon.2020.e03971] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 04/09/2020] [Accepted: 05/07/2020] [Indexed: 12/27/2022] Open
Abstract
Type 2 diabetes (T2D) is a prevalent non-communicable disease among the world's growing elderly population. The contribution of the gut microbiota to T2D in several Westernized countries has been established. However, there is little information on the role of the gut microbiota in T2D from the African continent where lifestyle and life expectancy are different. AIMS This study sought to investigate gut microbiota variation in relation to elderly people living with T2D. in Nigeria. METHODS Whole microbial community DNA were derived from the stool samples of healthy urban-dwelling elderly individuals and urban-dwelling elderly individuals with T2D. The V4 region of the 16S rRNA gene was Illumina-sequenced and analyzed using QIIME2. RESULTS Beta taxonomic diversity was significantly different between healthy elderly individuals and elderly individuals with T2D. However, no difference in the alpha taxonomic diversity and predicted functional alpha diversity of the gut microbiota was observed. The genus Ruminococcus (T2D versus Healthy: 2.89% vs 2.21%), families Coriobacteriaceae (Collinsella, T2D versus Healthy: 2.62 % vs 1.25%) and Bifidobacteriaceae were enriched in elderly individuals with T2D, while members of Clostridiaceae (Clostridium, Healthy versus T2D: 5.6% vs 3.2%) and Peptostreptococcaceae (Healthy versus T2D: 3.45% vs 1.99%) were enriched in healthy volunteers. Pathways involved in amino acid biosynthesis were enriched in elderly individuals with T2D, while pathways involved in respiration and the biosynthesis of vital building blocks were enriched in healthy volunteers. CONCLUSIONS The study demonstrated for the first time in an African elderly population that the abundance of Bifidobacteriaceae, Collinsella, and Ruminococcus within the gut varies in relation to T2D. Findings from this study suggest that the restoration of features associated with healthiness via the way of gut microbiota modification could be one step needed to improve elderly patient care.
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Affiliation(s)
- A.O. Afolayan
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - L.A. Adebusoye
- Chief Tony Anenih Geriatric Centre, University College Hospital, Ibadan, Oyo State, Nigeria
| | - E.O. Cadmus
- Chief Tony Anenih Geriatric Centre, University College Hospital, Ibadan, Oyo State, Nigeria
- Department of Community Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - F.A. Ayeni
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
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84
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Adigun O, Gcebe N, Jambwa K, Fasina F, Adesiyun AA. Molecular and phenotypic characterization of
Staphylococcus aureus
strains isolated from carcass swabs and carcass drips of chickens slaughtered in the informal market in Gauteng Province, South Africa. J Food Saf 2020. [DOI: 10.1111/jfs.12806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Oluwatola Adigun
- Department of Production Animal Studies, Faculty of Veterinary ScienceUniversity of Pretoria Pretoria South Africa
| | - Nomakorinte Gcebe
- Agriculture Research Council, Onderstepoort Veterinary ResearchBacteriology Laboratory Pretoria South Africa
| | - Kudakwashe Jambwa
- Agriculture Research Council, Onderstepoort Veterinary ResearchBacteriology Laboratory Pretoria South Africa
| | - Folorunso Fasina
- Department of Veterinary Tropical Disease, Faculty of Veterinary SciencesUniversity of Pretoria Pretoria South Africa
- ECTADFood and Agriculture Organization Dar es Salaam, Tanzania
| | - Abiodun A. Adesiyun
- Department of Production Animal Studies, Faculty of Veterinary ScienceUniversity of Pretoria Pretoria South Africa
- School of Veterinary Medicine, Faculty of Medical SciencesUniversity of the West Indies St. Augustine Trinidad and Tobago
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85
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Cowan CSM, Dinan TG, Cryan JF. Annual Research Review: Critical windows - the microbiota-gut-brain axis in neurocognitive development. J Child Psychol Psychiatry 2020; 61:353-371. [PMID: 31773737 DOI: 10.1111/jcpp.13156] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/26/2019] [Accepted: 10/09/2019] [Indexed: 02/06/2023]
Abstract
