601
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The Central Nervous System and the Gut Microbiome. Cell 2017; 167:915-932. [PMID: 27814521 DOI: 10.1016/j.cell.2016.10.027] [Citation(s) in RCA: 889] [Impact Index Per Article: 127.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/14/2016] [Accepted: 10/16/2016] [Indexed: 12/11/2022]
Abstract
Neurodevelopment is a complex process governed by both intrinsic and extrinsic signals. While historically studied by researching the brain, inputs from the periphery impact many neurological conditions. Indeed, emerging data suggest communication between the gut and the brain in anxiety, depression, cognition, and autism spectrum disorder (ASD). The development of a healthy, functional brain depends on key pre- and post-natal events that integrate environmental cues, such as molecular signals from the gut. These cues largely originate from the microbiome, the consortium of symbiotic bacteria that reside within all animals. Research over the past few years reveals that the gut microbiome plays a role in basic neurogenerative processes such as the formation of the blood-brain barrier, myelination, neurogenesis, and microglia maturation and also modulates many aspects of animal behavior. Herein, we discuss the biological intersection of neurodevelopment and the microbiome and explore the hypothesis that gut bacteria are integral contributors to development and function of the nervous system and to the balance between mental health and disease.
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602
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Abstract
PURPOSE OF THE REVIEW Evidence is rapidly accumulating implicating gut dysbiosis in hypertension (HTN). However, we are far from understanding whether this is a cause or consequence of HTN, and how to best translate this fundamental knowledge to advance the management of HTN. This review aims to summarize recent advances in the field, illustrate the connections between the gut and hypertension, and establish that the gut microbiota (GM)-gut interaction is centrally positioned for consideration as an innovative approach for HTN therapeutics. RECENT FINDINGS Animal models of HTN have shown that gut pathology occurs in HTN, and provides some clues to mechanisms linking the dysbiosis, gut pathology, and HTN. Circumstantial evidence links gut dysbiosis and HTN. Gut pathology, apparent in animal HTN models, has not been fully investigated in hypertensive patients. Objective evidence and an understanding of mechanisms could have a major impact for new antihypertensive therapies and/or improved applications of current ones.
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Affiliation(s)
- Elaine M Richards
- Departments of Physiology and Functional Genomics, University of Florida, PO Box 100274, Gainesville, FL, 32610-0274, USA
| | - Carl J Pepine
- Department of Medicine, Division of Cardiovascular Medicine, University of Florida, Gainesville, Florida, USA
| | - Mohan K Raizada
- Departments of Physiology and Functional Genomics, University of Florida, PO Box 100274, Gainesville, FL, 32610-0274, USA.
| | - Seungbum Kim
- Departments of Physiology and Functional Genomics, University of Florida, PO Box 100274, Gainesville, FL, 32610-0274, USA
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603
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Gray LEK, O'Hely M, Ranganathan S, Sly PD, Vuillermin P. The Maternal Diet, Gut Bacteria, and Bacterial Metabolites during Pregnancy Influence Offspring Asthma. Front Immunol 2017; 8:365. [PMID: 28408909 PMCID: PMC5374203 DOI: 10.3389/fimmu.2017.00365] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 03/14/2017] [Indexed: 01/04/2023] Open
Abstract
This review focuses on the current evidence that maternal dietary and gut bacterial exposures during pregnancy influence the developing fetal immune system and subsequent offspring asthma. Part 1 addresses exposure to a farm environment, antibiotics, and prebiotic and probiotic supplementation that together indicate the importance of bacterial experience in immune programming and offspring asthma. Part 2 outlines proposed mechanisms to explain these associations including bacterial exposure of the fetoplacental unit; immunoglobulin-related transplacental transport of gut bacterial components; cytokine signaling producing fetomaternal immune alignment; and immune programming via metabolites produced by gut bacteria. Part 3 focuses on the interplay between diet, gut bacteria, and bacterial metabolites. Maternal diet influences fecal bacterial composition, with dietary microbiota-accessible carbohydrates (MACs) selecting short-chain fatty acid (SCFA)-producing bacteria. Current evidence from mouse models indicates an association between increased maternal dietary MACs, SCFA exposure during pregnancy, and reduced offspring asthma that is, at least in part, mediated by the induction of regulatory T lymphocytes in the fetal lung. Part 4 discusses considerations for future studies investigating maternal diet-by-microbiome determinants of offspring asthma including the challenge of measuring dietary MAC intake; limitations of the existing measures of the gut microbiome composition and metabolic activity; measures of SCFA exposure; and the complexities of childhood respiratory health assessment.
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Affiliation(s)
- Lawrence E K Gray
- Barwon Infant Study, School of Medicine, Deakin University, Geelong, VIC, Australia.,Child Health Research Unit, Barwon Health, Geelong, VIC, Australia
| | - Martin O'Hely
- Barwon Infant Study, School of Medicine, Deakin University, Geelong, VIC, Australia.,Respiratory Diseases, Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Sarath Ranganathan
- Respiratory Diseases, Infection and Immunity Theme, Murdoch Children's Research Institute, Parkville, VIC, Australia.,Department of Respiratory and Sleep Medicine, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Peter David Sly
- Child Health Research Centre, The University of Queensland, Brisbane, QLD, Australia
| | - Peter Vuillermin
- Barwon Infant Study, School of Medicine, Deakin University, Geelong, VIC, Australia.,Child Health Research Unit, Barwon Health, Geelong, VIC, Australia
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604
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Lewis ZT, Mills DA. Differential Establishment of Bifidobacteria in the Breastfed Infant Gut. NESTLE NUTRITION INSTITUTE WORKSHOP SERIES 2017; 88:149-159. [PMID: 28346936 DOI: 10.1159/000455399] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The composition of an infant's gut microbiome can impact their immediate and long-term health. Bifdobacteria play a major role in structuring the gut microbiome of breastfed infants due to their ability to consume oligosaccharides found in human milk. However, recent studies have revealed that bifidobacteria are often absent in the gut microbiome of breastfed infants in some locations. This lack of colonization may be due either to differences in the environmental conditions in the gastrointestinal tract of uncolonized infants which prohibit the growth of bifidobacteria or a dearth of sources from which infants may acquire these specialized bacterial species. Potential mechanisms by which these broad factors may lead to lower colonization of infants by bifidobacteria are discussed herein. Environmental conditions which may select against bifidobacteria include low rates/duration of breastfeeding, milk glycan composition, and antimicrobial use. Routes of colonization by bifidobacteria which may be disrupted include maternal transfer via vaginal birth, fecal-oral routes, or via breast milk itself. A careful contemplation of the conditions experienced by bifidobacteria over human evolutionary history may lead to further hypotheses as to the causative factors of the differential colonization by this foundation genus in some contemporary locations.
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605
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Power ML, Quaglieri C, Schulkin J. Reproductive Microbiomes: A New Thread in the Microbial Network. Reprod Sci 2017; 24:1482-1492. [DOI: 10.1177/1933719117698577] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Michael L. Power
- Research Department, American College of Obstetricians and Gynecologists, Washington, DC, USA
- Nutrition Laboratory, Conservation Ecology Center, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Caroline Quaglieri
- Research Department, American College of Obstetricians and Gynecologists, Washington, DC, USA
| | - Jay Schulkin
- Research Department, American College of Obstetricians and Gynecologists, Washington, DC, USA
- Department of Obstetrics and Gynecology, University of Washington School of Medicine, Seattle, WA, USA
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606
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Knight R, Callewaert C, Marotz C, Hyde ER, Debelius JW, McDonald D, Sogin ML. The Microbiome and Human Biology. Annu Rev Genomics Hum Genet 2017; 18:65-86. [PMID: 28375652 DOI: 10.1146/annurev-genom-083115-022438] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past few years, microbiome research has dramatically reshaped our understanding of human biology. New insights range from an enhanced understanding of how microbes mediate digestion and disease processes (e.g., in inflammatory bowel disease) to surprising associations with Parkinson's disease, autism, and depression. In this review, we describe how new generations of sequencing technology, analytical advances coupled to new software capabilities, and the integration of animal model data have led to these new discoveries. We also discuss the prospects for integrating studies of the microbiome, metabolome, and immune system, with the goal of elucidating mechanisms that govern their interactions. This systems-level understanding will change how we think about ourselves as organisms.
