151
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Palleja A, Mikkelsen KH, Forslund SK, Kashani A, Allin KH, Nielsen T, Hansen TH, Liang S, Feng Q, Zhang C, Pyl PT, Coelho LP, Yang H, Wang J, Typas A, Nielsen MF, Nielsen HB, Bork P, Wang J, Vilsbøll T, Hansen T, Knop FK, Arumugam M, Pedersen O. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol 2018; 3:1255-1265. [PMID: 30349083 DOI: 10.1038/s41564-018-0257-9] [Citation(s) in RCA: 417] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/28/2018] [Indexed: 12/18/2022]
Abstract
To minimize the impact of antibiotics, gut microorganisms harbour and exchange antibiotics resistance genes, collectively called their resistome. Using shotgun sequencing-based metagenomics, we analysed the partial eradication and subsequent regrowth of the gut microbiota in 12 healthy men over a 6-month period following a 4-day intervention with a cocktail of 3 last-resort antibiotics: meropenem, gentamicin and vancomycin. Initial changes included blooms of enterobacteria and other pathobionts, such as Enterococcus faecalis and Fusobacterium nucleatum, and the depletion of Bifidobacterium species and butyrate producers. The gut microbiota of the subjects recovered to near-baseline composition within 1.5 months, although 9 common species, which were present in all subjects before the treatment, remained undetectable in most of the subjects after 180 days. Species that harbour β-lactam resistance genes were positively selected for during and after the intervention. Harbouring glycopeptide or aminoglycoside resistance genes increased the odds of de novo colonization, however, the former also decreased the odds of survival. Compositional changes under antibiotic intervention in vivo matched results from in vitro susceptibility tests. Despite a mild yet long-lasting imprint following antibiotics exposure, the gut microbiota of healthy young adults are resilient to a short-term broad-spectrum antibiotics intervention and their antibiotics resistance gene carriage modulates their recovery processes.
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Affiliation(s)
- Albert Palleja
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Clinical-Microbiomics A/S, Copenhagen, Denmark
| | - Kristian H Mikkelsen
- Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Sofia K Forslund
- Experimental and Clinical Research Center, Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany.,Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Charité-Universitätsmedizin Berlin , Freie Universität Berlin Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alireza Kashani
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Danish Diabetes Academy, Odense, Denmark
| | - Kristine H Allin
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Epidemiology, Bispebjerg and Frederiksberg Hospital, Copenhagen, Denmark
| | - Trine Nielsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tue H Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Suisha Liang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Qiang Feng
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Chenchen Zhang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Paul Theodor Pyl
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Luis Pedro Coelho
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Athanasios Typas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Morten F Nielsen
- Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | | | - Peer Bork
- Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Molecular Medicine Partnership Unit, University of Heidelberg and European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jun Wang
- iCarbonX, Shenzhen, China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Avenida Wai Long, Taipa Macau, China
| | - Tina Vilsbøll
- Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Filip K Knop
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Center for Diabetes Research, Gentofte Hospital, University of Copenhagen, Hellerup, Denmark. .,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Manimozhiyan Arumugam
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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152
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Wang B, Liu J, Zhang Y, Yan C, Wang H, Jiang F, Li F, Zhang J. Prenatal Exposure to Antibiotics and Risk of Childhood Obesity in a Multicenter Cohort Study. Am J Epidemiol 2018; 187:2159-2167. [PMID: 29893794 DOI: 10.1093/aje/kwy122] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 06/05/2018] [Indexed: 12/19/2022] Open
Abstract
Mounting evidence has linked postnatal antibiotic use with body mass index (BMI) in children, but the influence of prenatal antibiotic use on offspring obesity risk remains unclear. We aimed to assess the association between fetal exposure to antibiotics and obesity at ages 4 and 7 years among 43,332 children using a multicenter prospective cohort of the US Collaborative Perinatal Project (1959-1976). Antibiotic use was ascertained for mothers during pregnancy. Modified Poisson regression models were used to estimate risk ratios for obesity (BMI >95th percentile), and linear mixed models were applied to assess the association with BMI z score. Repeated prenatal exposure to antibiotics was associated with childhood obesity at age 7 years, and risk of obesity tended to increase with an increasing number of antibiotic exposures (for 2-3 exposures, risk ratio (RR) = 1.22, 95% confidence interval (CI): 1.04, 1.44; for ≥4 exposures, RR = 1.34, 95% CI: 1.03, 1.73). The magnitude of association was strongest for repeated exposures in the second trimester (RR = 1.40, 95% CI: 1.16, 1.71). Prenatal antibiotic use was not associated with obesity or BMI z score at age 4 years. These findings support an increased risk of mid-childhood obesity with repeated use of antibiotics during pregnancy.
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Affiliation(s)
- Bin Wang
- Ministry of Education–Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jihong Liu
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, South Carolina
| | - Yongjun Zhang
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chonghuai Yan
- Ministry of Education–Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fan Jiang
- Ministry of Education–Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Li
- Ministry of Education–Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Zhang
- Ministry of Education–Shanghai Key Laboratory of Children’s Environmental Health, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Neonatology, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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153
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Antibiotic treatment of rat dams affects bacterial colonization and causes decreased weight gain in pups. Commun Biol 2018; 1:145. [PMID: 30272021 PMCID: PMC6137057 DOI: 10.1038/s42003-018-0140-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 08/17/2018] [Indexed: 12/13/2022] Open
Abstract
Intergenerational transmission of bacteria during birth initiates the natural successional development of the intestinal microbiota in mammals. This process can be disrupted by antibiotic exposure, potentially affecting early-life microbiota-dependent metabolic programming. In the present study, we specifically investigate the metabolic consequences of exposing neonate Wistar rats to an antibiotic-perturbed low-diversity microbiota from birth until weaning, without exposing the pups directly to antibiotics. Here, we show that pups born from both amoxicillin and vancomycin-treated dams gain less weight than controls. This was concordant with lower feed intake as well as increased colonic expression of the PYY satiety hormone gene at weaning. The weight difference persists into adulthood even though the initial differences in gut microbiota subsided. Our results demonstrate that early-life exposure to an antibiotic-perturbed low-diversity microbiota is sufficient to cause changes in body weight persisting into adulthood.
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154
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Adami AJ, Bracken SJ, Guernsey LA, Rafti E, Maas KR, Graf J, Matson AP, Thrall RS, Schramm CM. Early-life antibiotics attenuate regulatory T cell generation and increase the severity of murine house dust mite-induced asthma. Pediatr Res 2018; 84:426-434. [PMID: 29967529 PMCID: PMC6258300 DOI: 10.1038/s41390-018-0031-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 03/29/2018] [Accepted: 04/10/2018] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Early-life exposure to antibiotics (ABX) has been linked to increases in asthma severity and prevalence in both children and laboratory animals. We explored the immunologic mechanisms behind this association using a mouse model of house dust mite (HDM)-induced asthma and early-life ABX exposure. METHODS Mice were exposed to three short courses of ABX following weaning and experimental asthma was thereafter induced. Airway cell counts and differentials; serum immunoglobulin E (IgE); pulmonary function; lung histopathology; pulmonary regulatory T cells (Tregs); and the fecal microbiome were characterized following ABX exposure and induction of experimental asthma. RESULTS Asthma severity was increased in mice exposed to ABX, including: airway eosinophilia, airway hyper-reactivity, serum HDM-specific IgE, and lung histopathology. ABX treatment led to sharp reduction in fecal microbiome diversity, including the loss of pro-regulatory organisms such as Lachnospira. Pulmonary Tregs were reduced with ABX treatment, and this reduction was directly proportional to diminished microbiome diversity. CONCLUSION Intermittent exposure to ABX early in life worsened the severity of experimental asthma and reduced pulmonary Tregs; the latter change correlated with decreased microbiome diversity. These data may suggest targets for immunologic or probiotic therapy to counteract the harmful effects of childhood ABX.
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Affiliation(s)
- Alexander J. Adami
- Department of Immunology, University of Connecticut Health, Farmington, CT
| | - Sonali J. Bracken
- Department of Immunology, University of Connecticut Health, Farmington, CT
| | - Linda A. Guernsey
- Department of Immunology, University of Connecticut Health, Farmington, CT,Department of Pediatrics, University of Connecticut Health, Farmington, CT
| | - Ektor Rafti
- Department of Pediatrics, University of Connecticut Health, Farmington, CT
| | - Kendra R. Maas
- Microbial Analysis, Resources, and Services Facility, University of Connecticut, Storrs, CT
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT
| | - Adam P. Matson
- Department of Immunology, University of Connecticut Health, Farmington, CT,Department of Pediatrics, University of Connecticut Health, Farmington, CT,Division of Neonatology, Connecticut Children’s Medical Center, Hartford, CT
| | - Roger S. Thrall
- Department of Immunology, University of Connecticut Health, Farmington, CT
| | - Craig M. Schramm
- Department of Pediatrics, University of Connecticut Health, Farmington, CT,Division of Pulmonary Medicine, Connecticut Children’s Medical Center, Hartford, CT,Corresponding Author: Craig M. Schramm, Connecticut Children’s Medical Center, 282 Washington
Street, Hartford, CT 06106; ; Telephone: 860-545- 9440; Fax: 860-545-9445
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155
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Ruggles KV, Wang J, Volkova A, Contreras M, Noya-Alarcon O, Lander O, Caballero H, Dominguez-Bello MG. Changes in the Gut Microbiota of Urban Subjects during an Immersion in the Traditional Diet and Lifestyle of a Rainforest Village. mSphere 2018; 3:3/4/e00193-18. [PMID: 30158281 PMCID: PMC6115531 DOI: 10.1128/msphere.00193-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
People living traditional lifestyles have higher gut microbiota diversity than urban subjects. We hypothesized that shifting lifestyles from an urban environment to a traditional rainforest village would lead to changes in the microbiota of visitors, which would become more similar to the microbiota of villagers. Here, we characterized at different time points the microbiota of 7 urban visitors (5 adults and 2 children) staying in a rainforest Amerindian village for 16 days and compared them with a reference collection of samples from age-matched local villagers. We performed a 16S rRNA gene survey of samples from multiple body sites (including fecal, oral, nasal, and skin samples) using Illumina MiSeq sequencing. The main factor segregating the microbiotas of each body site was the human group (i.e., visitors versus villagers), with the visitor microbiota tending to have lower alpha diversity; the lowered alpha diversity was statistically significant in the microbiota of skin and in the children's fecal and oral microbiota. During the rainforest period, all visitors experienced microbiota changes within their personal cloud of variation. For all body sites, the microbiota conformations in the visitor children better matched the microbiota conformations in villagers of the same age than did those of the visitor adults, which showed a lower "microbiota age" than the microbiota of the villagers. The results suggest higher stability in the adult microbiota, with the less resilient children's microbiota responding more to dietary changes.IMPORTANCE Despite the limitations of a small study, our results evidence higher resilience of the gut microbiota with respect to dietary manipulation in adults than in children and urge further studies to understand the extent of microbiota plasticity in response to dietary changes and the mechanisms underlying microbiota resilience. These studies are relevant to the potential of future human pre- and probiotics in preventing or curing microbiota-associated diseases.