The gut microbiota is a vast, complex, and fascinating ecosystem of microorganisms that resides in the human gastrointestinal tract. As an integral part of the microbiota-gut-brain axis, it is now being recognized that the microbiota is a modulator of brain and behavior, across species. Intriguingly, periods of change in the microbiota coincide with the development of other body systems and particularly the brain. We hypothesize that these times of parallel development are biologically relevant, corresponding to 'sensitive periods' or 'critical windows' in the development of the microbiota-gut-brain axis. Specifically, signals from the microbiota during these periods are hypothesized to be crucial for establishing appropriate communication along the axis throughout the life span. In other words, the microbiota is hypothesized to act like an expected input to calibrate the development of the microbiota-gut-brain axis. The absence or disruption of the microbiota during specific developmental windows would therefore be expected to have a disproportionate effect on specific functions or potentially for regulation of the system as a whole. Evidence for microbial modulation of neurocognitive development and neurodevelopmental risk is discussed in light of this hypothesis, finishing with a focus on the challenges that lay ahead for the future study of the microbiota-gut-brain axis during development.
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Affiliation(s)
| | - Timothy G Dinan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Psychiatry and Neurobehavioural Science, University College Cork, Cork, Ireland
| | - John F Cryan
- APC Microbiome Ireland, University College Cork, Cork, Ireland.,Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
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86
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Lokmer A, Aflalo S, Amougou N, Lafosse S, Froment A, Tabe FE, Poyet M, Groussin M, Said-Mohamed R, Ségurel L. Response of the human gut and saliva microbiome to urbanization in Cameroon. Sci Rep 2020; 10:2856. [PMID: 32071424 PMCID: PMC7028744 DOI: 10.1038/s41598-020-59849-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/05/2020] [Indexed: 12/22/2022] Open
Abstract
Urban populations from highly industrialized countries are characterized by a lower gut bacterial diversity as well as by changes in composition compared to rural populations from less industrialized countries. To unveil the mechanisms and factors leading to this diversity loss, it is necessary to identify the factors associated with urbanization-induced shifts at a smaller geographical scale, especially in less industrialized countries. To do so, we investigated potential associations between a variety of dietary, medical, parasitological and socio-cultural factors and the gut and saliva microbiomes of 147 individuals from three populations along an urbanization gradient in Cameroon. We found that the presence of Entamoeba sp., a commensal gut protozoan, followed by stool consistency, were major determinants of the gut microbiome diversity and composition. Interestingly, urban individuals have retained most of their gut eukaryotic and bacterial diversity despite significant changes in diet compared to the rural areas, suggesting that the loss of bacterial microbiome diversity observed in industrialized areas is likely associated with medication. Finally, we observed a weak positive correlation between the gut and the saliva microbiome diversity and composition, even though the saliva microbiome is mainly shaped by habitat-related factors.
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Affiliation(s)
- Ana Lokmer
- UMR7206 Eco-anthropologie, CNRS - MNHN - Université de Paris, Paris, France.
| | - Sophie Aflalo
- UMR7206 Eco-anthropologie, CNRS - MNHN - Université de Paris, Paris, France
| | - Norbert Amougou
- UMR7206 Eco-anthropologie, CNRS - MNHN - Université de Paris, Paris, France
| | - Sophie Lafosse
- UMR7206 Eco-anthropologie, CNRS - MNHN - Université de Paris, Paris, France
| | - Alain Froment
- UMR7206 Eco-anthropologie, CNRS - MNHN - Université de Paris, Paris, France
| | - Francis Ekwin Tabe
- Faculté de Médecine et des Sciences Biomédicales - Université Yaoundé 1, Yaoundé, Cameroun
| | - Mathilde Poyet
- Department of Biological Engineering/Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mathieu Groussin
- Department of Biological Engineering/Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rihlat Said-Mohamed
- SAMRC/WITS Developmental Pathways for Health Research Unit, Department of Paediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Laure Ségurel
- UMR7206 Eco-anthropologie, CNRS - MNHN - Université de Paris, Paris, France.