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Affiliation(s)
- Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093; .,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California 92093.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, California 92093
| | - Chris Callewaert
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093; .,Center for Microbial Ecology and Technology, Ghent University, 9000 Ghent, Belgium
| | - Clarisse Marotz
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093;
| | - Embriette R Hyde
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093;
| | - Justine W Debelius
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093;
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, California 92093;
| | - Mitchell L Sogin
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, Massachusetts 02543
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607
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Laursen MF, Bahl MI, Michaelsen KF, Licht TR. First Foods and Gut Microbes. Front Microbiol 2017; 8:356. [PMID: 28321211 PMCID: PMC5337510 DOI: 10.3389/fmicb.2017.00356] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/21/2017] [Indexed: 12/26/2022] Open
Abstract
The establishment of the human gut microbiota in early life has been associated with later health and disease. During the 1st months after birth, the microbial composition in the gut is known to be affected by the mode of delivery, use of antibiotics, geographical location and type of feeding (breast/formula). Consequently, the neonatal period and early infancy has attracted much attention. However, after this first period the gut microbial composition continues to develop until the age of 3 years, and these 1st years have been designated “a window of opportunity” for microbial modulation. The beginning and end of this window is currently debated, but it likely coincides with the complementary feeding period, marking the gradual transition from milk-based infant feeding to family diet usually occurring between 6 and 24 months. Furthermore, the ‘first 1000 days,’ i.e., the period from conception until age 2 years, are generally recognized to be of particular importance for the healthy development of children. While dietary changes are known to affect the adult gut microbiota, there is a gap in our knowledge on how the introduction of new dietary components into the diet of infants/young children affects the gut microbiota development. This perspective paper summarizes the currently very few studies addressing the effects of complementary diet on gut microbiota, and highlights the recent finding that transition to family foods greatly impacts the development of gut microbial diversity. Further, we discuss potential impacts on child health and the need for further studies on this important topic.
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Affiliation(s)
- Martin F Laursen
- National Food Institute, Technical University of Denmark Søborg, Denmark
| | - Martin I Bahl
- National Food Institute, Technical University of Denmark Søborg, Denmark
| | - Kim F Michaelsen
- Department of Nutrition, Exercise and Sports, University of Copenhagen Frederiksberg, Denmark
| | - Tine R Licht
- National Food Institute, Technical University of Denmark Søborg, Denmark
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608
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Silverman MA, Konnikova L, Gerber JS. Impact of Antibiotics on Necrotizing Enterocolitis and Antibiotic-Associated Diarrhea. Gastroenterol Clin North Am 2017; 46:61-76. [PMID: 28164853 PMCID: PMC5314436 DOI: 10.1016/j.gtc.2016.09.010] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Antibiotic treatment alters the composition and metabolic function of the intestinal microbiota. These alterations may contribute to the pathogenesis of necrotizing enterocolitis (NEC) and antibiotic-associated diarrhea (AAD). Recent studies are beginning to unravel the contribution of specific groups of microbes and their metabolic pathways to these diseases. Probiotics or other microbiota-targeted therapies may provide effect strategies to prevent and treat NEC and AAD.
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Affiliation(s)
- Michael A. Silverman
- Division of Infectious Diseases, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104
| | - Liza Konnikova
- Department of Pediatric and Newborn Medicine, Brigham and Women’s Hospital, Boston, MA 02115 and Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Jeffrey S. Gerber
- Center for Pediatric Clinical Effectiveness, Division of Infectious Diseases, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104 and Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
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609
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Hill DR, Spence JR. Gastrointestinal Organoids: Understanding the Molecular Basis of the Host-Microbe Interface. Cell Mol Gastroenterol Hepatol 2017; 3:138-149. [PMID: 28275681 PMCID: PMC5331777 DOI: 10.1016/j.jcmgh.2016.11.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/09/2016] [Indexed: 02/07/2023]
Abstract
In recent years, increasing attention has been devoted to the concept that microorganisms play an integral role in human physiology and pathophysiology. Despite this, the molecular basis of host-pathogen and host-symbiont interactions in the human intestine remains poorly understood owing to the limited availability of human tissue, and the biological complexity of host-microbe interactions. Over the past decade, technological advances have enabled long-term culture of organotypic intestinal tissue derived from human subjects and from human pluripotent stem cells, and these in vitro culture systems already have shown the potential to inform our understanding significantly of host-microbe interactions. Gastrointestinal organoids represent a substantial advance in structural and functional complexity over traditional in vitro cell culture models of the human gastrointestinal epithelium while retaining much of the genetic and molecular tractability that makes in vitro experimentation so appealing. The opportunity to model epithelial barrier dynamics, cellular differentiation, and proliferation more accurately in specific intestinal segments and in tissue containing a proportional representation of the diverse epithelial subtypes found in the native gut greatly enhances the translational potential of organotypic gastrointestinal culture systems. By using these tools, researchers have uncovered novel aspects of host-pathogen and host-symbiont interactions with the intestinal epithelium. Application of these tools promises to reveal new insights into the pathogenesis of infectious disease, inflammation, cancer, and the role of microorganisms in intestinal development. This review summarizes research on the use of gastrointestinal organoids as a model of the host-microbe interface.
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Key Words
- 3D, 3-dimensional
- CDI, Clostridium difficile infection
- ECM, extracellular matrix
- Enteroids
- Epithelium
- GI, gastrointestinal
- HIO, human intestinal organoids
- IFN, interferon
- IL, interleukin
- Intestine
- Model Systems
- NEC, necrotizing enterocolitis
- Pathogenesis
- SCFA, short-chain fatty acid
- Symbiosis
- TcdB, C difficile toxin B
- hPSC, human pluripotent stem cell
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Affiliation(s)
- David R. Hill
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jason R. Spence
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan
- Center for Organogenesis, University of Michigan Medical School, Ann Arbor, Michigan
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610
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Kong HH, Andersson B, Clavel T, Common JE, Jackson SA, Olson ND, Segre JA, Traidl-Hoffmann C. Performing Skin Microbiome Research: A Method to the Madness. J Invest Dermatol 2017; 137:561-568. [PMID: 28063650 PMCID: PMC5468751 DOI: 10.1016/j.jid.2016.10.033] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 10/27/2016] [Accepted: 10/31/2016] [Indexed: 02/07/2023]
Abstract
Growing interest in microbial contributions to human health and disease has increasingly led investigators to examine the microbiome in both healthy skin and cutaneous disorders, including acne, psoriasis, and atopic dermatitis. The need for common language, effective study design, and validated methods is critical for high-quality standardized research. Features, unique to skin, pose particular challenges when conducting microbiome research. This review discusses microbiome research standards and highlights important factors to consider, including clinical study design, skin sampling, sample processing, DNA sequencing, control inclusion, and data analysis.
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Affiliation(s)
- Heidi H Kong
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
| | - Björn Andersson
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Clavel
- Core Facility NGS/Microbiome, ZIEL Institute for Food and Health, Technical University of Munich, Freising, Germany
| | | | - Scott A Jackson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Nathan D Olson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Julia A Segre
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, USA
| | - Claudia Traidl-Hoffmann
- Institute of Environmental Medicine, UNIKA-T, Technical University of Munich and Helmholtz Zentrum München-German Research Center for Environmental Health, Augsburg, Germany; Christine Kühne Center for Allergy Research and Education, Davos, Switzerland
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611
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Vuong HE, Hsiao EY. Emerging Roles for the Gut Microbiome in Autism Spectrum Disorder. Biol Psychiatry 2017; 81:411-423. [PMID: 27773355 PMCID: PMC5285286 DOI: 10.1016/j.biopsych.2016.08.024] [Citation(s) in RCA: 344] [Impact Index Per Article: 49.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 07/28/2016] [Accepted: 08/18/2016] [Indexed: 01/16/2023]
Abstract
Autism spectrum disorder (ASD) is a serious neurodevelopmental disorder that affects one in 45 children in the United States, with a similarly striking prevalence in countries around the world. However, mechanisms underlying its etiology and manifestations remain poorly understood. Although ASD is diagnosed based on the presence and severity of impaired social communication and repetitive behavior, immune dysregulation and gastrointestinal issues are common comorbidities. The microbiome is an integral part of human physiology; recent studies show that changes in the gut microbiota can modulate gastrointestinal physiology, immune function, and even behavior. Links between particular bacteria from the indigenous gut microbiota and phenotypes relevant to ASD raise the important question of whether microbial dysbiosis plays a role in the development or presentation of ASD symptoms. Here we review reports of microbial dysbiosis in ASD. We further discuss potential effects of the microbiota on ASD-associated symptoms, drawing on signaling mechanisms for reciprocal interactions among the microbiota, immunity, gut function, and behavior. In addition, we discuss recent findings supporting a role for the microbiome as an interface between environmental and genetic risk factors that are associated with ASD. These studies highlight the integration of pathways across multiple body systems that together can impact brain and behavior and suggest that changes in the microbiome may contribute to symptoms of neurodevelopmental disease.
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Affiliation(s)
- Helen E. Vuong
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Elaine Y. Hsiao
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA,Correspondence to: ; 610 Charles E. Young Drive MSB 3825A; Los Angeles CA 90095; 310-825-0228
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612
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Abstract
Atopic dermatitis (AD) is a common chronic inflammatory skin disease affecting ~10–20% of the general population. AD is characterized by disturbances in epidermal barrier function and hyperactive immune response. Recently, changes in the skin and intestinal microbiome have been analyzed in more detail. The available data suggest a link between disturbed skin microbiome and course of the disease. Flares of the disease are associated with an expansion of Staphylococcus aureus on lesional skin and a substantial loss of biodiversity in skin microbiome. Staphylococci exoproteins and superantigens evoke inflammatory reactions in the host. Skin microbiome includes superficial stratum corneum that is affected by environmental factors such as exposure to germs and cleansing. Available evidence argues for a link between epidermal barrier impairment and disturbances in skin microbiome in AD. In contrast to skin microbiome, intestinal microbiome seems to become stabilized after infancy. There is also a significant heritable component for intestinal microbiome. The microbial taxa, relative percentages and quantities vary remarkably between the different parts of the intestinal tract. Early intestinal microbial colonization may be a critical step for prevention of further development of AD. Skin barrier-aimed topical treatments help to develop a neo-microbiome from deeper compartments. Probiotics, prebiotics and synbiotics have been investigated for the treatment of AD, but further investigations are needed. Targeted treatment options to normalize skin and intestinal microbiome in AD are under investigation.