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Affiliation(s)
- Kelly V Ruggles
- Department of Medicine, New York University Langone Medical Center, New York, New York, USA
| | - Jincheng Wang
- Department of Medicine, New York University Langone Medical Center, New York, New York, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Angelina Volkova
- Department of Medicine, New York University Langone Medical Center, New York, New York, USA
| | - Monica Contreras
- Center for Biophysics and Biochemistry, Venezuelan Institute of Scientific Research (IVIC), Caracas, Venezuela
| | - Oscar Noya-Alarcon
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
- Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho, Venezuela
| | - Orlana Lander
- Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas, Venezuela
| | - Hortensia Caballero
- Department of Anthropology, Venezuelan Institute of Scientific Research (IVIC), Caracas, Venezuela
| | - Maria G Dominguez-Bello
- Department of Medicine, New York University Langone Medical Center, New York, New York, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
- Department of Anthropology, New York University, New York, New York, USA
- Department of Anthropology, Rutgers University, New Brunswick, New Jersey, USA
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156
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Shi Y, Kellingray L, Zhai Q, Gall GL, Narbad A, Zhao J, Zhang H, Chen W. Structural and Functional Alterations in the Microbial Community and Immunological Consequences in a Mouse Model of Antibiotic-Induced Dysbiosis. Front Microbiol 2018; 9:1948. [PMID: 30186263 PMCID: PMC6110884 DOI: 10.3389/fmicb.2018.01948] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 08/02/2018] [Indexed: 12/11/2022] Open
Abstract
The aim of this study was to establish continuous therapeutic-dose ampicillin (CTDA)-induced dysbiosis in a mouse model, mimicking typical adult exposure, with a view to using this to assess its impact on gut microbiota, intestinal metabolites and host immune responses. Mice were exposed to ampicillin for 14 days and antibiotic-induced dysbiosis was evaluated by alteration of microbiota and gut permeability. The cecal index was increased in the CTDA group, and the gut permeability indicated by fluorescent dextran, endotoxin and D-Lactate in the serum was significantly increased after antibiotic use. The tight-junction proteins ZO-1 and occludin in the colon were reduced to half the control level in CTDA. We found that alpha-diversity was significantly decreased in mice receiving CTDA, and microbial community structure was altered compared with the control. Key taxa were identified as CTDA-specific, and the relative abundance of Enterococcus and Klebsiella was particularly enriched while Lachnospiraceae, Coprobacillus and Dorea were depleted after antibiotic treatment. In particular, a significant increase in succinate and a reduction in butyrate was detected in CTDA mice, and the triggering of NF-κB enhancement reflected that the host immune response was influenced by ampicillin use. The observed perturbation of the microbiota was accompanied by modulation of inflammatory state; this included increase in interferon-γ and RegIIIγ, and a decrease in secretory IgA in the colon mucosa. This study allowed us to identify the key taxa associated with an ampicillin-induced state of dysbiosis in mice and to characterize the microbial communities via molecular profiling. Thus, this work describes the bacterial ecology of antibiotic exposure model in combination with host physiological characteristics at a detailed level of microbial taxa.
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Affiliation(s)
- Ying Shi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Wuxi, China.,International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, China.,Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Lee Kellingray
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, United Kingdom.,UK-China Joint Centre on Probiotic Bacteria, Norwich, United Kingdom
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Wuxi, China.,International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, China
| | - Gwenaelle Le Gall
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Arjan Narbad
- Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, United Kingdom.,UK-China Joint Centre on Probiotic Bacteria, Norwich, United Kingdom
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Wuxi, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,National Engineering Research Center for Functional Food, Wuxi, China.,Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, China
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157
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Smith AH, Rehberger TG. Bacteria and fungi in day-old turkeys vary among companies, collection periods, and breeder flocks. Poult Sci 2018; 97:1400-1411. [PMID: 29390100 DOI: 10.3382/ps/pex429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/06/2017] [Indexed: 12/21/2022] Open
Abstract
Microbial colonization of the intestinal tract of commercial poultry is highly variable, likely due to the fact that poults and chicks are hatched and raised without exposure to adult birds and their microbiota. In industrial poultry production, it is hypothesized that most of the microbiota is obtained through horizontal transmission from the environment and very little by maternal transmission. The initial gut microbiota will therefore differ between flocks and companies based on environmental conditions at the hatchery. Day-old poults were collected from the hatchery of 2 companies at 3 different time points to monitor the initial colonizing microbiota by sequencing amplicons of marker genes for bacteria, lactic acid bacteria (LAB), fungi, and archaea. Bacterial colonizers were distinct by company (pseudo-F 38.7, P ≤ 0.05) with the predominant bacteria at Company A being clostridia, specifically Clostridium celatum group, C. paraputrificum, and C. tertium. Predominant bacteria at Company B were Enterobacteriaceae, belonging to 2 different groups, one that included Escherichia; Shigella and Salmonella and the other Klebsiella; Enterobacter; and others. The predominant LAB at both companies were Enterococcus faecalis and E. gallinarum, confirmed by sequencing the 16S ribosomal RNA (rRNA) gene of colonies picked from lactobacilli agar plate counts. The predominant fungi were Aspergillus niger and Saccharomyces cerevisiae, with Candida sake or Alterneria sp. in some samples of Company A. Archaeal sequences were detected only in a single poult from Company B. The initial gastrointestinal colonizers of poults vary across company and time, signifying a strong environmental effect on microbiota acquisition. There was an indication of maternal effects in certain breeder flocks from Company B. Further work is necessary to determine how this variability affects microbiota succession and impacts growth and production of the birds.
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Affiliation(s)
| | - T G Rehberger
- Arm and Hammer Animal Nutrition, W227 N752 Westmound Dr., Waukesha, WI 53186
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158
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Yoshida S, Ide K, Takeuchi M, Kawakami K. Prenatal and early-life antibiotic use and risk of childhood asthma: A retrospective cohort study. Pediatr Allergy Immunol 2018; 29:490-495. [PMID: 29604125 DOI: 10.1111/pai.12902] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/26/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND Although associations between antibiotic exposure in infants and asthma development are reported, few studies have examined the effects of prenatal exposure to antibiotics. We evaluated this association considering the antibiotic types using a large-scale claim database in Japan. METHODS This retrospective study using health insurance administrative claim data in Japan included children born between January 2005 and September 2014. We constructed 2 cohorts: initial cohort, with information on children's mothers, and sibling cohort, with at least one sibling. Cox proportional hazard regression and sibling-matched cohort analyses were performed to determine the association between exposure to antibiotics in utero or the first year of life and asthma development until age 6. RESULTS In the initial cohort, antibiotic exposure during the foetal period was associated with early asthma development (until age 3; HR: 1.18, 95% CI: 1.08-1.30). However, this association disappeared after 3 years. The association between antibiotic exposure in the first year of life and asthma was stronger in early (HR: 2.43, 95% CI: 2.20-2.69) than later (HR: 1.23, 95% CI: 1.11-1.36) life. In the sibling cohort, we observed positive associations between foetal exposure and asthma by adjusting for familial factors (HR: 1.34, 95% CI: 1.05-1.72), which remained during the first year of life (HR: 1.62, 95% CI: 1.27-2.07). CONCLUSIONS Exposure to antibiotics during the first year of life was associated with childhood asthma even after adjusting for familial factors. However, a weak association was observed between prenatal antibiotic exposure and asthma development.
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Affiliation(s)
- Satomi Yoshida
- Department of Pharmacoepidemiology, Graduate School of Medicine and Public Health, Kyoto University, Kyoto, Japan
| | - Kazuki Ide
- Department of Pharmacoepidemiology, Graduate School of Medicine and Public Health, Kyoto University, Kyoto, Japan
| | - Masato Takeuchi
- Department of Pharmacoepidemiology, Graduate School of Medicine and Public Health, Kyoto University, Kyoto, Japan
| | - Koji Kawakami
- Department of Pharmacoepidemiology, Graduate School of Medicine and Public Health, Kyoto University, Kyoto, Japan
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159
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Fu L, Qiu Y, Shen L, Cui C, Wang S, Wang S, Xie Y, Zhao X, Gao X, Ning G, Nie A, Gu Y. The delayed effects of antibiotics in type 2 diabetes, friend or foe? J Endocrinol 2018; 238:137-149. [PMID: 29929986 DOI: 10.1530/joe-17-0709] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 05/31/2018] [Indexed: 12/26/2022]
Abstract
An increasing amount of evidence suggests that the delayed effect of antibiotics (abx) on gut microbiota after its cessation is not as favorable as its immediate effect on host metabolism. However, it is not known how the diverse abx-dependent metabolic effects influence diabetic subjects and how gut microbiota is involved. Here, we treated db/db mice with abx cocktail for 12 days and discontinued for 24 days. We found that db/db mice showed decreased body weight and blood glucose after abx treatment, which rapidly caught up after abx cessation. Twenty-four days after abx withdrawal, db/db mice exhibit increased plasma, hepatic total cholesterol (TC) levels and liver weight. The gut microbiota composition at that time showed decreased relative abundances (RAs) of Desulfovibrionaceae and Rikenellaceae, increased RA of Erysipelotrichaceae and Mogibacteriaceae, which were correlating with the reduced short-chain fatty acids (SCFAs) in gut content, such as propionic acid and valeric acid and with the elevated fecal taurine-conjugated bile acids (BAs) levels. The molecular biology studies showed inhibited hepatic BA synthesis from cholesterol, impeded intracellular transportation and biliary excretion of cholesterol that all conferred to liver TC accumulation. The associations among alterations of gut microbiota composition, microbial metabolite profiles and host phenotypes suggested the existence of gut microbiota-linked mechanisms that mediate the unfavorable delayed effects of abx on db/db mice cholesterol metabolism. Thus, we call upon the caution of applying abx in diabetic animal models for studying microbiota-host interaction and in type 2 diabetes subjects for preventing chronic cardiovascular consequences.