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87
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Chew C, Barros KV, Weffort VRS, Maranhão HDS, Laranjeira M, Knol J, Roeselers G, de Morais MB. Gut Microbiota of Young Children Living in Four Brazilian Cities. Front Pediatr 2020; 8:573815. [PMID: 33365290 PMCID: PMC7751462 DOI: 10.3389/fped.2020.573815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022] Open
Abstract
Recent studies have demonstrated that gut microbiota development is influenced by human biogeographic factors such as race, ethnicity, diet, lifestyle or culture-specific variations, and other environmental influences. However, biogeographic variation in gut microbiota assembly remains largely unexplored in Latin America. In this paper, we compared food recall information and microbiota composition of toddlers living in geographically separated urban populations within four states of Brazil. 16S RNA gene sequencing revealed that alpha diversity was similar between the four different populations. Gut microbiota compositions were dominated by members of the phyla Firmicutes and Bacteroidetes, resembling a more adult-like microbiota as compared with those of Western European toddlers of similar age. These findings suggest that inter-individual and nutrition-induced differences were apparent in the fecal microbiota. We conclude that urban dietary pattern plays a larger role in influencing the gut microbiota composition than do biogeographic factors.
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Affiliation(s)
- Charmaine Chew
- Danone Nutricia Research, Singapore, Singapore.,Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands
| | | | | | | | | | - Jan Knol
- Laboratory of Microbiology, Wageningen University, Wageningen, Netherlands.,Danone Nutricia Research, Utrecht, Netherlands
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88
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Vojinovic D, Radjabzadeh D, Kurilshikov A, Amin N, Wijmenga C, Franke L, Ikram MA, Uitterlinden AG, Zhernakova A, Fu J, Kraaij R, van Duijn CM. Relationship between gut microbiota and circulating metabolites in population-based cohorts. Nat Commun 2019; 10:5813. [PMID: 31862950 PMCID: PMC6925111 DOI: 10.1038/s41467-019-13721-1] [Citation(s) in RCA: 146] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 11/13/2019] [Indexed: 12/29/2022] Open
Abstract
Gut microbiota has been implicated in major diseases affecting the human population and has also been linked to triglycerides and high-density lipoprotein levels in the circulation. Recent development in metabolomics allows classifying the lipoprotein particles into more details. Here, we examine the impact of gut microbiota on circulating metabolites measured by Nuclear Magnetic Resonance technology in 2309 individuals from the Rotterdam Study and the LifeLines-DEEP cohort. We assess the relationship between gut microbiota and metabolites by linear regression analysis while adjusting for age, sex, body-mass index, technical covariates, medication use, and multiple testing. We report an association of 32 microbial families and genera with very-low-density and high-density subfractions, serum lipid measures, glycolysis-related metabolites, ketone bodies, amino acids, and acute-phase reaction markers. These observations provide insights into the role of microbiota in host metabolism and support the potential of gut microbiota as a target for therapeutic and preventive interventions.
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Affiliation(s)
- Dina Vojinovic
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Alexander Kurilshikov
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Cisca Wijmenga
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Lude Franke
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Alexandra Zhernakova
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
| | - Jingyuan Fu
- University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen and University Medical Center Groningen, Groningen, The Netherlands
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
- Nuffield Department of Population Health, University of Oxford, Oxford, UK.