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Affiliation(s)
- Uwe Wollina
- Department of Dermatology and Allergology, Academic Teaching Hospital Dresden-Friedrichstadt, Dresden, Germany
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613
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Doré J, Multon MC, Béhier JM, Affagard H, Andremont A, Barthélémy P, Batista R, Bonneville M, Bonny C, Boyaval G, Chamaillard M, Chevalier MP, Cordaillat-Simmons M, Cournarie F, Diaz I, Guillaume E, Guyard C, Jouvin-Marche E, Martin FP, Petiteau D. Microbiote intestinal : qu’en attendre au plan physiologique et thérapeutique ? Therapie 2017; 72:1-19. [PMID: 28214070 DOI: 10.1016/j.therap.2017.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/22/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Joël Doré
- INRA, Metagenopolis, 78350 Jouy-en-Josas, France
| | | | | | | | | | - Antoine Andremont
- Hôpital Bichat, université Paris Diderot, AP-HP, 92240 Malakoff, France
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614
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Lynch JP, Sikder MAA, Curren BF, Werder RB, Simpson J, Cuív PÓ, Dennis PG, Everard ML, Phipps S. The Influence of the Microbiome on Early-Life Severe Viral Lower Respiratory Infections and Asthma-Food for Thought? Front Immunol 2017; 8:156. [PMID: 28261214 PMCID: PMC5311067 DOI: 10.3389/fimmu.2017.00156] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 01/30/2017] [Indexed: 12/24/2022] Open
Abstract
Severe viral lower respiratory infections are a major cause of infant morbidity. In developing countries, respiratory syncytial virus (RSV)-bronchiolitis induces significant mortality, whereas in developed nations the disease represents a major risk factor for subsequent asthma. Susceptibility to severe RSV-bronchiolitis is governed by gene-environmental interactions that affect the host response to RSV infection. Emerging evidence suggests that the excessive inflammatory response and ensuing immunopathology, typically as a consequence of insufficient immunoregulation, leads to long-term changes in immune cells and structural cells that render the host susceptible to subsequent environmental incursions. Thus, the initial host response to RSV may represent a tipping point in the balance between long-term respiratory health or chronic disease (e.g., asthma). The composition and diversity of the microbiota, which in humans stabilizes in the first year of life, critically affects the development and function of the immune system. Hence, perturbations to the maternal and/or infant microbiota are likely to have a profound impact on the host response to RSV and susceptibility to childhood asthma. Here, we review recent insights describing the effects of the microbiota on immune system homeostasis and respiratory disease and discuss the environmental factors that promote microbial dysbiosis in infancy. Ultimately, this knowledge will be harnessed for the prevention and treatment of severe viral bronchiolitis as a strategy to prevent the onset and development of asthma.
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Affiliation(s)
- Jason P. Lynch
- Laboratory of Respiratory Mucosal Immunity, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Md. Al Amin Sikder
- Laboratory of Respiratory Mucosal Immunity, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Bodie F. Curren
- Laboratory of Respiratory Mucosal Immunity, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Rhiannon B. Werder
- Laboratory of Respiratory Mucosal Immunity, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Jennifer Simpson
- Laboratory of Respiratory Mucosal Immunity, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Páraic Ó Cuív
- Translational Research Institute, The University of Queensland Diamantina Institute, The University of Queensland, St. Lucia, QLD, Australia
| | - Paul G. Dennis
- The School of Agriculture and Food Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Mark L. Everard
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA, Australia
| | - Simon Phipps
- Laboratory of Respiratory Mucosal Immunity, School of Biomedical Sciences, The University of Queensland, St. Lucia, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, QLD, Australia
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615
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Ward TL, Knights D, Gale CA. Infant fungal communities: current knowledge and research opportunities. BMC Med 2017; 15:30. [PMID: 28190400 PMCID: PMC5304398 DOI: 10.1186/s12916-017-0802-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 01/24/2017] [Indexed: 12/16/2022] Open
Abstract
The microbes colonizing the infant gastrointestinal tract have been implicated in later-life disease states such as allergies and obesity. Recently, the medical research community has begun to realize that very early colonization events may be most impactful on future health, with the presence of key taxa required for proper immune and metabolic development. However, most studies to date have focused on bacterial colonization events and have left out fungi, a clinically important sub-population of the microbiota. A number of recent findings indicate the importance of host-associated fungi (the mycobiota) in adult and infant disease states, including acute infections, allergies, and metabolism, making characterization of early human mycobiota an important frontier of medical research. This review summarizes the current state of knowledge with a focus on factors influencing infant mycobiota development and associations between early fungal exposures and health outcomes. We also propose next steps for infant fungal mycobiome research, including longitudinal studies of mother-infant pairs while monitoring long-term health outcomes, further exploration of bacterium-fungus interactions, and improved methods and databases for mycobiome quantitation.
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Affiliation(s)
- Tonya L Ward
- Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA
| | - Dan Knights
- Biotechnology Institute, University of Minnesota, Saint Paul, MN, USA.,Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Cheryl A Gale
- Department of Pediatrics, University of Minnesota, 2450 Riverside Ave, Minneapolis, MN, 55454, USA.
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616
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Li J, Yang K, Ju T, Ho T, McKay CA, Gao Y, Forget SK, Gartner SR, Field CJ, Chan CB, Willing BP. Early life antibiotic exposure affects pancreatic islet development and metabolic regulation. Sci Rep 2017; 7:41778. [PMID: 28150721 PMCID: PMC5288777 DOI: 10.1038/srep41778] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 12/30/2016] [Indexed: 12/12/2022] Open
Abstract
Childhood antibiotic exposure has been recently linked with increased risk of metabolic disease later in life. A better understanding of this association would potentially provide strategies to reduce the childhood chronic disease epidemic. Therefore, we explored the underlying mechanisms using a swine model that better mimics human infants than rodents, and demonstrated that early life antibiotic exposure affects glucose metabolism 5 weeks after antibiotic withdrawal, which was associated with changes in pancreatic development. Antibiotics exerted a transient impact on postnatal gut microbiota colonization and microbial metabolite production, yet changes in the expression of key genes involved in short-chain fatty acid signaling and pancreatic development were detected in later life. These findings suggest a programming effect of early life antibiotic exposure that merits further investigation.
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Affiliation(s)
- Jiaying Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Kaiyuan Yang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Tingting Ju
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Tracy Ho
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Catharine A McKay
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Yanhua Gao
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Shay K Forget
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Stephanie R Gartner
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Catherine J Field
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
| | - Catherine B Chan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada.,Department of Physiology, University of Alberta, Edmonton, AB, T6G 2H7, Canada
| | - Benjamin P Willing
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5, Canada
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617
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Chin AM, Hill DR, Aurora M, Spence JR. Morphogenesis and maturation of the embryonic and postnatal intestine. Semin Cell Dev Biol 2017; 66:81-93. [PMID: 28161556 DOI: 10.1016/j.semcdb.2017.01.011] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 12/12/2022]
Abstract
The intestine is a vital organ responsible for nutrient absorption, bile and waste excretion, and a major site of host immunity. In order to keep up with daily demands, the intestine has evolved a mechanism to expand the absorptive surface area by undergoing a morphogenetic process to generate finger-like units called villi. These villi house specialized cell types critical for both absorbing nutrients from food, and for protecting the host from commensal and pathogenic microbes present in the adult gut. In this review, we will discuss mechanisms that coordinate intestinal development, growth, and maturation of the small intestine, starting from the formation of the early gut tube, through villus morphogenesis and into early postnatal life when the intestine must adapt to the acquisition of nutrients through food intake, and to interactions with microbes.
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Affiliation(s)
- Alana M Chin
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - David R Hill
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Megan Aurora
- Department of Pediatrics, Division of Neonatal-Perinatal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI, United States; Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI, United States; Center for Organogenesis, University of Michigan Medical School, Ann Arbor, MI, United States.