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Affiliation(s)
- Lihong Fu
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yixuan Qiu
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Linyan Shen
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Endocrinology, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Canqi Cui
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Shujie Wang
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Xie
- Department of Cardiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xinjie Zhao
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Xianfu Gao
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guang Ning
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Aifang Nie
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanyun Gu
- Shanghai National Research Center for Endocrine and Metabolic Diseases, Shanghai Institute for Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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160
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Zhang XS, Li J, Krautkramer KA, Badri M, Battaglia T, Borbet TC, Koh H, Ng S, Sibley RA, Li Y, Pathmasiri W, Jindal S, Shields-Cutler RR, Hillmann B, Al-Ghalith GA, Ruiz VE, Livanos A, van 't Wout AB, Nagalingam N, Rogers AB, Sumner SJ, Knights D, Denu JM, Li H, Ruggles KV, Bonneau R, Williamson RA, Rauch M, Blaser MJ. Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. eLife 2018; 7:37816. [PMID: 30039798 PMCID: PMC6085123 DOI: 10.7554/elife.37816] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/12/2018] [Indexed: 12/18/2022] Open
Abstract
The early-life intestinal microbiota plays a key role in shaping host immune system development. We found that a single early-life antibiotic course (1PAT) accelerated type 1 diabetes (T1D) development in male NOD mice. The single course had deep and persistent effects on the intestinal microbiome, leading to altered cecal, hepatic, and serum metabolites. The exposure elicited sex-specific effects on chromatin states in the ileum and liver and perturbed ileal gene expression, altering normal maturational patterns. The global signature changes included specific genes controlling both innate and adaptive immunity. Microbiome analysis revealed four taxa each that potentially protect against or accelerate T1D onset, that were linked in a network model to specific differences in ileal gene expression. This simplified animal model reveals multiple potential pathways to understand pathogenesis by which early-life gut microbiome perturbations alter a global suite of intestinal responses, contributing to the accelerated and enhanced T1D development.
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Affiliation(s)
- Xue-Song Zhang
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Jackie Li
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Kimberly A Krautkramer
- Department of Biomolecular Chemistry, Wisconsin Institute for Discovery, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Michelle Badri
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States.,Center for Data Science, New York University, New York, United States
| | - Thomas Battaglia
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Timothy C Borbet
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Hyunwook Koh
- Department of Population Health, New York University Langone Medical Center, New York, United States
| | - Sandy Ng
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Rachel A Sibley
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Yuanyuan Li
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Wimal Pathmasiri
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Shawn Jindal
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Robin R Shields-Cutler
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Ben Hillmann
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Gabriel A Al-Ghalith
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - Victoria E Ruiz
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Alexandra Livanos
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Angélique B van 't Wout
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Nabeetha Nagalingam
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Arlin B Rogers
- Department of Biomedical Sciences, Cummings School of Veterinary Medicine, Tufts University, North Grafton, United States
| | - Susan Jenkins Sumner
- Nutrition Research Institute, University of North Carolina at Chapel Hill School of Public Health, Kannapolis, United States
| | - Dan Knights
- Computer Science and Engineering, BioTechnology Institute, University of Minnesota, St. Paul, United States
| | - John M Denu
- Department of Biomolecular Chemistry, Wisconsin Institute for Discovery, University of Wisconsin School of Medicine and Public Health, Madison, United States
| | - Huilin Li
- Department of Population Health, New York University Langone Medical Center, New York, United States
| | - Kelly V Ruggles
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States
| | - Richard Bonneau
- Center for Data Science, New York University, New York, United States
| | - R Anthony Williamson
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Marcus Rauch
- Janssen Prevention Center London, Janssen Pharmaceutical Companies of Johnson and Johnson, London, United Kingdom
| | - Martin J Blaser
- Department of Medicine, New York University Langone Medical Center, New York, United States.,Human Microbiome Program, New York University Langone Medical Center, New York, United States.,Department of Microbiology, New York Uniersity Langone Medical Center, New York, United States
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161
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Hu J, Koh H, He L, Liu M, Blaser MJ, Li H. A two-stage microbial association mapping framework with advanced FDR control. MICROBIOME 2018; 6:131. [PMID: 30045760 PMCID: PMC6060480 DOI: 10.1186/s40168-018-0517-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 07/11/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND In microbiome studies, it is important to detect taxa which are associated with pathological outcomes at the lowest definable taxonomic rank, such as genus or species. Traditionally, taxa at the target rank are tested for individual association, followed by the Benjamini-Hochberg (BH) procedure to control for false discovery rate (FDR). However, this approach neglects the dependence structure among taxa and may lead to conservative results. The taxonomic tree of microbiome data represents alignment from phylum to species rank and characterizes evolutionary relationships across microbial taxa. Taxa that are closer on the tree usually have similar responses to the exposure (environment). The statistical power in microbial association tests can be enhanced by efficiently employing the prior evolutionary information via the taxonomic tree. METHODS We propose a two-stage microbial association mapping framework (massMap) which uses grouping information from the taxonomic tree to strengthen statistical power in association tests at the target rank. massMap first screens the association of taxonomic groups at a pre-selected higher taxonomic rank using a powerful microbial group test OMiAT. The method then proceeds to test the association for each candidate taxon at the target rank within the significant taxonomic groups identified in the first stage. Hierarchical BH (HBH) and selected subset testing (SST) procedures are evaluated to control the FDR for the two-stage structured tests. RESULTS Our simulations show that massMap incorporating OMiAT and the advanced FDR controlling methodologies largely alleviates the multiplicity issue. It is statistically more powerful than the traditional association mapping directly at the target rank while controlling the FDR at desired levels under most scenarios. In our real data analyses, massMap detects more or the same amount of associated species with smaller adjusted p values compared to the traditional method, which further illustrates the efficiency of the proposed framework. The R package of massMap is publicly available at https://sites.google.com/site/huilinli09/software and https://github.com/JiyuanHu/ . CONCLUSIONS massMap is a novel microbial association mapping framework and achieves additional efficiency by utilizing the intrinsic taxonomic structure of microbiome data.
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Affiliation(s)
- Jiyuan Hu
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016 USA
- Shanghai Center for Mathematical Sciences, Fudan University, Shanghai, 200433 China
| | - Hyunwook Koh
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016 USA
| | - Linchen He
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016 USA
| | - Menghan Liu
- Department of Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Martin J. Blaser
- Department of Medicine, New York University School of Medicine, New York, NY 10016 USA
| | - Huilin Li
- Division of Biostatistics, Department of Population Health, New York University School of Medicine, New York, NY 10016 USA
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162
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Ribado JV, Ley C, Haggerty TD, Tkachenko E, Bhatt AS, Parsonnet J. Household triclosan and triclocarban effects on the infant and maternal microbiome. EMBO Mol Med 2018; 9:1732-1741. [PMID: 29030459 PMCID: PMC5709730 DOI: 10.15252/emmm.201707882] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In 2016, the US Food and Drug Administration banned the use of specific microbicides in some household and personal wash products due to concerns that these chemicals might induce antibiotic resistance or disrupt human microbial communities. Triclosan and triclocarban (referred to as TCs) are the most common antimicrobials in household and personal care products, but the extent to which TC exposure perturbs microbial communities in humans, particularly during infant development, was unknown. We conducted a randomized intervention of TC‐containing household and personal care products during the first year following birth to characterize whether TC exposure from wash products perturbs microbial communities in mothers and their infants. Longitudinal survey of the gut microbiota using 16S ribosomal RNA amplicon sequencing showed that TC exposure from wash products did not induce global reconstruction or loss of microbial diversity of either infant or maternal gut microbiotas. Broadly antibiotic‐resistant species from the phylum Proteobacteria, however, were enriched in stool samples from mothers in TC households after the introduction of triclosan‐containing toothpaste. When compared by urinary triclosan level, agnostic to treatment arm, infants with higher triclosan levels also showed an enrichment of Proteobacteria species. Despite the minimal effects of TC exposure from wash products on the gut microbial community of infants and adults, detected taxonomic differences highlight the need for consumer safety testing of antimicrobial self‐care products on the human microbiome and on antibiotic resistance.
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Affiliation(s)
| | - Catherine Ley
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Thomas D Haggerty
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ekaterina Tkachenko
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA .,Division of Hematology, Department of Medicine, Stanford University, Stanford, CA, USA
| | - Julie Parsonnet
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, CA, USA .,Division of Epidemiology, Department of Health Research and Policy, Stanford University, Stanford, CA, USA
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163
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Nyangahu DD, Lennard KS, Brown BP, Darby MG, Wendoh JM, Havyarimana E, Smith P, Butcher J, Stintzi A, Mulder N, Horsnell W, Jaspan HB. Disruption of maternal gut microbiota during gestation alters offspring microbiota and immunity. MICROBIOME 2018; 6:124. [PMID: 29981583 PMCID: PMC6035804 DOI: 10.1186/s40168-018-0511-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 07/02/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Early life microbiota is an important determinant of immune and metabolic development and may have lasting consequences. The maternal gut microbiota during pregnancy or breastfeeding is important for defining infant gut microbiota. We hypothesized that maternal gut microbiota during pregnancy and breastfeeding is a critical determinant of infant immunity. To test this, pregnant BALB/c dams were fed vancomycin for 5 days prior to delivery (gestation; Mg), 14 days postpartum during nursing (Mn), or during gestation and nursing (Mgn), or no vancomycin (Mc). We analyzed adaptive immunity and gut microbiota in dams and pups at various times after delivery. RESULTS In addition to direct alterations to maternal gut microbial composition, pup gut microbiota displayed lower α-diversity and distinct community clusters according to timing of maternal vancomycin. Vancomycin was undetectable in maternal and offspring sera, therefore the observed changes in the microbiota of stomach contents (as a proxy for breastmilk) and pup gut signify an indirect mechanism through which maternal intestinal microbiota influences extra-intestinal and neonatal commensal colonization. These effects on microbiota influenced both maternal and offspring immunity. Maternal immunity was altered, as demonstrated by significantly higher levels of both total IgG and IgM in Mgn and Mn breastmilk when compared to Mc. In pups, lymphocyte numbers in the spleens of Pg and Pn were significantly increased compared to Pc. This increase in cellularity was in part attributable to elevated numbers of both CD4+ T cells and B cells, most notable Follicular B cells. CONCLUSION Our results indicate that perturbations to maternal gut microbiota dictate neonatal adaptive immunity.