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89
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Spencer SP, Fragiadakis GK, Sonnenburg JL. Pursuing Human-Relevant Gut Microbiota-Immune Interactions. Immunity 2019; 51:225-239. [PMID: 31433970 DOI: 10.1016/j.immuni.2019.08.002] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The gut microbiota is a complex and plastic network of diverse organisms intricately connected with human physiology. Recent advances in profiling approaches of both the microbiota and the immune system now enable a deeper exploration of immunity-microbiota connections. An important next step is to elucidate a human-relevant "map" of microbial-immune wiring while focusing on animal studies to probe a prioritized subset of interactions. Here, we provide an overview of this field's current status and discuss two approaches for establishing priorities for detailed investigation: (1) longitudinal intervention studies in humans probing the dynamics of both the microbiota and the immune system and (2) the study of traditional populations to assess lost features of human microbial identity whose absence may be contributing to the rise of immunological disorders. These human-centered approaches offer a judicious path forward to understand the impact of the microbiota in immune development and function.
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Affiliation(s)
- Sean P Spencer
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | | | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA; Center for Human Microbiome Studies, Stanford University, Stanford, CA, USA.
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90
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Abstract
Pancreatic cancer (PC) is a leading cause of cancer-related death in developed countries, and since most patients have incurable disease at the time of diagnosis, developing a screening method for early detection is of high priority. Due to its metabolic importance, alterations in pancreatic functions may affect the composition of the gut microbiota, potentially yielding biomarkers for PC. However, the usefulness of these biomarkers may be limited if they are specific for advanced stages of disease, which may involve comorbidities such as biliary obstruction or diabetes. In this study we analyzed the fecal microbiota of 30 patients with pancreatic adenocarcinoma, 6 patients with pre-cancerous lesions, 13 healthy subjects and 16 with non-alcoholic fatty liver disease, using amplicon sequencing of the bacterial 16S rRNA gene. Fourteen bacterial features discriminated between PC and controls, and several were shared with findings from a recent Chinese cohort. A Random Forest model based on the microbiota classified PC and control samples with an AUC of 82.5%. However, inter-subject variability was high, and only a small part of the PC-associated microbial signals were also observed in patients with pre-cancerous pancreatic lesions, implying that microbiome-based early detection of such lesions will be challenging.
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91
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Waters JL, Ley RE. The human gut bacteria Christensenellaceae are widespread, heritable, and associated with health. BMC Biol 2019; 17:83. [PMID: 31660948 PMCID: PMC6819567 DOI: 10.1186/s12915-019-0699-4] [Citation(s) in RCA: 351] [Impact Index Per Article: 70.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 12/18/2022] Open
Abstract
The Christensenellaceae, a recently described family in the phylum Firmicutes, is emerging as an important player in human health. The relative abundance of Christensenellaceae in the human gut is inversely related to host body mass index (BMI) in different populations and multiple studies, making its relationship with BMI the most robust and reproducible link between the microbial ecology of the human gut and metabolic disease reported to date. The family is also related to a healthy status in a number of other different disease contexts, including obesity and inflammatory bowel disease. In addition, Christensenellaceae is highly heritable across multiple populations, although specific human genes underlying its heritability have so far been elusive. Further research into the microbial ecology and metabolism of these bacteria should reveal mechanistic underpinnings of their host-health associations and enable their development as therapeutics.
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Affiliation(s)
- Jillian L Waters
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tuebingen, Germany
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tuebingen, Germany.