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618
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Maturation of the infant microbiome community structure and function across multiple body sites and in relation to mode of delivery. Nat Med 2017; 23:314-326. [PMID: 28112736 PMCID: PMC5345907 DOI: 10.1038/nm.4272] [Citation(s) in RCA: 641] [Impact Index Per Article: 91.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 12/26/2022]
Abstract
Human microbial communities are characterized by their taxonomic, metagenomic, and metabolic diversity, which varies by distinct body sites and influences human physiology. However, when and how microbial communities within each body niche acquire unique taxonomical and functional signatures in early life remains underexplored. We thus sought to assess the taxonomic composition and potential metabolic function of the neonatal and early infant microbiota across multiple body sites, and assess the impact of mode of delivery and its potential confounders or modifiers. A cohort of pregnant women in their early 3rd trimester (n=81) were prospectively enrolled for longitudinal sampling through 6 weeks post-delivery, and a second matched cross-sectional cohort (n=81) was additionally recruited for sampling once at delivery. Samples were collected for each maternal-infant dyad across multiple body sites, including stool, oral gingiva, nares, skin and vagina. 16S rRNA gene sequencing analysis and whole genome shotgun sequencing was performed to interrogate the composition and function of the neonatal and maternal microbiota. We found that the neonatal microbiota and its associated functional pathways were relatively homogenous across all body sites at delivery, with the notable exception of neonatal meconium. However, by 6 weeks, the infant microbiota structure and function had significantly expanded and diversified, with body site serving as the primary determinant of the bacterial community composition and its functional capacity. Although minor variations in the neonatal (immediately at birth) microbiota community structure were associated with Cesarean delivery in some body sites (oral, nares, and skin; R2 = 0.038), this was not true in neonatal stool (meconium, Mann-Whitney p>0.05) and there was no observable difference in community function regardless of delivery mode. By 6 weeks of age, the infant microbiota structure and function had expanded and diversified with demonstrable body site specificity (p<0.001, R2 = 0.189), and no discernable differences in neither community structure nor function by Cesarean delivery were identifiable (p=0.057, R2 = 0.007). We conclude that within the first 6 weeks of life, the infant microbiota undergoes significant reorganization that is primarily driven by body site and not by mode of delivery.
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619
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Prevalence of Antibiotic Resistance Genes among Human Gut-Derived Bifidobacteria. Appl Environ Microbiol 2017; 83:AEM.02894-16. [PMID: 27864179 DOI: 10.1128/aem.02894-16] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 11/17/2016] [Indexed: 12/11/2022] Open
Abstract
The microbiota of the human gastrointestinal tract (GIT) may regularly be exposed to antibiotics, which are used to prevent and treat infectious diseases caused by bacteria and fungi. Bacterial communities of the gut retain a reservoir of antibiotic resistance (AR) genes, and antibiotic therapy thus positively selects for those microorganisms that harbor such genetic features, causing microbiota modulation. During the first months following birth, bifidobacteria represent some of the most dominant components of the human gut microbiota, although little is known about their AR gene complement (or resistome). In the current study, we assessed the resistome of the Bifidobacterium genus based on phenotypic and genotypic data of members that represent all currently recognized bifidobacterial (sub)species. Moreover, a comparison between the bifidobacterial resistome and gut metagenome data sets from adults and infants shows that the bifidobacterial community present at the first week following birth possesses a reduced AR arsenal compared to that present in the infant bifidobacterial population in subsequent weeks of the first year of life. Our findings reinforce the concept that the early infant gut microbiota is more susceptible to disturbances by antibiotic treatment than the gut microbiota developed at a later life stage. IMPORTANCE The spread of resistance to antibiotics among bacterial communities has represented a major concern since their discovery in the last century. The risk of genetic transfer of resistance genes between microorganisms has been extensively investigated due to its relevance to human health. In contrast, there is only limited information available on antibiotic resistance among human gut commensal microorganisms such as bifidobacteria, which are widely exploited by the food industry as health-promoting microorganisms or probiotic ingredients. In the current study, we explored the occurrence of antibiotic resistance genes in the genomes of bifidobacteria and evaluated their genetic mobility to other human gut commensal microorganisms.
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620
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Dinan TG, Cryan JF. Gut instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration. J Physiol 2017; 595:489-503. [PMID: 27641441 PMCID: PMC5233671 DOI: 10.1113/jp273106] [Citation(s) in RCA: 457] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Accepted: 09/13/2016] [Indexed: 12/16/2022] Open
Abstract
There is a growing realisation that the gut-brain axis and its regulation by the microbiota may play a key role in the biological and physiological basis of neurodevelopmental, age-related and neurodegenerative disorders. The routes of communication between the microbiota and brain are being unravelled and include the vagus nerve, gut hormone signalling, the immune system, tryptophan metabolism or by way of microbial metabolites such as short chain fatty acids. The importance of early life gut microbiota in shaping future health outcomes is also emerging. Disturbances of this composition by way of antibiotic exposure, lack of breastfeeding, infection, stress and the environmental influences coupled with the influence of host genetics can result in long-term effects on physiology and behaviour, at least in animal models. It is also worth noting that mode of delivery at birth influences microbiota composition with those born by Caesarean section having a distinctly different microbiota in early life to those born per vaginum. At the other extreme of life, ageing is associated with a narrowing in microbial diversity and healthy ageing correlates with a diverse microbiome. Recently, the gut microbiota has been implicated in a variety of conditions including depression, autism, schizophrenia and Parkinson's disease. There is still considerable debate as to whether or not the gut microbiota changes are core to the pathophysiology of such conditions or are merely epiphenomenal. It is plausible that such neuropsychiatric disorders might be treated in the future by targeting the microbiota either by microbiota transplantation, antibiotics or psychobiotics.
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Affiliation(s)
- Timothy G. Dinan
- APC Microbiome InstituteUniversity College CorkIreland
- Department of Psychiatry and Neurobehavioural ScienceUniversity College CorkIreland
| | - John F. Cryan
- APC Microbiome InstituteUniversity College CorkIreland
- Department of Anatomy and NeuroscienceUniversity College CorkIreland
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Davis JCC, Lewis ZT, Krishnan S, Bernstein RM, Moore SE, Prentice AM, Mills DA, Lebrilla CB, Zivkovic AM. Growth and Morbidity of Gambian Infants are Influenced by Maternal Milk Oligosaccharides and Infant Gut Microbiota. Sci Rep 2017; 7:40466. [PMID: 28079170 PMCID: PMC5227965 DOI: 10.1038/srep40466] [Citation(s) in RCA: 137] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 12/06/2016] [Indexed: 12/25/2022] Open
Abstract
Human milk oligosaccharides (HMOs) play an important role in the health of an infant as substrate for beneficial gut bacteria. Little is known about the effects of HMO composition and its changes on the morbidity and growth outcomes of infants living in areas with high infection rates. Mother's HMO composition and infant gut microbiota from 33 Gambian mother/infant pairs at 4, 16, and 20 weeks postpartum were analyzed for relationships between HMOs, microbiota, and infant morbidity and growth. The data indicate that lacto-N-fucopentaose I was associated with decreased infant morbidity, and 3'-sialyllactose was found to be a good indicator of infant weight-for-age. Because HMOs, gut microbiota, and infant health are interrelated, the relationship between infant health and their microbiome were analyzed. While bifidobacteria were the dominant genus in the infant gut overall, Dialister and Prevotella were negatively correlated with morbidity, and Bacteroides was increased in infants with abnormal calprotectin. Mothers nursing in the wet season (July to October) produced significantly less oligosaccharides compared to those nursing in the dry season (November to June). These results suggest that specific types and structures of HMOs are sensitive to environmental conditions, protective of morbidity, predictive of growth, and correlated with specific microbiota.
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Affiliation(s)
- Jasmine C. C. Davis
- Department of Chemistry, University of California, Davis, CA 95616, United States
- Foods for Health Institute, University of California, Davis, CA 95616, United States
| | - Zachery T. Lewis
- Foods for Health Institute, University of California, Davis, CA 95616, United States
- Department of Food Science and Technology, University of California, Davis, CA 95616, United States
| | - Sridevi Krishnan
- Department of Nutrition, University of California, Davis, CA 95616, United States
| | - Robin M. Bernstein
- Department of Anthropology, University of Colorado, Boulder, CO 80309, United States
- Health and Society Program, Institute of Behavioral Science, University of Colorado, Boulder, CO 80309, United States
| | - Sophie E. Moore
- Medical Research Council (MRC) Human Nutrition Research, Cambridge, UK
- MRC Unit, The Gambia and MRC International Nutrition Group, London School of Hygiene & Tropical Medicine, London, UK
| | - Andrew M. Prentice
- MRC Unit, The Gambia and MRC International Nutrition Group, London School of Hygiene & Tropical Medicine, London, UK
| | - David A. Mills
- Foods for Health Institute, University of California, Davis, CA 95616, United States
- Department of Food Science and Technology, University of California, Davis, CA 95616, United States
- Department of Viticulture and Enology, University of California, Davis, CA 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, CA 95616, United States
- Foods for Health Institute, University of California, Davis, CA 95616, United States
| | - Angela M. Zivkovic
- Foods for Health Institute, University of California, Davis, CA 95616, United States
- Department of Nutrition, University of California, Davis, CA 95616, United States
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622
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Blackwood BP, Hunter CJ, Grabowski J. Variability in Antibiotic Regimens for Surgical Necrotizing Enterocolitis Highlights the Need for New Guidelines. Surg Infect (Larchmt) 2017; 18:215-220. [PMID: 28048964 DOI: 10.1089/sur.2016.163] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Necrotizing enterocolitis or NEC is the most common gastrointestinal emergency in the newborn. The etiology of NEC remains unknown, and treatment consists of antibiotic therapy and supportive care with the addition of surgical intervention as necessary. Unlike most surgical diseases, clear guidelines for the type and duration of peri-operative antibiotic therapy have not been established. Our aim was to review the antibiotic regimen(s) applied to surgical patients with NEC within a single neonatal intensive care unit (NICU) and to evaluate outcomes and help develop guidelines for antibiotic administration in this patient population. PATIENTS AND METHODS A single-center retrospective review was performed of all patients who underwent surgical intervention for NEC from August 1, 2005 through August 1, 2015. Relevant data were extracted including gestational age, age at diagnosis, gender, pre-operative antibiotic treatment, post-operative antibiotic treatment, development of stricture, and mortality. Patients were excluded if there was incomplete data documentation. RESULTS A total of 90 patients were identified who met inclusion criteria. There were 56 male patients and 34 female patients. The average gestational age was 30 5/7 wks and average age of diagnosis 16.7 d. A total of 22 different pre-operative antibiotic regimens were identified with an average duration of 10.6 d. The most common pre-operative regimen was ampicillin, gentamicin, and metronidazole for 14 d. A total of 15 different post-operative antibiotic regimens were identified with an average duration of 6.6 d. The most common post-operative regimen was ampicillin, gentamicin, and metronidazole for two days. There were 26 strictures and 15 deaths. No regimen or duration proved superior. CONCLUSION We found that there is a high degree of variability in the antibiotic regimen for the treatment of NEC, even within a single NICU, with no regimen appearing superior over another. As data emerge that demonstrate the adverse effects of antibiotic overuse, our findings highlight the need for guidelines in the antibiotic treatment of NEC and suggest that an abbreviated course of post-operative antibiotics may be safe.