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Affiliation(s)
- Donald D Nyangahu
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Division of Immunology, University of Cape Town, Cape Town, South Africa
- Present Address: Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Katie S Lennard
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Division of Computational Biology, University of Cape Town, Cape Town, South Africa
| | - Bryan P Brown
- Duke University, Durham, NC, USA
- Present Address: Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Matthew G Darby
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Jerome M Wendoh
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Enock Havyarimana
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Peter Smith
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - James Butcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ontario, CA, USA
| | - Alain Stintzi
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ontario, CA, USA
| | - Nicola Mulder
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Division of Computational Biology, University of Cape Town, Cape Town, South Africa
| | - William Horsnell
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Division of Immunology, University of Cape Town, Cape Town, South Africa
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
- Laboratory of Molecular and Experimental Immunology and Neurogenetics, UMR 7355, CNRS-University of Orleans and Le Studium Institute for Advanced Studies, Rue Dupanloup, 45000, Orléans, France
| | - Heather B Jaspan
- Institute of Infectious Diseases and Molecular Medicine, Department of Pathology, Division of Immunology, University of Cape Town, Cape Town, South Africa.
- Department of Pediatrics and Global Health, University of Washington and Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, USA.
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164
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Roca-Saavedra P, Rodriguez JA, Lamas A, Miranda JM, Nebot C, Cardelle-Cobas A, Franco CM, Cepeda A. Low-dosage antibiotic intake can disturb gut microbiota in mice. CYTA - JOURNAL OF FOOD 2018. [DOI: 10.1080/19476337.2018.1474264] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Paula Roca-Saavedra
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jose A. Rodriguez
- Área Académica de Química, Universidad Autónoma del Estado de Hidalgo, Pachuca, México
| | - Alexandre Lamas
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jose Manuel Miranda
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, Lugo, Spain
| | - Carolina Nebot
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, Lugo, Spain
| | - Alejandra Cardelle-Cobas
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, Lugo, Spain
| | - Carlos M. Franco
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, Lugo, Spain
| | - Alberto Cepeda
- Laboratorio de Higiene Inspección y Control de Alimentos. Dpto. de Química Analítica, Nutrición y Bromatología, Universidade de Santiago de Compostela, Lugo, Spain
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165
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The Microbiome and Metabolome of Preterm Infant Stool Are Personalized and Not Driven by Health Outcomes, Including Necrotizing Enterocolitis and Late-Onset Sepsis. mSphere 2018; 3:3/3/e00104-18. [PMID: 29875143 PMCID: PMC5990886 DOI: 10.1128/msphere.00104-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/17/2018] [Indexed: 01/28/2023] Open
Abstract
Preterm infants face health problems likely related to microbial exposures, including sepsis and necrotizing enterocolitis. However, the role of the gut microbiome in preterm infant health is poorly understood. Microbial colonization differs from that of healthy term babies because it occurs in the NICU and is often perturbed by antibiotics. We measured bacterial compositions and metabolomic profiles of 77 fecal samples from 32 preterm infants to investigate the differences between microbiomes in health and disease. Rather than finding microbial signatures of disease, we found that both the preterm infant microbiome and the metabolome were personalized and that the preterm infant gut microbiome is enriched in microbes that commonly dominate in the presence of antibiotics. These results contribute to the growing knowledge of the preterm infant microbiome and emphasize that a personalized view will be important to disentangle the health consequences of the preterm infant microbiome. The assembly and development of the gut microbiome in infants have important consequences for immediate and long-term health. Preterm infants represent an abnormal case for bacterial colonization because of early exposure to bacteria and frequent use of antibiotics. To better understand the assembly of the gut microbiota in preterm infants, fecal samples were collected from 32 very low birth weight preterm infants over the first 6 weeks of life. Infant health outcomes included health, late-onset sepsis, and necrotizing enterocolitis (NEC). We characterized bacterial compositions by 16S rRNA gene sequencing and metabolomes by untargeted gas chromatography-mass spectrometry. Preterm infant fecal samples lacked beneficial Bifidobacterium spp. and were dominated by Enterobacteriaceae, Enterococcus, and Staphylococcus organisms due to nearly uniform antibiotic administration. Most of the variance between the microbial community compositions could be attributed to the baby from which the sample derived (permutational multivariate analysis of variance [PERMANOVA] R2 = 0.48, P < 0.001), while clinical status (health, NEC, or late-onset sepsis) and overlapping times in the neonatal intensive care unit (NICU) did not explain a significant amount of variation in bacterial composition. Fecal metabolomes were also found to be unique to the individual (PERMANOVA R2 = 0.43, P < 0.001) and weakly associated with bacterial composition (Mantel statistic r = 0.23 ± 0.05, P < 0.05). No measured metabolites were found to be associated with necrotizing enterocolitis, late-onset sepsis, or a healthy outcome. Overall, preterm infant gut microbial communities were personalized and reflected antibiotic usage. IMPORTANCE Preterm infants face health problems likely related to microbial exposures, including sepsis and necrotizing enterocolitis. However, the role of the gut microbiome in preterm infant health is poorly understood. Microbial colonization differs from that of healthy term babies because it occurs in the NICU and is often perturbed by antibiotics. We measured bacterial compositions and metabolomic profiles of 77 fecal samples from 32 preterm infants to investigate the differences between microbiomes in health and disease. Rather than finding microbial signatures of disease, we found that both the preterm infant microbiome and the metabolome were personalized and that the preterm infant gut microbiome is enriched in microbes that commonly dominate in the presence of antibiotics. These results contribute to the growing knowledge of the preterm infant microbiome and emphasize that a personalized view will be important to disentangle the health consequences of the preterm infant microbiome.
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166
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Cignarella F, Cantoni C, Ghezzi L, Salter A, Dorsett Y, Chen L, Phillips D, Weinstock GM, Fontana L, Cross AH, Zhou Y, Piccio L. Intermittent Fasting Confers Protection in CNS Autoimmunity by Altering the Gut Microbiota. Cell Metab 2018; 27:1222-1235.e6. [PMID: 29874567 PMCID: PMC6460288 DOI: 10.1016/j.cmet.2018.05.006] [Citation(s) in RCA: 327] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 12/15/2017] [Accepted: 05/03/2018] [Indexed: 12/29/2022]
Abstract
Multiple sclerosis (MS) is more common in western countries with diet being a potential contributing factor. Here we show that intermittent fasting (IF) ameliorated clinical course and pathology of the MS model, experimental autoimmune encephalomyelitis (EAE). IF led to increased gut bacteria richness, enrichment of the Lactobacillaceae, Bacteroidaceae, and Prevotellaceae families and enhanced antioxidative microbial metabolic pathways. IF altered T cells in the gut with a reduction of IL-17 producing T cells and an increase in regulatory T cells. Fecal microbiome transplantation from mice on IF ameliorated EAE in immunized recipient mice on a normal diet, suggesting that IF effects are at least partially mediated by the gut flora. In a pilot clinical trial in MS patients, intermittent energy restriction altered blood adipokines and the gut flora resembling protective changes observed in mice. In conclusion, IF has potent immunomodulatory effects that are at least partially mediated by the gut microbiome.
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Affiliation(s)
- Francesca Cignarella
- Department of Neurology, Washington University School of Medicine, Campus Box 8111, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Claudia Cantoni
- Department of Neurology, Washington University School of Medicine, Campus Box 8111, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Laura Ghezzi
- Department of Neurology, Washington University School of Medicine, Campus Box 8111, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Neurology Unit, Department of Pathophysiology and Transplantation, University of Milan, Fondazione Cà Granda, IRCCS Ospedale Policlinico, Milan, Italy
| | - Amber Salter
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yair Dorsett
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Lei Chen
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Daniel Phillips
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Luigi Fontana
- Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Department of Clinical and Experimental Sciences, Brescia University Medical School, Brescia, Italy; CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Anne H Cross
- Department of Neurology, Washington University School of Medicine, Campus Box 8111, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA
| | - Yanjiao Zhou
- Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
| | - Laura Piccio
- Department of Neurology, Washington University School of Medicine, Campus Box 8111, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Hope Center for Neurological Disorders, Washington University School of Medicine, St Louis, MO, USA.