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92
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Zambrana LE, McKeen S, Ibrahim H, Zarei I, Borresen EC, Doumbia L, Boré A, Cissoko A, Douyon S, Koné K, Perez J, Perez C, Hess A, Abdo Z, Sangaré L, Maiga A, Becker-Dreps S, Yuan L, Koita O, Vilchez S, Ryan EP. Rice bran supplementation modulates growth, microbiota and metabolome in weaning infants: a clinical trial in Nicaragua and Mali. Sci Rep 2019; 9:13919. [PMID: 31558739 PMCID: PMC6763478 DOI: 10.1038/s41598-019-50344-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 09/11/2019] [Indexed: 12/12/2022] Open
Abstract
Rice bran supplementation provides nutrients, prebiotics and phytochemicals that enhance gut immunity, reduce enteric pathogens and diarrhea, and warrants attention for improvement of environmental enteric dysfunction (EED) in children. EED is a subclinical condition associated with stunting due to impaired nutrient absorption. This study investigated the effects of rice bran supplementation on weight for age and length for age z-scores (WAZ, LAZ), EED stool biomarkers, as well as microbiota and metabolome signatures in weaning infants from 6 to 12 months old that reside in Nicaragua and Mali. Healthy infants were randomized to a control (no intervention) or a rice bran group that received daily supplementation with increasing doses at each month (1–5 g/day). Stool microbiota were characterized using 16S rDNA amplicon sequencing. Stool metabolomes were analyzed using ultra-high-performance liquid-chromatography tandem mass-spectrometry. Statistical comparisons were completed at 6, 8, and 12 months of age. Daily consumption of rice bran was safe and feasible to support changes in LAZ from 6–8 and 8–12 months of age in Nicaragua and Mali infants when compared to control. WAZ was significantly improved only for Mali infants at 8 and 12 months. Mali and Nicaraguan infants showed major differences in the overall gut microbiota and metabolome composition and structure at baseline, and thus each country cohort demonstrated distinct microbial and metabolite profile responses to rice bran supplementation when compared to control. Rice bran is a practical dietary intervention strategy that merits development in rice-growing regions that have a high prevalence of growth stunting due to malnutrition and diarrheal diseases. Rice is grown as a staple food, and the bran is used as animal feed or wasted in many low- and middle-income countries where EED and stunting is prevalent.
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Affiliation(s)
- Luis E Zambrana
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA.,Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León (UNAN-León), León, Nicaragua
| | - Starin McKeen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Hend Ibrahim
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA.,Department of Medical Biochemistry, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Iman Zarei
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Erica C Borresen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Lassina Doumbia
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Abdoulaye Boré
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Alima Cissoko
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Seydou Douyon
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Karim Koné
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Johann Perez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León (UNAN-León), León, Nicaragua
| | - Claudia Perez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León (UNAN-León), León, Nicaragua
| | - Ann Hess
- Department of Statistics, Colorado State University, Fort Collins, CO, 80523, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80521, USA
| | - Lansana Sangaré
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Ababacar Maiga
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Sylvia Becker-Dreps
- Departments of Family Medicine and Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7595, USA
| | - Lijuan Yuan
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Ousmane Koita
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali.
| | - Samuel Vilchez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León (UNAN-León), León, Nicaragua.
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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Kolodziejczyk AA, Zheng D, Elinav E. Diet–microbiota interactions and personalized nutrition. Nat Rev Microbiol 2019; 17:742-753. [DOI: 10.1038/s41579-019-0256-8] [Citation(s) in RCA: 357] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2019] [Indexed: 12/12/2022]
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94
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Afolayan AO, Ayeni FA, Moissl-Eichinger C, Gorkiewicz G, Halwachs B, Högenauer C. Impact of a Nomadic Pastoral Lifestyle on the Gut Microbiome in the Fulani Living in Nigeria. Front Microbiol 2019; 10:2138. [PMID: 31572342 PMCID: PMC6753190 DOI: 10.3389/fmicb.2019.02138] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 08/30/2019] [Indexed: 12/23/2022] Open
Abstract