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Affiliation(s)
- Brian P Blackwood
- 1 Division of Pediatric Surgery, Ann and Robert H. Lurie Children's Hospital of Chicago , Chicago, Illinois.,2 Department of General Surgery, Rush University Medical Center , Chicago, Illinois
| | - Catherine J Hunter
- 1 Division of Pediatric Surgery, Ann and Robert H. Lurie Children's Hospital of Chicago , Chicago, Illinois
| | - Julia Grabowski
- 1 Division of Pediatric Surgery, Ann and Robert H. Lurie Children's Hospital of Chicago , Chicago, Illinois
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Doré J, Multon MC, Béhier JM. The human gut microbiome as source of innovation for health: Which physiological and therapeutic outcomes could we expect? Therapie 2017; 72:21-38. [PMID: 28131442 DOI: 10.1016/j.therap.2016.12.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/22/2016] [Indexed: 12/12/2022]
Abstract
From the moment of birth, each human being builds a microbe-host symbiosis which is key for the preservation of its health and well-being. This personal symbiotic coexistence is the result of progressive enrichments in microorganism diversity through external supplies. This diversity is nowadays massively overthrown by drastic changes related to clinical practice in birth management, environmental exposure, nutrition and healthcare behaviors. The last two generations have been the frame of massive modifications in life and food habits, with people being more and more sedentary, overfed and permeated with drugs and pollutants. We are now able to measure the impact of these changes on the gut microbiota diversity. Concomitantly, these modifications of lifestyle were associated with a dramatic increase in incidence of immune-mediated diseases including metabolic, allergic and inflammatory diseases and most likely neurodegenerative and psychiatric disorders. Microbiota is becoming a hot topic in the scientific community and in the mainstream media. The number of scientific publications increased by up to a factor three over the last five years, with gastrointestinal and metabolic diseases being the most productive areas. In the intellectual property landscape, the patent families on microbiota have more than doubled in the meantime. In parallel, funding either from National Institutes (e.g. from NIH which funds research mainly in the field of allergies, infections, cancer and cardiovascular diseases, from the White House which launched the national microbiome initiative) or by pharmaceutical companies follow the same trend, showing a boost and a strong support in the research field on microbiota. All major health players are investing in microbiome research as shown by the number of deals signed and by funding during 2015. The Giens round table addressed how the medicine of tomorrow, considering human beings as a human-microbe symbiotic supraorganism, could leverage microbiome knowledge and tools. The rationale for our working group has been structured around four domains of innovation that could derive from ongoing efforts in deciphering the interactions between human cells and intestinal microbiome as a central component of human health, namely: (1) development of stratification and monitoring tools; (2) identification of new target and drug discovery, as a part of our supra-genome; (4) exploitation of microbiota as a therapeutic target that can be modulated; (4) and finally as a source of live biotherapeutics and adjuvants. These four streams will exemplify how microbiota has changed the way we consider a wide range of chronic and incurable diseases and the consequences of long-lasting dysbiosis. In-depth microbiota analysis is opening one of the broadest fields of investigation for improving human and animal health and will be a source of major therapeutic innovations for tackling today's medical unmet needs. We thus propose a range of recommendations for basic researchers, care givers as well as for health authorities to gain reliability in microbiome analysis and accelerate discovery processes and their translation into applications for the benefits of the people. Finally, les Ateliers de Giens round table on microbiota benefited from the richness of the French ecosystem. France represents a center of excellence in the microbiota research field, with French institutions as Institut national de la recherche agronomique (INRA [Metagenopolis, Micalis]), Centre national de la recherché scientifique (CNRS), Unité de recherche sur les maladies infectieuses et tropicales émergentes (URMITE), Institut of Cardiometabolism and Nutrition (ICAN), Institut des maladies métaboliques et cardiovasculaires (I2MC), Institut national de la santé et de la recherche médicale (Inserm), Pasteur Institute and Gustave-Roussy being top-players for the number of publications.
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Affiliation(s)
- Joël Doré
- Institut national de la recherche agronomique (INRA), Metagenopolis, 78350 Jouy-en-Josas, France
| | - Marie-Christine Multon
- Sanofi R&D, unité sciences translationnelles, 13, quai Jules-Guesde, 94403 Vitry sur Seine, France.
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624
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张 惠, 樊 蕊, 张 静, 陶 小, 孙 新. [Association between risk factors during maternal pregnancy and the neonatal period and childhood bronchial asthma]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2017; 19:49-53. [PMID: 28100322 PMCID: PMC7390120 DOI: 10.7499/j.issn.1008-8830.2017.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/16/2016] [Indexed: 06/06/2023]
Abstract
OBJECTIVE To study the association of the risk factors during maternal pregnancy and the neonatal period with childhood bronchial asthma. METHODS A total of 306 children with asthma (asthma group) and 250 healthy children (control group) were enrolled. Their clinical data during the neonatal period and the maternal data during pregnancy were retrospectively studied. RESULTS The univariate analysis showed that there were significant differences in the rates of maternal use of antibiotics during pregnancy, use of antibiotics and probiotics during the neonatal period, preterm birth, cesarean section, low birth weight, and breast feeding (>6 months) between the asthma and control groups (P<0.05). The multivariate logistic regression analysis showed that use of antibiotics during pregnancy (OR=3.908, 95%CI: 1.277-11.962), use of antibiotics during neonatal period (OR=24.154, 95%CI: 7.864-74.183), preterm birth (OR=8.535, 95%CI: 2.733-26.652), and cesarean section (OR=4.588, 95%CI: 2.887-7.291) were independent risk factors for childhood asthma. The use of probiotics during the neonatal period (OR=0.014, 95%CI: 0.004-0.046) and breast feeding (>6 months) (OR=0.161, 95%CI: 0.103-0.253) were protective factors for childhood asthma. CONCLUSIONS The early prevention of childhood asthma can be improved by reducing the use of antibiotics during pregnancy, reducing cesarean section, avoiding abuse of antibiotics during the neonatal period, trying breast feeding and taking probiotics in early stage.
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Affiliation(s)
- 惠琴 张
- />第四军医大学西京医院儿科, 陕西 西安 710032Department of Pediatrics, Xijing Hospital of Fourth Military Medical University, Xi'an 710032, China
| | - 蕊 樊
- />第四军医大学西京医院儿科, 陕西 西安 710032Department of Pediatrics, Xijing Hospital of Fourth Military Medical University, Xi'an 710032, China
| | - 静静 张
- />第四军医大学西京医院儿科, 陕西 西安 710032Department of Pediatrics, Xijing Hospital of Fourth Military Medical University, Xi'an 710032, China
| | - 小娟 陶
- />第四军医大学西京医院儿科, 陕西 西安 710032Department of Pediatrics, Xijing Hospital of Fourth Military Medical University, Xi'an 710032, China
| | - 新 孙
- />第四军医大学西京医院儿科, 陕西 西安 710032Department of Pediatrics, Xijing Hospital of Fourth Military Medical University, Xi'an 710032, China
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625
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Stewart CJ, Embleton ND, Clements E, Luna PN, Smith DP, Fofanova TY, Nelson A, Taylor G, Orr CH, Petrosino JF, Berrington JE, Cummings SP. Cesarean or Vaginal Birth Does Not Impact the Longitudinal Development of the Gut Microbiome in a Cohort of Exclusively Preterm Infants. Front Microbiol 2017. [PMID: 28634475 DOI: 10.3389/fmicb.2017.01008/full] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
The short and long-term impact of birth mode on the developing gut microbiome in neonates has potential implications for the health of infants. In term infants, the microbiome immediately following birth across multiple body sites corresponds to birth mode, with increased Bacteroides in vaginally delivered infants. We aimed to determine the impact of birth mode of the preterm gut microbiome over the first 100 days of life and following neonatal intensive care unit (NICU) discharge. In total, 867 stool samples from 46 preterm infants (21 cesarean and 25 vaginal), median gestational age 27 weeks, were sequenced (V4 region 16S rRNA gene, Illumina MiSeq). Of these, 776 samples passed quality filtering and were included in the analysis. The overall longitudinal alpha-diversity and within infant beta-diversity was comparable between cesarean and vaginally delivered infants. Vaginally delivered infants kept significantly more OTUs from 2 months of life and following NICU discharge, but OTUs lost, gained, and regained were not different based on birth mode. Furthermore, the temporal progression of dominant genera was comparable between birth modes and no significant difference was found for any genera following adjustment for covariates. Lastly, preterm gut community types (PGCTs) showed some moderate differences in very early life, but progressed toward a comparable pattern by week 5. No PGCT was significantly associated with cesarean or vaginal birth. Unlike term infants, birth mode was not significantly associated with changes in microbial diversity, composition, specific taxa, or overall microbial development in preterm infants. This may result from the dominating effects of NICU exposures including the universal use of antibiotics immediately following birth and/or the lack of Bacteroides colonizing preterm infants.