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167
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Torres MDT, Silva AF, Pedron CN, Capurro ML, de la Fuente‐Nunez C, Junior VXO. Peptide Design Enables Reengineering of an Inactive Wasp Venom Peptide into Synthetic Antiplasmodial Agents. ChemistrySelect 2018. [DOI: 10.1002/slct.201800529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Marcelo D. T. Torres
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABC
- Synthetic Biology Group
- Research Laboratory of Electronics
- Department of Biological Engineering and Department of Electrical Engineering and Computer ScienceMassachusetts Institute of TechnologyCambridge, MassachusettsUnited States of America
- Broad Institute of MIT and Harvard, Cambridge, MassachusettsUnited States of America
| | - Adriana F. Silva
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABC
| | - Cibele N. Pedron
- Centro de Ciências Naturais e HumanasUniversidade Federal do ABC
| | | | - Cesar de la Fuente‐Nunez
- Synthetic Biology Group
- Research Laboratory of Electronics
- Department of Biological Engineering and Department of Electrical Engineering and Computer ScienceMassachusetts Institute of TechnologyCambridge, MassachusettsUnited States of America
- Broad Institute of MIT and Harvard, Cambridge, MassachusettsUnited States of America
- The Center for Microbiome Informatics and Therapeutics, Cambridge, Massachusetts, United States of America
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168
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Probiotic Lactobacillus Paracasei Expressing a Nucleic Acid-Hydrolyzing Minibody (3D8 Scfv) Enhances Probiotic Activities in Mice Intestine as Revealed by Metagenomic Analyses. Genes (Basel) 2018; 9:genes9060276. [PMID: 29844265 PMCID: PMC6027128 DOI: 10.3390/genes9060276] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 05/17/2018] [Accepted: 05/17/2018] [Indexed: 01/13/2023] Open
Abstract
Probiotics are well known for their beneficial effects for animals, including humans and livestock. Here, we tested the probiotic activity of Lactobacillus paracasei expressing 3D8 scFv, a nucleic acid-hydrolyzing mini-antibody, in mice intestine. A total of 18 fecal samples derived from three different conditions at two different time points were subjected to high-throughput 16S ribosomal RNA (rRNA) metagenomic analyses. Bioinformatic analyses identified an average of 290 operational taxonomic units. After administration of L. paracasei, populations of the probiotics L. paracasei, Lactobacillus reuteri, and Pediococcus acidilactici increased, whereas the population of harmful bacteria such as Helicobacter species decreased. Furthermore, continuous administration of L. paracasei resulted in L. paracasei emerging as the dominant probiotic after competition with other existing probiotics. Expression of 3D8 scFv protein specifically increased the population of P. acidilactici, which is another probiotic. In summary, our results showed that L. paracasei expressing 3D8 scFv protein enhanced probiotic activity in mice intestine with no observable side effects. Thus, the system developed in this study may be a good tool for the expression of recombinant protein using probiotics.
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169
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Yoon H, Schaubeck M, Lagkouvardos I, Blesl A, Heinzlmeir S, Hahne H, Clavel T, Panda S, Ludwig C, Kuster B, Manichanh C, Kump P, Haller D, Hörmannsperger G. Increased Pancreatic Protease Activity in Response to Antibiotics Impairs Gut Barrier and Triggers Colitis. Cell Mol Gastroenterol Hepatol 2018; 6:370-388.e3. [PMID: 30182050 PMCID: PMC6121113 DOI: 10.1016/j.jcmgh.2018.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/15/2018] [Indexed: 12/19/2022]
Abstract
Background & Aims Antibiotic (ABx) therapy is associated with increased risk for Crohn's disease but underlying mechanisms are unknown. We observed high fecal serine protease activity (PA) to be a frequent side effect of ABx therapy. The aim of the present study was to unravel whether this rise in large intestinal PA may promote colitis development via detrimental effects on the large intestinal barrier. Methods Transwell experiments were used to assess the impact of high PA in ABx-treated patients or vancomycin/metronidazole-treated mice on the epithelial barrier. Serine protease profiling was performed using liquid chromatography-mass spectrometry/mass spectrometry analysis. The impact of high large intestinal PA on the intestinal barrier in wild-type and interleukin (IL)10-/- mice and on colitis development in IL10-/- mice was investigated using vancomycin/metronidazole with or without oral serine protease inhibitor (AEBSF) treatment. Results The ABx-induced, high large intestinal PA was caused by significantly increased levels of pancreatic proteases and impaired epithelial barrier integrity. In wild-type mice, the rise in PA caused a transient increase in intestinal permeability but did not affect susceptibility to chemically induced acute colitis. In IL10-/- mice, increased PA caused a consistent impairment of the intestinal barrier associated with inflammatory activation in the large intestinal tissue. In the long term, the vancomycin/metronidazole-induced lasting increase in PA aggravated colitis development in IL10-/- mice. Conclusions High large intestinal PA is a frequent adverse effect of ABx therapy, which is detrimental to the large intestinal barrier and may contribute to the development of chronic intestinal inflammation in susceptible individuals.
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Key Words
- ABx, antibiotics
- AEBSF, 4-(2-aminoethyl) benzenesulfonyl fluoride hydrochloride
- DSS, dextran sulfate sodium
- Epithelial Barrier
- GF, germ-free
- Gut Microbiota
- IBD, inflammatory bowel diseases
- IL, interleukin
- Inflammatory Bowel Diseases
- LC-MS/MS, liquid chromatography–mass spectrometry/mass spectrometry
- PA, protease activity
- PBS, phosphate-buffered saline
- PMSF, phenylmethane-sulfonylfluoride
- SPF, specific pathogen-free
- Serine Proteases
- TEER, transepithelial electrical resistance
- V/M, vancomycin/metronidazole
- WT, wild-type
- cecal-sup, cecal-supernatants
- ctr, control
- stool-sup, stool-supernatants
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Affiliation(s)
- Hongsup Yoon
- Technische Universität München, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
| | - Monika Schaubeck
- Max Planck Institute of Neurobiology, Department of Neuroimmunology, Martinsried, Germany
| | - Ilias Lagkouvardos
- Technische Universität München, Junior Research Group Microbial Bioinformatics, ZIEL – Institute for Food and Health, Freising-Weihenstephan, Germany
- Technische Universität München, ZIEL – Institute for Food & Health, Freising-Weihenstephan, Germany
| | - Andreas Blesl
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Stephanie Heinzlmeir
- Technische Universität München, Chair of Proteomics and Bioanalytics, Freising-Weihenstephan, Germany
- Technische Universität München, Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising-Weihenstephan, Germany
| | - Hannes Hahne
- Technische Universität München, Chair of Proteomics and Bioanalytics, Freising-Weihenstephan, Germany
- OmicScouts GmbH, Freising, Germany
| | - Thomas Clavel
- Technische Universität München, ZIEL – Institute for Food & Health, Freising-Weihenstephan, Germany
- RWTH University Hospital, Institute of Medical Microbiology, Functional Microbiome Research Group, Aachen, Germany
| | - Suchita Panda
- Vall d'Hebron Research Institute, Digestive Research Unit, Barcelona, Spain
| | - Christina Ludwig
- Technische Universität München, Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising-Weihenstephan, Germany
| | - Bernhard Kuster
- Technische Universität München, Chair of Proteomics and Bioanalytics, Freising-Weihenstephan, Germany
- Technische Universität München, Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Freising-Weihenstephan, Germany
| | | | - Patrizia Kump
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Dirk Haller
- Technische Universität München, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
- Technische Universität München, ZIEL – Institute for Food & Health, Freising-Weihenstephan, Germany
| | - Gabriele Hörmannsperger
- Technische Universität München, Chair of Nutrition and Immunology, Freising-Weihenstephan, Germany
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170
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van de Guchte M, Blottière HM, Doré J. Humans as holobionts: implications for prevention and therapy. MICROBIOME 2018; 6:81. [PMID: 29716650 PMCID: PMC5928587 DOI: 10.1186/s40168-018-0466-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/23/2018] [Indexed: 05/27/2023]
Abstract
The human gut microbiota is increasingly recognized for its important or even decisive role in health. As it becomes clear that microbiota and host mutually affect and depend on each other in an intimate relationship, a holistic view of the gut microbiota-host association imposes itself. Ideally, a stable state of equilibrium, homeostasis, is maintained and serves health, but signs are that perturbation of this equilibrium beyond the limits of resilience can propel the system into an alternative stable state, a pre-disease state, more susceptible to the development of chronic diseases. The microbiota-host equilibrium of a large and growing proportion of individuals in Western society may represent such a pre-disease state and explain the explosive development of chronic diseases such as inflammatory bowel disease, obesity, and other inflammatory diseases. These diseases themselves represent other alternative stable states again and are therefore hard to cure. The holistic view of the microbiota-host association where feedback loops between microbiota and host are thought to maintain the system in a stable state-be it a healthy, pre-disease, or disease state-implies that integrated approaches, addressing host processes and microbiota, should be used to treat or prevent (pre-)disease.
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Affiliation(s)
- Maarten van de Guchte
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
| | - Hervé M Blottière
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- MetaGenoPolis, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Joël Doré
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- MetaGenoPolis, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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171
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Abstract
PURPOSE OF REVIEW This review focuses on the recent discoveries about the impact of intestinal microbiota on mammalian host juvenile growth. RECENT FINDINGS Intestinal microbiota is a powerful modulator of many facets of multicellular host's physiology. Recent results from human field studies and animal research have clearly shown that not only the nutrition, but also the intestinal microbiota impacts host postnatal growth kinetics. Absence of microbiome leads to stunted growth in mammalian gnotobiotic models and changes in the composition of the intestinal microbiota can impact the postnatal growth kinetics both positively and negatively under normal nutritional conditions as well as in undernutrition. Strikingly, specific bacterial strains are able to interact with GH/IGF-1 somatotropic axis activity, thus directly impacting host juvenile development. SUMMARY Intestinal microbiota dictates the pace of host postnatal growth. This newly described role envisages that therapy with specific bacterial strains, together with re-nutritional strategies, might successfully alleviate the long-term sequelae of undernutrition during childhood in humans.
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Affiliation(s)
- Martin Schwarzer
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Novy Hradek, Czech Republic
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172
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Hsu E, Pacifici R. From Osteoimmunology to Osteomicrobiology: How the Microbiota and the Immune System Regulate Bone. Calcif Tissue Int 2018; 102:512-521. [PMID: 29018933 PMCID: PMC5893441 DOI: 10.1007/s00223-017-0321-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/05/2017] [Indexed: 12/13/2022]
Abstract
Osteomicrobiology refers to the role of microbiota in bone health and the mechanisms by which the microbiota regulates post-natal skeletal development, bone aging, and pathologic bone loss. Here, we review recent reports linking gut microbiota to changes in bone phenotype. A pro-inflammatory cytokine milieu drives bone resorption in conditions such as sex steroid hormone deficiency. The response of the immune system to activation by the microbiome results in increased circulating osteoclastogenic cytokines in a T cell-dependent mechanism. Additionally, gut microbiota affect bone homeostasis through nutrient absorption, mediation of the IGF-1 pathway, and short chain fatty acid and metabolic products. Manipulation of microbiota through prebiotics or probiotics reduces inflammatory cytokine production, leading to changes in bone density. One mechanism of probiotic action is through upregulating tight junction proteins, increasing the strength of the gut epithelial layer, and leading to less antigen presentation and less activation of intestinal immune cells. Thus, prebiotics or probiotics may represent a future therapeutic avenue for ameliorating the risk of postmenopausal bone loss in humans.