The co-evolution of the gut microbiota with its human host has revolutionized our current scientific viewpoint about the contribution of diet and lifestyle on human health. Most studies so far have focused on populations living in the United States and Europe or compared those with communities from other geographic areas in the world. In order to determine the taxonomic and predicted functional profile of the gut microbiome of a hitherto unstudied human community, we investigated the phylogenetic diversity of the gut microbiota in a community of Fulani nomadic pastoralists, and their semi-urbanized neighbors - the Jarawa. The Jarawa reside in a city (Jos) in the north-central part of Nigeria, and are adapted in part to a westernized lifestyle. The nomadic Fulani lifestyle resembles a mix of Paleolithic and Neolithic lifestyle patterns with a greater predisposition to diseases. The fecal microbiota of the Fulani and the Jarawa were characterized by paired-end Illumina MiSeq sequencing of the 16S rRNA gene, followed by downstream bioinformatics analysis of the sequence reads. The Fulani harbored increased numbers of signatures of microbes that are known to be associated with a foraging lifestyle such as the Bacteroidetes, Spirochaetes, and Prevotellaceae, while the Jarawa were dominated by signatures of Firmicutes, Ruminococcaceae, Lachnospiraceae, and Christensenellaceae. Notably, the gut microbiota of the Fulani showed less taxonomic diversity than those of the Jarawa. Although they reside in the same geographical zone, microbial community composition was significantly different between the two groups. Pathogens were predicted to be more abundant in the gut microbiota of the Fulani than of the Jarawa. Predicted pathogenic pathways and pathways associated with the breakdown of fiber-rich diet were enriched in the Fulani, including glutathione metabolism, while pathways associated with the consumption of low-fiber diet and xenobiotics, including fructose and mannose metabolic pathways, and nitrotoluene degradation pathways, respectively, were enriched in the Jarawa. Significant differences in composition between both groups were likely due to differences in diet and lifestyle and exposure to pathogens. These results suggest that microbial diversity may not always be higher in non-industrialized societies than in westernized societies, as previously assumed.
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Affiliation(s)
- Ayorinde O. Afolayan
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Funmilola A. Ayeni
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Christine Moissl-Eichinger
- Division of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Graz, Austria
- BioTechMed, Interuniversity Cooperation, Graz, Austria
| | - Gregor Gorkiewicz
- BioTechMed, Interuniversity Cooperation, Graz, Austria
- Institute of Pathology, Medical University of Graz, Graz, Austria
- Theodor Escherich Laboratory for Microbiome Research, Graz, Austria
| | - Bettina Halwachs
- BioTechMed, Interuniversity Cooperation, Graz, Austria
- Institute of Pathology, Medical University of Graz, Graz, Austria
- Theodor Escherich Laboratory for Microbiome Research, Graz, Austria
| | - Christoph Högenauer
- Institute of Pathology, Medical University of Graz, Graz, Austria
- Theodor Escherich Laboratory for Microbiome Research, Graz, Austria
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
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95
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Fiori J, Turroni S, Candela M, Gotti R. Assessment of gut microbiota fecal metabolites by chromatographic targeted approaches. J Pharm Biomed Anal 2019; 177:112867. [PMID: 31614303 DOI: 10.1016/j.jpba.2019.112867] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 02/08/2023]
Abstract
Gut microbiota, the specific microbial community of the gastrointestinal tract, by means of the production of microbial metabolites provides the host with several functions affecting metabolic and immunological homeostasis. Insights into the intricate relationships between gut microbiota and the host require not only the understanding of its structure and function but also the measurement of effector molecules acting along the gut microbiota axis. This article reviews the literature on targeted chromatographic approaches in analysis of gut microbiota specific metabolites in feces as the most accessible biological matrix which can directly probe the connection between intestinal bacteria and the (patho)physiology of the holobiont. Together with a discussion on sample collection and preparation, the chromatographic methods targeted to determination of some classes of microbiota-derived metabolites (e.g., short-chain fatty acids, bile acids, low molecular masses amines and polyamines, vitamins, neurotransmitters and related compounds) are discussed and their main characteristics, summarized in Tables.
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Affiliation(s)
- Jessica Fiori
- Department of Chemistry "Giacomo Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Silvia Turroni
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Roberto Gotti
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy.