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Affiliation(s)
- Christopher J Stewart
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Nicholas D Embleton
- Newcastle Neonatal ServiceRoyal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Elizabeth Clements
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Pamela N Luna
- Department of Statistics, Rice University, HoustonTX, United States
| | - Daniel P Smith
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Tatiana Y Fofanova
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Andrew Nelson
- Faculty of Health and Life Sciences, Northumbria UniversityNewcastle upon Tyne, United Kingdom
| | - Gillian Taylor
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Caroline H Orr
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, HoustonTX, United States
| | - Janet E Berrington
- Newcastle Neonatal ServiceRoyal Victoria Infirmary, Newcastle upon Tyne, United Kingdom
| | - Stephen P Cummings
- School of Science and Engineering, Teesside UniversityMiddlesbrough, United Kingdom
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626
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Noecker C, McNally CP, Eng A, Borenstein E. High-resolution characterization of the human microbiome. Transl Res 2017; 179:7-23. [PMID: 27513210 PMCID: PMC5164958 DOI: 10.1016/j.trsl.2016.07.012] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 12/29/2022]
Abstract
The human microbiome plays an important and increasingly recognized role in human health. Studies of the microbiome typically use targeted sequencing of the 16S rRNA gene, whole metagenome shotgun sequencing, or other meta-omic technologies to characterize the microbiome's composition, activity, and dynamics. Processing, analyzing, and interpreting these data involve numerous computational tools that aim to filter, cluster, annotate, and quantify the obtained data and ultimately provide an accurate and interpretable profile of the microbiome's taxonomy, functional capacity, and behavior. These tools, however, are often limited in resolution and accuracy and may fail to capture many biologically and clinically relevant microbiome features, such as strain-level variation or nuanced functional response to perturbation. Over the past few years, extensive efforts have been invested toward addressing these challenges and developing novel computational methods for accurate and high-resolution characterization of microbiome data. These methods aim to quantify strain-level composition and variation, detect and characterize rare microbiome species, link specific genes to individual taxa, and more accurately characterize the functional capacity and dynamics of the microbiome. These methods and the ability to produce detailed and precise microbiome information are clearly essential for informing microbiome-based personalized therapies. In this review, we survey these methods, highlighting the challenges each method sets out to address and briefly describing methodological approaches.
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Affiliation(s)
- Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Colin P McNally
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Computer Science and Engineering, University of Washington, Seattle, WA
- Santa Fe Institute, Santa Fe, NM
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627
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Mancini N, Greco R, Pasciuta R, Barbanti MC, Pini G, Morrow OB, Morelli M, Vago L, Clementi N, Giglio F, Lupo Stanghellini MT, Forcina A, Infurnari L, Marktel S, Assanelli A, Carrabba M, Bernardi M, Corti C, Burioni R, Peccatori J, Sormani MP, Banfi G, Ciceri F, Clementi M. Enteric Microbiome Markers as Early Predictors of Clinical Outcome in Allogeneic Hematopoietic Stem Cell Transplant: Results of a Prospective Study in Adult Patients. Open Forum Infect Dis 2017. [PMID: 29226172 DOI: 10.1093/ofid/ofx215/4367678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Infections and graft-vs-host disease (GvHD) still represent major, not easily predictable complications in allogeneic hematopoietic stem cell transplant (allo-HSCT). Both conditions have been correlated to altered enteric microbiome profiles during the peritransplant period. The main objective of this study was to identify possible early microbiome-based markers useful in pretransplant risk stratification. METHODS Stool samples were collected from 96 consecutive patients at the beginning of the pretransplant conditioning regimen (T0) and at 10 (T1) and 30 (T2) days following transplant. When significant in univariate analysis, the identified microbiome markers were used in multivariate regression analyses, together with other significant clinical variables for allo-HSCT-related risk stratification. Four main outcomes were addressed: (1) septic complications, (2) GvHD, (3) relapse of the underlying disease, and (4) mortality. RESULTS The presence of >5% proinflammatory Enterobacteriaceae at T0 was the only significant marker for the risk of microbiologically confirmed sepsis. Moreover, ≤10% Lachnospiraceae at T0 was the only significant factor for increased risk of overall mortality, including death from both infectious and noninfectious causes.Finally, a low bacterial alpha-diversity (Shannon index ≤ 1.3) at T1 was the only variable significantly correlating with an increased risk of GvHD within 30 days. CONCLUSIONS Microbiome markers can be useful in the very early identification of patients at risk for major transplant-related complications, offering new tools for individualized preemptive or therapeutic strategies to improve allo-HSCT outcomes.
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Affiliation(s)
- Nicasio Mancini
- Laboratory of Microbiology and Virology, San Raffaele Scientific Institute, Milan, Italy
- Department of Microbiology and Virology, University "Vita-Salute" San Raffaele, Milan, Italy
| | - Raffaella Greco
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | - Renée Pasciuta
- Laboratory of Microbiology and Virology, San Raffaele Scientific Institute, Milan, Italy
| | - Maria Chiara Barbanti
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | - Giacomo Pini
- Laboratory of Microbiology and Virology, San Raffaele Scientific Institute, Milan, Italy
| | - Olivia Beatrice Morrow
- Laboratory of Microbiology and Virology, San Raffaele Scientific Institute, Milan, Italy
| | - Mara Morelli
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | - Luca Vago
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | - Nicola Clementi
- Department of Microbiology and Virology, University "Vita-Salute" San Raffaele, Milan, Italy
| | - Fabio Giglio
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | - Maria Teresa Lupo Stanghellini
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Forcina
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | - Laura Infurnari
- Laboratory of Microbiology and Virology, San Raffaele Scientific Institute, Milan, Italy
| | - Sarah Marktel
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | - Andrea Assanelli
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Carrabba
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | - Massimo Bernardi
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | - Consuelo Corti
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | - Roberto Burioni
- Laboratory of Microbiology and Virology, San Raffaele Scientific Institute, Milan, Italy
- Department of Microbiology and Virology, University "Vita-Salute" San Raffaele, Milan, Italy
| | - Jacopo Peccatori
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
| | | | - Giuseppe Banfi
- Galeazzi Scientific Institute and University "Vita-Salute" San Raffaele, Milan, Italy
| | - Fabio Ciceri
- Hematology and Bone Marrow Transplantation Unit, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan, Italy
- Department of Hematology and Bone Marrow Transplantation, University "Vita-Salute" San Raffaele, Milan, Italy
| | - Massimo Clementi
- Laboratory of Microbiology and Virology, San Raffaele Scientific Institute, Milan, Italy
- Department of Microbiology and Virology, University "Vita-Salute" San Raffaele, Milan, Italy
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628
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Yasmin F, Tun HM, Konya TB, Guttman DS, Chari RS, Field CJ, Becker AB, Mandhane PJ, Turvey SE, Subbarao P, Sears MR, Scott JA, Dinu I, Kozyrskyj AL. Cesarean Section, Formula Feeding, and Infant Antibiotic Exposure: Separate and Combined Impacts on Gut Microbial Changes in Later Infancy. Front Pediatr 2017; 5:200. [PMID: 29018787 PMCID: PMC5622971 DOI: 10.3389/fped.2017.00200] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/31/2017] [Indexed: 12/11/2022] Open
Abstract
Established during infancy, our complex gut microbial community is shaped by medical interventions and societal preferences, such as cesarean section, formula feeding, and antibiotic use. We undertook this study to apply the significance analysis of microarrays (SAM) method to quantify changes in gut microbial composition during later infancy following the most common birth and postnatal exposures affecting infant gut microbial composition. Gut microbiota of 166 full-term infants in the Canadian Healthy Infant Longitudinal Development birth cohort were profiled using 16S high-throughput gene sequencing. Infants were placed into groups according to mutually exclusive combinations of birth mode (vaginal/cesarean birth), breastfeeding status (yes/no), and antibiotic use (yes/no) by 3 months of age. Based on repeated permutations of data and adjustment for the false discovery rate, the SAM statistic identified statistically significant changes in gut microbial abundance between 3 months and 1 year of age within each infant group. We observed well-known patterns of microbial phyla succession in later infancy (declining Proteobacteria; increasing Firmicutes and Bacteroidetes) following vaginal birth, breastfeeding, and no antibiotic exposure. Genus Lactobacillus, Roseburia, and Faecalibacterium species appeared in the top 10 increases to microbial abundance in these infants. Deviations from this pattern were evident among infants with other perinatal co-exposures; notably, the largest number of microbial species with unchanged abundance was seen in gut microbiota following early cessation of breastfeeding in infants. With and without antibiotic exposure, the absence of a breast milk diet by 3 months of age following vaginal birth yielded a higher proportion of unchanged abundance of Bacteroidaceae and Enterobacteriaceae in later infancy, and a higher ratio of unchanged Enterobacteriaceae to Alcaligenaceae microbiota. Gut microbiota of infants born vaginally and exclusively formula fed became less enriched with family Veillonellaceae and Clostridiaceae, showed unchanging levels of Ruminococcaceae, and exhibited a greater decline in the Rikenellaceae/Bacteroidaceae ratio compared to their breastfed, vaginally delivered counterparts. These changes were also evident in cesarean-delivered infants to a lesser extent. The clinical relevance of these trajectories of microbial change is that they culminate in taxon-specific abundances in the gut microbiota of later infancy, which we and others have observed to be associated with food sensitization.