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Affiliation(s)
- Emory Hsu
- Division of Endocrinology, Metabolism and Lipids, Department of Medicine, Emory University, 101 Woodruff Circle, Room 1309, Atlanta, GA, 30322, USA
| | - Roberto Pacifici
- Division of Endocrinology, Metabolism and Lipids, Department of Medicine, Emory University, 101 Woodruff Circle, Room 1309, Atlanta, GA, 30322, USA.
- Immunology and Molecular Pathogenesis Program, Emory University, Atlanta, GA, USA.
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173
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Abstract
Exposed surfaces of mammals are colonized with 100 trillion indigenous bacteria, fungi, and viruses, creating a diverse ecosystem known as the microbiome. The gastrointestinal tract harbors the greatest numbers of these microorganisms, which regulate human nutrition, metabolism, and immune system function. Moreover, the intestinal microbiota contains pro- and anti-inflammatory products that modulate immune responses and may play a role in maintaining gut barrier function. Therefore, the community composition of the microbiota has profound effects on the immune status of the host and impacts the development and/or progression of inflammatory diseases. Accordingly, numerous studies have shown differences in the microbiota of patients with and without a given inflammatory condition. There is now strong evidence that the gut microbiome regulates bone homeostasis in health and disease, and that prebiotic and probiotics protect against bone loss. Herein, the evidence supporting the role of the microbiota and the effects of prebiotic and probiotics will be reviewed.
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Affiliation(s)
- Roberto Pacifici
- Division of Endocrinology, Metabolism and Lipids, Department of Medicine, and Immunology and Molecular Pathogenesis Program, Emory University, Atlanta, Georgia 30322
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174
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den Hartigh LJ, Gao Z, Goodspeed L, Wang S, Das AK, Burant CF, Chait A, Blaser MJ. Obese Mice Losing Weight Due to trans-10,cis-12 Conjugated Linoleic Acid Supplementation or Food Restriction Harbor Distinct Gut Microbiota. J Nutr 2018; 148:562-572. [PMID: 29659960 PMCID: PMC6251681 DOI: 10.1093/jn/nxy011] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 11/28/2017] [Accepted: 01/09/2018] [Indexed: 12/28/2022] Open
Abstract
Background trans-10,cis-12 Conjugated linoleic acid (t10,c12-CLA) is a dietary supplement that promotes weight loss by increasing fat oxidation and energy expenditure. We previously reported that in the absence of t10,c12-CLA, mice forced to lose equivalent body weight by food restriction (FR) do not exhibit increases in fat oxidation or energy expenditure but have improved glucose metabolism, consistent with FR as a metabolically healthy weight-loss method. Objective Because diet is a primary determinant of gut bacterial populations, we hypothesized that the disparate metabolic effects accompanying weight loss from t10,c12-CLA or FR could be related to altered intestinal microbiota. Methods Ten-week-old male LDL receptor-deficient (Ldlr-/-) mice were fed a high-fat, high-sucrose diet (HFHS; 36% lard fat, 36.2% sucrose + 0.15% cholesterol) for 12 wk (baseline), then switched to the HFHS diet alone (obese control), HFHS + 1% c9,t11-CLA (obese fatty acid control), HFHS + 1% t10,c12-CLA (weight-loss-inducing fatty acid), or HFHS + FR (weight-loss control group with 75-85% ad libitum HFHS food intake) for a further 8 wk. Fecal microbial content, short-chain fatty acids (butyrate, acetate), tissue CLA concentrations, and intestinal nutrient transporter expression were quantified. Results Mice fed t10,c12-CLA or assigned to FR lost 14.5% of baseline body weight. t10,c12-CLA-fed mice had elevated concentrations of fecal butyrate (2-fold) and plasma acetate (1.5-fold) compared with HFHS-fed controls. Fecal α diversity decreased by 7.6-14% in all groups. Butyrivibrio and Roseburia, butyrate-producing microbes, were enriched over time by t10,c12-CLA. By comparing with each control group, we also identified bacterial genera significantly enriched in the t10,c12-CLA recipients, including Lactobacillus, Actinobacteria, and the newly identified Ileibacterium valens of the Allobaculum genus, whereas other taxa were enriched by FR, including Clostridiales and Bacteroides. Conclusion Modalities resulting in equivalent weight loss but with divergent metabolic effects are associated with compositional differences in the mouse intestinal microbiota.
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Affiliation(s)
- Laura J den Hartigh
- Division of Metabolism, Endocrinology, and Nutrition, Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Zhan Gao
- Department of Medicine, New York University School of Medicine, New York, NY
| | - Leela Goodspeed
- Division of Metabolism, Endocrinology, and Nutrition, Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Shari Wang
- Division of Metabolism, Endocrinology, and Nutrition, Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Arun K Das
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | - Alan Chait
- Division of Metabolism, Endocrinology, and Nutrition, Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Martin J Blaser
- Department of Medicine, New York University School of Medicine, New York, NY
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175
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Abstract
The gut microbiota (GM) is the whole of commensal, symbiotic, and pathogenic microorganisms living in our intestine. The GM-host interactions contribute to the maturation of the host immune system, modulating its systemic response. It is well documented that GM can interact with non-enteral cells such as immune cells, dendritic cells, and hepatocytes, producing molecules such as short-chain fatty acids, indole derivatives, polyamines, and secondary bile acid. The receptors for some of these molecules are expressed on immune cells, and modulate the differentiation of T effector and regulatory cells: this is the reason why dysbiosis is correlated with several autoimmune, metabolic, and neurodegenerative diseases. Due to the close interplay between immune and bone cells, GM has a central role in maintaining bone health and influences bone turnover and density. GM can improve bone health also increasing calcium absorption and modulating the production of gut serotonin, a molecule that interacts with bone cells and has been suggested to act as a bone mass regulator. Thus, GM manipulation by consumption of antibiotics, changes in dietary habits, and the use of pre- and probiotics may affect bone health. This review summarizes evidences on the influence of GM on immune system and on bone turnover and density and how GM manipulation may influence bone health.
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Affiliation(s)
- P D'Amelio
- Gerontology and Bone Metabolic Diseases Section, Department of Medical Science, University of Torino, CorsoDogliotti 14, 10126, Turin, Italy.
| | - F Sassi
- Gerontology and Bone Metabolic Diseases Section, Department of Medical Science, University of Torino, CorsoDogliotti 14, 10126, Turin, Italy
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176
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Schwarzer M, Strigini M, Leulier F. Gut Microbiota and Host Juvenile Growth. Calcif Tissue Int 2018; 102:387-405. [PMID: 29214457 DOI: 10.1007/s00223-017-0368-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/18/2017] [Indexed: 02/07/2023]
Abstract
Good genes, good food, good friends. That is what parents hope will sustain and nurture the harmonious growth of their children. The impact of the genetic background and nutrition on postnatal growth has been in the spot light for long, but the good friends have come to the scene only recently. Among the good friends perhaps the most crucial ones are those that we are carrying within ourselves. They comprise the trillions of microbes that collectively constitute each individual's intestinal microbiota. Indeed, recent epidemiological and field studies in humans, supported by extensive experimental data on animal models, demonstrate a clear role of the intestinal microbiota on their host's juvenile growth, especially under suboptimal nutrient conditions. Genuinely integrative approaches applicable to invertebrate and vertebrate systems combine tools from genetics, developmental biology, microbiology, nutrition, and physiology to reveal how gut microbiota affects growth both positively and negatively, in healthy and pathological conditions. It appears that certain natural or engineered gut microbiota communities can positively impact insulin/IGF-1 and steroid hormone signaling, thus contributing to the host juvenile development and maturation.
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Affiliation(s)
- Martin Schwarzer
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, 69364, Lyon Cedex 07, France.
- Laboratory of Gnotobiology, Institute of Microbiology of the Czech Academy of Sciences, Nový Hrádek, Czech Republic.
| | - Maura Strigini
- INSERM, U1059, Sainbiose, Université de Lyon, Université Jean Monnet, Faculté de Médecine, Campus Santé Innovation, 42023, Saint-Étienne, France.
| | - François Leulier
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Université Claude Bernard Lyon 1, 69364, Lyon Cedex 07, France
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177
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Stiemsma LT, Michels KB. The Role of the Microbiome in the Developmental Origins of Health and Disease. Pediatrics 2018; 141:e20172437. [PMID: 29519955 PMCID: PMC5869344 DOI: 10.1542/peds.2017-2437] [Citation(s) in RCA: 211] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/29/2017] [Indexed: 12/15/2022] Open
Abstract
Although the prominent role of the microbiome in human health has been established, the early-life microbiome is now being recognized as a major influence on long-term human health and development. Variations in the composition and functional potential of the early-life microbiome are the result of lifestyle factors, such as mode of birth, breastfeeding, diet, and antibiotic usage. In addition, variations in the composition of the early-life microbiome have been associated with specific disease outcomes, such as asthma, obesity, and neurodevelopmental disorders. This points toward this bacterial consortium as a mediator between early lifestyle factors and health and disease. In addition, variations in the microbial intrauterine environment may predispose neonates to specific health outcomes later in life. A role of the microbiome in the Developmental Origins of Health and Disease is supported in this collective research. Highlighting the early-life critical window of susceptibility associated with microbiome development, we discuss infant microbial colonization, beginning with the maternal-to-fetal exchange of microbes in utero and up through the influence of breastfeeding in the first year of life. In addition, we review the available disease-specific evidence pointing toward the microbiome as a mechanistic mediator in the Developmental Origins of Health and Disease.