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96
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Cheng D, Song J, Xie M, Song D. The bidirectional relationship between host physiology and microbiota and health benefits of probiotics: A review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.07.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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97
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Rhoades N, Barr T, Hendrickson S, Prongay K, Haertel A, Gill L, Garzel L, Whiteson K, Slifka M, Messaoudi I. Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease. Genome Biol 2019; 20:173. [PMID: 31451108 PMCID: PMC6709555 DOI: 10.1186/s13059-019-1789-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 08/09/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Diarrhea is the second leading cause of death in children under 5 years of age. Enhanced understanding of causal pathways, pathogenesis, and sequelae of diarrhea is urgently needed. Although the gut microbiota is believed to play a role in susceptibility to diarrheal diseases, our understanding of this association remains incomplete. Infant rhesus macaques (Macaca mulatta) are susceptible to diarrhea making them an ideal model to address this question. RESULTS The maturation of the infant rhesus macaque gut microbiome throughout the first 8 months of life occurs in a similar pattern as that described for human infants. Moreover, the microbiome of the captive reared infant rhesus macaque more closely resembles that of human infants in the developing world than in the western world. Importantly, prior to disease onset, the gut microbiome of infants that later develop diarrhea is enriched in pathways of immunomodulatory metabolite synthesis, while those of infants that remain asymptomatic are enriched in pathways for short-chain fatty acid production. We identify Prevotella strains that are more abundant at 1 month in infants that later develop diarrhea. At 8 months, the microbiomes of animals that experience diarrhea show increased abundance of Campylobacter and a reduction in Helicobacter macacae. CONCLUSION The composition of the microbial community could provide a phenotypic marker of an infant's susceptibility to diarrheal disease. Given the significant physiological and immunological similarities between human and nonhuman primates, these findings provide potential markers of susceptibility to diarrhea that could be modulated to improve infant health, especially in the developing world.
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Affiliation(s)
- Nicholas Rhoades
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Tasha Barr
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Sara Hendrickson
- Division of Neuroscience, Oregon National Primate Research Center, Portland, OR, USA
| | - Kamm Prongay
- Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University West Campus, Portland, OR, USA
| | - Andrew Haertel
- Division of Comparative Medicine, Oregon National Primate Research Center, Oregon Health and Science University West Campus, Portland, OR, USA
| | - Leanne Gill
- California National Primate Research Center, Davis, CA, USA
| | - Laura Garzel
- California National Primate Research Center, Davis, CA, USA
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Mark Slifka
- Division of Neuroscience, Oregon National Primate Research Center, Portland, OR, USA
| | - Ilhem Messaoudi
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA.
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98
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Barone M, Turroni S, Rampelli S, Soverini M, D’Amico F, Biagi E, Brigidi P, Troiani E, Candela M. Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context. PLoS One 2019; 14:e0220619. [PMID: 31393934 PMCID: PMC6687155 DOI: 10.1371/journal.pone.0220619] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 07/18/2019] [Indexed: 02/07/2023] Open
Abstract
The modern Paleolithic diet (MPD), featured by the consumption of vegetables, fruit, nuts, seeds, eggs, fish and lean meat, while excluding grains, dairy products, salt and refined sugar, has gained substantial public attention in recent years because of its potential multiple health benefits. However, to date little is known about the actual impact of this dietary pattern on the gut microbiome (GM) and its implications for human health. In the current scenario where Western diets, low in fiber while rich in industrialized and processed foods, are considered one of the leading causes of maladaptive GM changes along human evolution, likely contributing to the increasing incidence of chronic non-communicable diseases, we hypothesize that the MPD could modulate the Western GM towards a more “ancestral” configuration. In an attempt to shed light on this, here we profiled the GM structure of urban Italian subjects adhering to the MPD, and compared data with other urban Italians following a Mediterranean Diet (MD), as well as worldwide traditional hunter-gatherer populations from previous publications. Notwithstanding a strong geography effect on the GM structure, our results show an unexpectedly high degree of biodiversity in MPD subjects, which well approximates that of traditional populations. The GM of MPD individuals also shows some peculiarities, including a high relative abundance of bile-tolerant and fat-loving microorganisms. The consumption of plant-based foods–albeit with the exclusion of grains and pulses–along with the minimization of the intake of processed foods, both hallmarks of the MPD, could therefore contribute to partially rewild the GM but caution should be taken in adhering to this dietary pattern in the long term.