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Affiliation(s)
- Farzana Yasmin
- Department of Public Health Sciences, University of Alberta, Edmonton, AB, Canada
| | - Hein Min Tun
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | | | - David S Guttman
- Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada
| | - Radha S Chari
- Department of Obstetrics and Gynecology, University of Alberta, Edmonton, AB, Canada
| | - Catherine J Field
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Allan B Becker
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, MB, Canada
| | - Piush J Mandhane
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Stuart E Turvey
- Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Padmaja Subbarao
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Malcolm R Sears
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | | | - James A Scott
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Irina Dinu
- Department of Public Health Sciences, University of Alberta, Edmonton, AB, Canada
| | - Anita L Kozyrskyj
- Department of Public Health Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Pediatrics, University of Alberta, Edmonton, AB, Canada.,Department of Obstetrics and Gynecology, University of Alberta, Edmonton, AB, Canada
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629
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Rogers MB, Firek B, Shi M, Yeh A, Brower-Sinning R, Aveson V, Kohl BL, Fabio A, Carcillo JA, Morowitz MJ. Disruption of the microbiota across multiple body sites in critically ill children. MICROBIOME 2016; 4:66. [PMID: 28034303 PMCID: PMC5200963 DOI: 10.1186/s40168-016-0211-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/24/2016] [Indexed: 05/10/2023]
Abstract
BACKGROUND Despite intense interest in the links between the microbiome and human health, little has been written about dysbiosis among ICU patients. We characterized microbial diversity in samples from 37 children in a pediatric ICU (PICU). Standard measures of alpha and beta diversity were calculated, and results were compared with data from adult and pediatric reference datasets. RESULTS Bacterial 16S rRNA gene sequences were analyzed from 71 total tongue swabs, 50 skin swabs, and 77 stool samples or rectal swabs. The mean age of the PICU patients was 2.9 years (range 1-9 years), and many were chronically ill children that had previously been hospitalized in the PICU. Relative to healthy adults and children, alpha diversity was decreased in PICU GI and tongue but not skin samples. Measures of beta diversity indicated differences in community membership at each body site between PICU, adult, and pediatric groups. Taxonomic alterations in the PICU included enrichment of gut pathogens such as Enterococcus and Staphylococcus at multiple body sites and depletion of commensals such as Faecalibacterium and Ruminococcus from GI samples. Alpha and beta diversity were unstable over time in patients followed longitudinally. We observed the frequent presence of "dominant" pathogens in PICU samples at relative abundance >50%. PICU samples were characterized by loss of site specificity, with individual taxa commonly present simultaneously at three sample sites on a single individual. Some pathogens identified by culture of tracheal aspirates were commonly observed in skin samples from the same patient. CONCLUSIONS We conclude that the microbiota in critically ill children differs sharply from the microbiota of healthy children and adults. Acknowledgement of dysbiosis associated with critical illness could provide opportunities to modulate the microbiota with precision and thereby improve patient outcomes.
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Affiliation(s)
- Matthew B. Rogers
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Brian Firek
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Min Shi
- Division of Pediatric General and Thoracic Surgery, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, USA
| | - Andrew Yeh
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Rachel Brower-Sinning
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Victoria Aveson
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Brittany L. Kohl
- Division of Pediatric Critical Care Medicine, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, USA
| | - Anthony Fabio
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, USA
| | - Joseph A. Carcillo
- Division of Pediatric Critical Care Medicine, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, USA
- Department of Critical Care Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, USA
| | - Michael J. Morowitz
- Division of Pediatric Surgery, Children’s Hospital of Pittsburgh of UPMC, 4401 Penn Avenue, 7th Floor Faculty Pavilion, Pittsburgh, PA 15244 USA
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630
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Zhao X, Jiang Z, Yang F, Wang Y, Gao X, Wang Y, Chai X, Pan G, Zhu Y. Sensitive and Simplified Detection of Antibiotic Influence on the Dynamic and Versatile Changes of Fecal Short-Chain Fatty Acids. PLoS One 2016; 11:e0167032. [PMID: 27907030 PMCID: PMC5132400 DOI: 10.1371/journal.pone.0167032] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 11/08/2016] [Indexed: 12/13/2022] Open
Abstract
Short-chain fatty acids (SCFAs), produced by anaerobic fermentation of mainly indigestible dietary carbohydrates by gut microbiota, have a profound influence on intestinal function and host energy metabolism. Antibiotics may seriously disturb the balance of fecal SCFAs. To evaluate the impacts of antibiotics on fecal SCFAs produced by gut microbiota, a simple, reproducible and accurate gas chromatography (GC) method, which can simultaneously analyze seven SCFAs in fecal samples, was developed and validated. The ranges of detection and quantitation of the SCFAs reached 0.0868 ~ 0.393 and 0.261 ~ 1.18 μg·mL-1 respectively, in an optimized protocol for SCFAs extraction and analysis that used 10 mL 75% ethanol aqueous solution containing 1% HCl, without ultrasonication. The technique exhibited excellent intra-day (relative standard deviation (RSD) ≤ 2.54%) and inter-day (RSD ≤ 4.33%) precisions for all the SCFAs. Later, we administered broad-spectrum antibiotics, cefdinir or azithromycin to rats and analyzed the alterations in fecal SCFAs. The total amount, types and distribution of nearly all fecal SCFAs were significantly altered during the administration and even after withdrawal of the antibiotics in rats. The effects of cefdinir on the SCFAs were more pronounced than those of azithromycin. Our findings suggest SCFAs may serve as sensitive indicators to monitor the influences of antibiotics on SCFAs originated by intestinal bacteria. Our improved SCFAs analysis method is a potential platform for a standard clinical test of the effects of new antibiotics on SCFAs.
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Affiliation(s)
- Xiaoya Zhao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Zhenzuo Jiang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Fan Yang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Yan Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Xiumei Gao
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yuefei Wang
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
- * E-mail: (YFW); (YZ)
| | - Xin Chai
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Guixiang Pan
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
| | - Yan Zhu
- Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
- Research and Development Center of TCM, Tianjin International Joint Academy of Biotechnology and Medicine, Tianjin, China
- * E-mail: (YFW); (YZ)
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631
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Aagaard K, Stewart CJ, Chu D. Una destinatio, viae diversae: Does exposure to the vaginal microbiota confer health benefits to the infant, and does lack of exposure confer disease risk? EMBO Rep 2016; 17:1679-1684. [PMID: 27884820 PMCID: PMC5283592 DOI: 10.15252/embr.201643483] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
There are lingering concerns that Cesarean surgery could impede on the child's health due to a lack of exposure to the mother's vaginal microbiota. However, the evidence so far is not sufficient to affirm whether the mode of birth influences disease risk or whether it is other causes.![]()
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Affiliation(s)
- Kjersti Aagaard
- Division of Maternal Fetal Medicine, Department of Obstetrics & Gynecology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.,Center for Metagenomics & Microbiome Research, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.,Department of Molecular & Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.,Department of Molecular & Cell Biology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Christopher J Stewart
- Division of Maternal Fetal Medicine, Department of Obstetrics & Gynecology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA.,Center for Metagenomics & Microbiome Research, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Derrick Chu
- Division of Maternal Fetal Medicine, Department of Obstetrics & Gynecology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
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632
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633
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Willmann M, Peter S. Translational metagenomics and the human resistome: confronting the menace of the new millennium. J Mol Med (Berl) 2016; 95:41-51. [PMID: 27766372 PMCID: PMC5225160 DOI: 10.1007/s00109-016-1478-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 09/19/2016] [Accepted: 09/26/2016] [Indexed: 12/21/2022]
Abstract
The increasing threat of antimicrobial resistance poses one of the greatest challenges to modern medicine. The collection of all antimicrobial resistance genes carried by various microorganisms in the human body is called the human resistome and represents the source of resistance in pathogens that can eventually cause life-threatening and untreatable infections. A deep understanding of the human resistome and its multilateral interaction with various environments is necessary for developing proper measures that can efficiently reduce the spread of resistance. However, the human resistome and its evolution still remain, for the most part, a mystery to researchers. Metagenomics, particularly in combination with next-generation-sequencing technology, provides a powerful methodological approach for studying the human microbiome as well as the pathogenome, the virolume and especially the resistome. We summarize below current knowledge on how the human resistome is shaped and discuss how metagenomics can be employed to improve our understanding of these complex processes, particularly as regards a rapid translation of new findings into clinical diagnostics, infection control and public health.