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Affiliation(s)
- Leah T Stiemsma
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
| | - Karin B Michels
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, California
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178
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Ji S, Jiang T, Yan H, Guo C, Liu J, Su H, Alugongo GM, Shi H, Wang Y, Cao Z, Li S. Ecological Restoration of Antibiotic-Disturbed Gastrointestinal Microbiota in Foregut and Hindgut of Cows. Front Cell Infect Microbiol 2018; 8:79. [PMID: 29594071 PMCID: PMC5859144 DOI: 10.3389/fcimb.2018.00079] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 02/27/2018] [Indexed: 12/28/2022] Open
Abstract
Antibiotically disturbed gastrointestinal microbiota needs a long period time to be restored to normal, which may cause a series of problems to the host. The understanding of restoration of the biased microbiota by antibiotics remains largely unknown. Here, we investigated the microbiota shift in foregut (rumen) and hindgut (rectum) of lactating cows after antibiotics exposure as well as after antibiotics withdrawal with (Microbiota transplantation, MT group) or without (Control, CON group) microbiota transplantation. We were able to demonstrate that microbiota in both foregut and hindgut significantly changed after 3 or 14 days of antibiotics exposure, and the changes persisted over long period of time (>18 days) after withdrawing the antibiotics. We further observed a faster restoration of microbiota in both foregut and hindgut of MT group than CON group, microbiota in foregut was mainly benefited from microbiota transplantation by restoring the alpha-diversity as well as within-group similarity, while microbiota in hindgut was primarily benefited from microbiota transplantation by reestablishing the co-occurrence network (nodes number, edges number, density, modularity as well as closeness centrality). These results together expanded our understanding of restoration of the biased microbiota by antibiotics, and may also be instructive to deal with the delayed microbiota restoration at least in cows.
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Affiliation(s)
- Shoukun Ji
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Tao Jiang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Laboratory of Animal Nutrition, College of Animal Science, Tarim University, Alar, China
| | - Hui Yan
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chunyan Guo
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Laboratory of Animal Nutrition, College of Animal Science and Technology, Shihezi University, Shihezi, China
| | - Jingjing Liu
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huawei Su
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Gibson M Alugongo
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Haitao Shi
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yajing Wang
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhijun Cao
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shengli Li
- State Key Laboratory of Animal Nutrition, Beijing Engineering Technology Research Center of Raw Milk Quality and Safety Control, College of Animal Science and Technology, China Agricultural University, Beijing, China
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179
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Obata F, Fons CO, Gould AP. Early-life exposure to low-dose oxidants can increase longevity via microbiome remodelling in Drosophila. Nat Commun 2018; 9:975. [PMID: 29515102 PMCID: PMC5841413 DOI: 10.1038/s41467-018-03070-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 01/16/2018] [Indexed: 02/07/2023] Open
Abstract
Environmental stresses experienced during development exert many long-term effects upon health and disease. For example, chemical oxidants or genetic perturbations that induce low levels of reactive oxygen species can extend lifespan in several species. In some cases, the beneficial effects of low-dose oxidants are attributed to adaptive protective mechanisms such as mitohormesis, which involve long-term increases in the expression of stress response genes. Here we show in Drosophila that transient exposure to low concentrations of oxidants during development leads to an extension of adult lifespan. Surprisingly, this depends upon oxidants acting in an antibiotic-like manner to selectively deplete the microbiome of Acetobacter proteobacteria. We demonstrate that the presence of Acetobacter species, such as A. aceti, in the indigenous microbiota increases age-related gut dysfunction and shortens lifespan. This study demonstrates that low-dose oxidant exposure during early life can extend lifespan via microbiome remodelling rather than mitohormesis.
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Affiliation(s)
- Fumiaki Obata
- Physiology and Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Genetics, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Clara O Fons
- Physiology and Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alex P Gould
- Physiology and Metabolism Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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180
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Xiong W, Wang Y, Sun Y, Ma L, Zeng Q, Jiang X, Li A, Zeng Z, Zhang T. Antibiotic-mediated changes in the fecal microbiome of broiler chickens define the incidence of antibiotic resistance genes. MICROBIOME 2018; 6:34. [PMID: 29439741 PMCID: PMC5811963 DOI: 10.1186/s40168-018-0419-2] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 01/30/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Antimicrobial agents have been widely used in animal farms to prevent and treat animal diseases and to promote growth. Antimicrobial agents may change the bacterial community and enhance the resistome in animal feces. We used metagenome-wide analysis to investigate the changes in bacterial community, variations in antibiotic resistance genes (ARGs), and their bacterial hosts in the feces of broiler chickens over a full-treatment course of chlortetracycline at low and therapeutic dose levels. RESULTS The effects of chlortetracycline on resistome were dependent on the specific ARG subtypes and not simply the overall community-level ARGs. Therapeutic dose of chlortetracycline promoted the abundance of tetracycline resistance genes (tetA and tetW) and inhibited multidrug resistance genes (mdtA, mdtC, mdtK, ompR, and TolC). The therapeutic dose of chlortetracycline led to loss of Proteobacteria mainly due to the decrease of Escherichia/Shigella (from 72 to 58%). Inhibition of Escherichia by chlortetracycline was the primary reason for the decrease of genes resistant to multiple drugs in the therapeutic dose group. The ARG host Bifidobacterium were enriched due to tetW harbored by Bifidobacterium under chlortetracycline treatment. Escherichia was always the major host for multidrug resistance genes, whereas the primary host was changed from Escherichia to Klebsiella for aminoglycoside resistance genes with the treatment of therapeutic dose of chlortetracycline. CONCLUSIONS We provided the first metagenomic insights into antibiotic-mediated alteration of ARG-harboring bacterial hosts at community-wide level in chicken feces. These results indicated that the changes in the structure of antibiotic-induced feces microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the feces microbiota. These findings will help to optimize therapeutic schemes for the effective treatment of antibiotic resistant pathogens in poultry farms. Resistome variations in faecal microbiome of chickens exposed to chlortetracycline.
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Affiliation(s)
- Wenguang Xiong
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yulin Wang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Liping Ma
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Qinglin Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Xiaotao Jiang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Andong Li
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
| | - Zhenling Zeng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs (SCAU) and Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, 483 Wushan Road, Guangzhou, 510642 China
| | - Tong Zhang
- Environmental Biotechnology Laboratory, The University of Hong Kong, Pokfulam Road, Hong Kong, China
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181
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Antibiotic treatment and stewardship in the era of microbiota-oriented diagnostics. Eur J Clin Microbiol Infect Dis 2018; 37:795-798. [PMID: 29411188 DOI: 10.1007/s10096-018-3198-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 01/20/2018] [Indexed: 12/22/2022]
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182
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Shi Y, Zhao X, Zhao J, Zhang H, Zhai Q, Narbad A, Chen W. A mixture of Lactobacillus species isolated from traditional fermented foods promote recovery from antibiotic-induced intestinal disruption in mice. J Appl Microbiol 2018; 124:842-854. [PMID: 29314490 DOI: 10.1111/jam.13687] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/30/2017] [Accepted: 12/12/2017] [Indexed: 12/18/2022]
Abstract
AIMS This study evaluated the antibiotic-induced changes in microbial ecology, intestinal dysbiosis and low-grade inflammation; and the combined effect of four different Lactobacillus species on recovery of microbiota composition and improvement of gut barrier function in mice. METHODS AND RESULTS Administration of the antibiotic ampicillin for 2 weeks decreased microbial community diversity, induced caecum tumefaction and increased gut permeability in mice. Application of a probiotic cocktail of four Lactobacillus species (JUP-Y4) modulated the microbiota community structure and promoted the abundance of potentially beneficial bacteria such as Akkermansia. Ampicillin administration led to a decline in Bacteroidetes from 46·6 ± 3·91% to 0·264 ± 0·0362%; the addition of JUP-Y4 restored this to 41·4 ± 2·87%. This probiotic supplementation was more effective than natural restoration, where the levels of Bacteroidetes were only restored to 29·3 ± 2·07%. Interestingly, JUP-Y4 treatment was more effective in the restoration of microbiota in faecal samples than in caecal samples. JUP-Y4 also significantly reduced the levels of d-lactate and endotoxin (lipopolysaccharide, LPS) in the serum of mice, and increased the expression of tight-junction proteins while reducing the production of inflammatory cytokines (TNF-α, IL-6, MCP-1, IFN-γ and IL-1β) in the ileum and the colon of antibiotic-treated mice. CONCLUSIONS JUP-Y4 not only promoted recovery from antibiotic-induced gut dysbiosis, but also enhanced the function of the gut barrier, reduced inflammation and lowered levels of circulating endotoxin in mice. SIGNIFICANCE AND IMPACT OF THE STUDY Consumption of a mixture of Lactobacillus species may encourage faster recovery from antibiotic-induced gut dysbiosis and gut microbiota-related immune disturbance.
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Affiliation(s)
- Y Shi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China
| | - X Zhao
- School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - J Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - H Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,National Engineering Research Centre for Functional Food, Wuxi, Jiangsu, China
| | - Q Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu, China.,National Engineering Research Centre for Functional Food, Wuxi, Jiangsu, China
| | - A Narbad
- UK-China Joint Centre on Probiotic Bacteria, Norwich, UK.,Gut Health and Food Safety Programme, Quadram Institute Bioscience, Norwich, UK
| | - W Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China.,National Engineering Research Centre for Functional Food, Wuxi, Jiangsu, China.,Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, China
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183
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Maturation of the gut microbiome and risk of asthma in childhood. Nat Commun 2018; 9:141. [PMID: 29321519 PMCID: PMC5762761 DOI: 10.1038/s41467-017-02573-2] [Citation(s) in RCA: 311] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 12/07/2017] [Indexed: 02/08/2023] Open
Abstract
The composition of the human gut microbiome matures within the first years of life. It has been hypothesized that microbial compositions in this period can cause immune dysregulations and potentially cause asthma. Here we show, by associating gut microbial composition from 16S rRNA gene amplicon sequencing during the first year of life with subsequent risk of asthma in 690 participants, that 1-year-old children with an immature microbial composition have an increased risk of asthma at age 5 years. This association is only apparent among children born to asthmatic mothers, suggesting that lacking microbial stimulation during the first year of life can trigger their inherited asthma risk. Conversely, adequate maturation of the gut microbiome in this period may protect these pre-disposed children. Colonization of commensal bacteria is thought to impact immune development, especially in the earliest years of life. Here, the authors show, by analyzing the development of the gut microbiome of 690 children, that microbial composition at the age of 1 year is associated with asthma diagnosed in the first 5 years of life.