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Affiliation(s)
- Monica Barone
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Silvia Turroni
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
- * E-mail:
| | - Simone Rampelli
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Matteo Soverini
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Federica D’Amico
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Elena Biagi
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Patrizia Brigidi
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Emidio Troiani
- Primary Care Unit and Territorial Health, Social Security Institute, Cailungo, Republic of San Marino
| | - Marco Candela
- Unit of Microbial Ecology of Health, Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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99
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Porras AM, Brito IL. The internationalization of human microbiome research. Curr Opin Microbiol 2019; 50:50-55. [PMID: 31683111 PMCID: PMC6907006 DOI: 10.1016/j.mib.2019.09.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 12/27/2022]
Abstract
The human microbiome has now been linked with myriad diseases, yet most of this research has been conducted on American and European populations that make up only 1/6th of the world's population. With growing recognition that human microbiomes differ tremendously across global populations, it is especially important to understand how these compositional differences impact health outcomes. Recent advances in infectious disease and malnutrition research have demonstrated the potential for microbiome-based strategies to address the biggest challenges in global health. This review highlights major advances toward understanding microbiome diversity across the world and its contributions to disease, and outlines key questions, challenges, and opportunities to broaden the scope of and promote inclusivity within microbiome research.
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Affiliation(s)
- Ana Maria Porras
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14850, United States
| | - Ilana Lauren Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14850, United States.
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100
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Malmuthuge N, Griebel PJ. A Novel Animal Model for Regional Microbial Dysbiosis of the Pioneer Microbial Community. Front Microbiol 2019; 10:1706. [PMID: 31396198 PMCID: PMC6668574 DOI: 10.3389/fmicb.2019.01706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/10/2019] [Indexed: 01/17/2023] Open
Abstract
Pioneer microbiota colonizing the newborn gastrointestinal tract has long-lasting effects on host health. Restoration of the gut microbial community, following dysbiosis during the neonatal period, may be one strategy to prevent undesirable health outcomes linked to an altered neonatal gut microbiome. Without appropriate animal models that recreate the prolonged human neonatal developmental period it is not possible to effectively analyze interventions designed to restore regional microbial populations. Our study used a lamb model in which intestinal segments were surgically isolated (blind-ended) in fetal lambs to create early microbial dysbiosis by delaying post-natal exposure to intestinal ingesta. Intestinal segments isolated in utero retained blood flow, innervation, and lymphatic drainage through the mesenteric attachment. Continuity of the fetal gastro-intestinal tract was re-established by side-to-side anastomosis of intestine proximal and distal to each isolated intestinal segment. Microbial restoration was then implemented in neonatal lambs by reconnecting a portion of the in utero isolated intestinal segments to adjacent intestinal tract 1 and 7 days after birth. Bacterial communities colonizing the adjacent intestine, in utero isolated intestinal segments, and reconnected intestinal segments were profiled using 16S amplicon sequencing on days 1, 7, and 56 of age. The in utero isolated intestinal segments were colonized 1 day after birth but the density of active bacteria was reduced and community composition altered when compared to adjacent intestine. Proteobacteria dominated the adjacent small intestine at early time points (day 1 and day 7) with a shift to primarily Firmicutes on day 56, consistent with establishment of an anaerobic bacterial community. In contrast, Proteobacteria persisted as the predominant community for 56 days in the in utero isolated intestinal segments. There was, however, almost full restoration of the microbial community composition in the in utero isolated intestinal segments following reconnection to the adjacent intestine. The density of beneficial bacteria, especially Bifidobacterium, remained significantly lower in the reconnected intestinal segments at 56 days when compared to adjacent intestine. Post-natal persistence of a stable pioneer community (Proteobacteria) in the in utero isolated intestinal segments provides a model system to study the temporal effects of regional microbial dysbiosis throughout a prolonged neonatal period.
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Affiliation(s)
- Nilusha Malmuthuge
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Philip J. Griebel
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK, Canada
- School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
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