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Affiliation(s)
- Matthias Willmann
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Elfriede-Aulhorn-Str. 6, 72076, Tuebingen, Germany. .,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany.
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Elfriede-Aulhorn-Str. 6, 72076, Tuebingen, Germany.,German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
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634
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Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res 2016; 26:1612-1625. [PMID: 27803195 PMCID: PMC5088602 DOI: 10.1101/gr.201863.115] [Citation(s) in RCA: 301] [Impact Index Per Article: 37.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Accepted: 09/08/2016] [Indexed: 01/19/2023]
Abstract
We present the Metagenomic Intra-species Diversity Analysis System (MIDAS), which is an integrated computational pipeline for quantifying bacterial species abundance and strain-level genomic variation, including gene content and single-nucleotide polymorphisms (SNPs), from shotgun metagenomes. Our method leverages a database of more than 30,000 bacterial reference genomes that we clustered into species groups. These cover the majority of abundant species in the human microbiome but only a small proportion of microbes in other environments, including soil and seawater. We applied MIDAS to stool metagenomes from 98 Swedish mothers and their infants over one year and used rare SNPs to track strains between hosts. Using this approach, we found that although species compositions of mothers and infants converged over time, strain-level similarity diverged. Specifically, early colonizing bacteria were often transmitted from an infant’s mother, while late colonizing bacteria were often transmitted from other sources in the environment and were enriched for spore-formation genes. We also applied MIDAS to 198 globally distributed marine metagenomes and used gene content to show that many prevalent bacterial species have population structure that correlates with geographic location. Strain-level genetic variants present in metagenomes clearly reveal extensive structure and dynamics that are obscured when data are analyzed at a coarser taxonomic resolution.
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Affiliation(s)
- Stephen Nayfach
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, California 94158, USA.,Gladstone Institutes, San Francisco, California 94158, USA
| | | | - Nandita Garud
- Gladstone Institutes, San Francisco, California 94158, USA
| | - Katherine S Pollard
- Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, California 94158, USA.,Gladstone Institutes, San Francisco, California 94158, USA.,Institute for Human Genetics, Institute for Computational Health Sciences, and Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California 94158, USA
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635
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Do T. Insights into microbial ecosystems using a new computational approach. Oral Dis 2016; 23:817-819. [PMID: 27718300 DOI: 10.1111/odi.12591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thuy Do
- Division of Oral Biology, School of Dentistry, University of Leeds, Leeds, UK
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636
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Eeckhaut V, Wang J, Van Parys A, Haesebrouck F, Joossens M, Falony G, Raes J, Ducatelle R, Van Immerseel F. The Probiotic Butyricicoccus pullicaecorum Reduces Feed Conversion and Protects from Potentially Harmful Intestinal Microorganisms and Necrotic Enteritis in Broilers. Front Microbiol 2016; 7:1416. [PMID: 27708624 PMCID: PMC5030265 DOI: 10.3389/fmicb.2016.01416] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 08/26/2016] [Indexed: 01/21/2023] Open
Abstract
Probiotics which do not result in the development and spread of microbial resistance are among the candidate replacements for antibiotics previously used as growth promotors. In this study the effect of in-feed supplementation of the butyrate producing Butyricicoccus pullicaecorum strain 25-3T on performance, intestinal microbiota and prevention of necrotic enteritis (NE), a disease caused by Clostridium perfringens was evaluated in broilers. For the performance study, day old Ross 308 chicks were randomly allocated into two treatment groups and fed either a non-supplemented diet or a diet supplemented with 109 cfu lyophilized B. pullicaecorum per kg feed for 40 days. On day 40 broilers administered B. pullicaecorum had a significant lower bodyweight (2675 g vs. 2762 g; p = 0.0025) but supplementation of B. pullicaecorum decreased the feed conversion ratio significantly (1.518 vs. 1.632; p < 0.0001). Additionally, ingestion of the Butyricicoccus strain significantly lowered the abundance of Campylobacter spp. in the caecum and Enterococcus and Escherichia/Shigella spp. in the ileum at day 40. In feed supplementation of B. pullicaecorum in the NE trials resulted in a significant decrease in the number of birds with necrotic lesions compared with the untreated control group. These studies show that supplementation of B. pullicaecorum is able to improve feed conversion, to reduce the abundance of some potentially important pathogens in the caeca and ileum and to contribute to the prevention of NE in broilers, making the strain a potential valuable probiotic.
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Affiliation(s)
- Venessa Eeckhaut
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University Merelbeke, Belgium
| | - Jun Wang
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU LeuvenLeuven, Belgium; Center for the Biology of Disease, Vlaams Instituut voor BiotechnologieLeuven, Belgium
| | - Alexander Van Parys
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University Merelbeke, Belgium
| | - Marie Joossens
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU LeuvenLeuven, Belgium; Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit BrusselBrussels, Belgium
| | - Gwen Falony
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU LeuvenLeuven, Belgium; Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit BrusselBrussels, Belgium
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU LeuvenLeuven, Belgium; Microbiology Unit, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit BrusselBrussels, Belgium
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University Merelbeke, Belgium
| | - Filip Van Immerseel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University Merelbeke, Belgium
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637
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Raymond F, Déraspe M, Boissinot M, Bergeron MG, Corbeil J. Partial recovery of microbiomes after antibiotic treatment. Gut Microbes 2016; 7:428-34. [PMID: 27494088 PMCID: PMC5154369 DOI: 10.1080/19490976.2016.1216747] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 07/14/2016] [Accepted: 07/19/2016] [Indexed: 02/03/2023] Open
Abstract
Antibiotics profoundly affect the gut microbiome and modulate microbial communities. We recently observed that antimicrobial drugs also impact the abundance and distribution of antibiotic resistance genes. In this addendum, we reanalyze our ∼1 trillion nucleotide shotgun metagenomic dataset to quantify comprehensive genomic differences at the sequence level before and after antibiotic treatment. We show that 7 day exposure to cefprozil leads to a statistically significant loss of metagenome sequences. Recovery of gut microbiomes 3 months after antibiotherapy was characterized by the emergence of new genome sequences not observed prior to antibiotic exposure. Participants with low initial gut microbiome diversity had an increased amount of sequences related to antibiotic resistance. Therefore, we suggest that while the taxonomical composition of microbiomes is partially affected by the antibiotic, the genomic content and population structure of bacterial communities is noticeably impacted.
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Affiliation(s)
- Frédéric Raymond
- Centre de Recherche en Infectiologie, CHU de
Québec-Université Laval, Québec,
Canada
- Big Data Research Center, Université
Laval, Québec, Canada
| | - Maxime Déraspe
- Centre de Recherche en Infectiologie, CHU de
Québec-Université Laval, Québec,
Canada
- Big Data Research Center, Université
Laval, Québec, Canada
| | - Maurice Boissinot
- Centre de Recherche en Infectiologie, CHU de
Québec-Université Laval, Québec,
Canada
| | - Michel G. Bergeron
- Centre de Recherche en Infectiologie, CHU de
Québec-Université Laval, Québec,
Canada
- Département de
microbiologie-infectiologie et d'immunologie, Université
Laval, Québec, Canada
| | - Jacques Corbeil
- Centre de Recherche en Infectiologie, CHU de
Québec-Université Laval, Québec,
Canada
- Big Data Research Center, Université
Laval, Québec, Canada
- Département de médecine
moléculaire, Université Laval, Québec,
Canada
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Abstract
The gut microbiome research is going from a descriptive into an intervention phase. To optimize beneficial microbe–host interaction, we need to understand how to steer the system by modulating the nutrient input with which the system is literally fed (e.g. diets, fibres, prebiotics, human milk oligosaccharides), and we must learn how to modulate the composition of the gut microbiota by adding beneficial microbes (e.g. probiotics, faecal transplants) and by eliminating disturbing microbial members using, for example, bacteriophages in this highly complex ecosystem. The current status of the field is reviewed together with an outlook what might be expected until 2020, highlighting obstacles to progress and possible solutions to these problems.
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Affiliation(s)
- Harald Brüssow
- Nestlé Research Center, Nutrition and Health Research, Host-Microbe Interaction, Vers-chez-les-Blanc, CH-1000, Lausanne 26, Switzerland
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