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184
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Edwards MR, Walton RP, Jackson DJ, Feleszko W, Skevaki C, Jartti T, Makrinoti H, Nikonova A, Shilovskiy IP, Schwarze J, Johnston SL, Khaitov MR. The potential of anti-infectives and immunomodulators as therapies for asthma and asthma exacerbations. Allergy 2018; 73:50-63. [PMID: 28722755 PMCID: PMC7159495 DOI: 10.1111/all.13257] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2017] [Indexed: 12/30/2022]
Abstract
Asthma is responsible for approximately 25,000 deaths annually in Europe despite available medicines that maintain asthma control and reduce asthma exacerbations. Better treatments are urgently needed for the control of chronic asthma and reduction in asthma exacerbations, the major cause of asthma mortality. Much research spanning >20 years shows a strong association between microorganisms including pathogens in asthma onset, severity and exacerbation, yet with the exception of antibiotics, few treatments are available that specifically target the offending pathogens. Recent insights into the microbiome suggest that modulating commensal organisms within the gut or lung may also be a possible way to treat/prevent asthma. The European Academy of Allergy & Clinical Immunology Task Force on Anti-infectives in Asthma was initiated to investigate the potential of anti-infectives and immunomodulators in asthma. This review provides a concise summary of the current literature and aimed to identify and address key questions that concern the use of anti-infectives and both microbe- and host-based immunomodulators and their feasibility for use in asthma.
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Affiliation(s)
- M. R. Edwards
- Airway Disease Infection Section National Heart Lung Institute Imperial College London London UK
- MRC and Asthma UK Centre for Allergic Mechanisms of Asthma London UK
| | - R. P. Walton
- Airway Disease Infection Section National Heart Lung Institute Imperial College London London UK
- MRC and Asthma UK Centre for Allergic Mechanisms of Asthma London UK
| | - D. J. Jackson
- Airway Disease Infection Section National Heart Lung Institute Imperial College London London UK
- MRC and Asthma UK Centre for Allergic Mechanisms of Asthma London UK
- Division of Asthma, Allergy & Lung Biology King's College London & Guy's and St Thomas' NHS Trust London UK
| | - W. Feleszko
- Department of Pediatric Respiratory Diseases and Allergy The Medical University of Warsaw Warsaw Poland
| | - C. Skevaki
- Institute of Laboratory Medicine and Pathobiochemistry, Molecular Diagnostics Philipps University Marburg & University Hospital Giessen Marburg Germany
| | - T. Jartti
- The Department of Pediatrics Turku University Hospital Turku Finland
| | - H. Makrinoti
- Airway Disease Infection Section National Heart Lung Institute Imperial College London London UK
- MRC and Asthma UK Centre for Allergic Mechanisms of Asthma London UK
| | - A. Nikonova
- National Research Center Institute of Immunology of Federal Medicobiological Agency Moscow Russia
- Mechnikov Research Institute of Vaccines and Sera Moscow Russia
| | - I. P. Shilovskiy
- National Research Center Institute of Immunology of Federal Medicobiological Agency Moscow Russia
| | - J. Schwarze
- Centre for Inflammation Research University of Edinburgh The Queens Medical Research Institute Edinburgh Edinburgh UK
| | - S. L. Johnston
- Airway Disease Infection Section National Heart Lung Institute Imperial College London London UK
- MRC and Asthma UK Centre for Allergic Mechanisms of Asthma London UK
| | - M. R. Khaitov
- National Research Center Institute of Immunology of Federal Medicobiological Agency Moscow Russia
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185
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Nogacka AM, Salazar N, Arboleya S, Suárez M, Fernández N, Solís G, de Los Reyes-Gavilán CG, Gueimonde M. Early microbiota, antibiotics and health. Cell Mol Life Sci 2018; 75:83-91. [PMID: 28988290 PMCID: PMC11105232 DOI: 10.1007/s00018-017-2670-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 09/29/2017] [Indexed: 12/19/2022]
Abstract
The colonization of the neonatal digestive tract provides a microbial stimulus required for an adequate maturation towards the physiological homeostasis of the host. This colonization, which is affected by several factors, begins with facultative anaerobes and continues with anaerobic genera. Accumulating evidence underlines the key role of the early neonatal period for this microbiota-induced maturation, being a key determinant factor for later health. Therefore, understanding the factors that determine the establishment of the microbiota in the infant is of critical importance. Exposure to antibiotics, either prenatally or postnatally, is common in early life mainly due to the use of intrapartum prophylaxis or to the administration of antibiotics in C-section deliveries. However, we are still far from understanding the impact of early antibiotics and their long-term effects. Increased risk of non-communicable diseases, such as allergies or obesity, has been observed in individuals exposed to antibiotics during early infancy. Moreover, the impact of antibiotics on the establishment of the infant gut resistome, and on the role of the microbiota as a reservoir of resistance genes, should be evaluated in the context of the problems associated with the increasing number of antibiotic resistant pathogenic strains. In this article, we review and discuss the above-mentioned issues with the aim of encouraging debate on the actions needed for understanding the impact of early life antibiotics upon human microbiota and health and for developing strategies aimed at minimizing this impact.
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Affiliation(s)
- Alicja M Nogacka
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Nuria Salazar
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Silvia Arboleya
- APC Microbiome Institute, University College Cork, Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Fermoy, Cork, Ireland
| | - Marta Suárez
- Pediatrics Service, Hospital Universitario Central de Asturias, SESPA, Oviedo, Asturias, Spain
| | - Nuria Fernández
- Pediatrics Service, Hospital Universitario Central de Asturias, SESPA, Oviedo, Asturias, Spain
| | - Gonzalo Solís
- Pediatrics Service, Hospital Universitario Central de Asturias, SESPA, Oviedo, Asturias, Spain
| | - Clara G de Los Reyes-Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300, Villaviciosa, Asturias, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias, Consejo Superior de Investigaciones Científicas (IPLA-CSIC), Paseo Rio Linares s/n, 33300, Villaviciosa, Asturias, Spain.
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186
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Xia Y, Sun J, Chen DG. Introductory Overview of Statistical Analysis of Microbiome Data. STATISTICAL ANALYSIS OF MICROBIOME DATA WITH R 2018. [DOI: 10.1007/978-981-13-1534-3_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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187
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Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, D Lieber A, Wu F, Perez-Perez GI, Chen Y, Schweizer W, Zheng X, Contreras M, Dominguez-Bello MG, Blaser MJ. Antibiotics, birth mode, and diet shape microbiome maturation during early life. Sci Transl Med 2017; 8:343ra82. [PMID: 27306664 DOI: 10.1126/scitranslmed.aad7121] [Citation(s) in RCA: 869] [Impact Index Per Article: 124.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 05/27/2016] [Indexed: 12/11/2022]
Abstract
Early childhood is a critical stage for the foundation and development of both the microbiome and host. Early-life antibiotic exposures, cesarean section, and formula feeding could disrupt microbiome establishment and adversely affect health later in life. We profiled microbial development during the first 2 years of life in a cohort of 43 U.S. infants and identified multiple disturbances associated with antibiotic exposures, cesarean section, and formula feeding. These exposures contributed to altered establishment of maternal bacteria, delayed microbiome development, and altered α-diversity. These findings illustrate the complexity of early-life microbiome development and its sensitivity to perturbation.
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Affiliation(s)
- Nicholas A Bokulich
- Department of Medicine, New York University Langone Medical Center, New York, NY 10016, USA
| | - Jennifer Chung
- Department of Medicine, New York University Langone Medical Center, New York, NY 10016, USA
| | - Thomas Battaglia
- Department of Medicine, New York University Langone Medical Center, New York, NY 10016, USA
| | - Nora Henderson
- Department of Medicine, New York University Langone Medical Center, New York, NY 10016, USA
| | - Melanie Jay
- Department of Medicine, New York University Langone Medical Center, New York, NY 10016, USA. Department of Population Health, New York University Langone Medical Center, New York, NY 10016, USA
| | - Huilin Li
- Division of Biostatistics, Department of Population Health and Department of Environmental Medicine, New York University Langone Medical Center, New York, NY 10016, USA
| | - Arnon D Lieber
- Department of Medicine, New York University Langone Medical Center, New York, NY 10016, USA
| | - Fen Wu
- Department of Medicine, New York University Langone Medical Center, New York, NY 10016, USA. Department of Population Health, New York University Langone Medical Center, New York, NY 10016, USA
| | - Guillermo I Perez-Perez
- Department of Medicine, New York University Langone Medical Center, New York, NY 10016, USA. Department of Microbiology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Yu Chen
- Department of Medicine, New York University Langone Medical Center, New York, NY 10016, USA. Department of Population Health, New York University Langone Medical Center, New York, NY 10016, USA
| | - William Schweizer
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Xuhui Zheng
- Department of Microbiology, New York University Langone Medical Center, New York, NY 10016, USA
| | - Monica Contreras
- Department of Medicine, New York University Langone Medical Center, New York, NY 10016, USA
| | | | - Martin J Blaser
- Department of Medicine, New York University Langone Medical Center, New York, NY 10016, USA. Department of Microbiology, New York University Langone Medical Center, New York, NY 10016, USA. New York Harbor Department of Veterans Affairs Medical Center, New York, NY 10010, USA.
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188
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Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M, Xavier RJ. Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability. Sci Transl Med 2017; 8:343ra81. [PMID: 27306663 DOI: 10.1126/scitranslmed.aad0917] [Citation(s) in RCA: 624] [Impact Index Per Article: 89.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 05/27/2016] [Indexed: 12/12/2022]
Abstract
The gut microbial community is dynamic during the first 3 years of life, before stabilizing to an adult-like state. However, little is known about the impact of environmental factors on the developing human gut microbiome. We report a longitudinal study of the gut microbiome based on DNA sequence analysis of monthly stool samples and clinical information from 39 children, about half of whom received multiple courses of antibiotics during the first 3 years of life. Whereas the gut microbiome of most children born by vaginal delivery was dominated by Bacteroides species, the four children born by cesarean section and about 20% of vaginally born children lacked Bacteroides in the first 6 to 18 months of life. Longitudinal sampling, coupled with whole-genome shotgun sequencing, allowed detection of strain-level variation as well as the abundance of antibiotic resistance genes. The microbiota of antibiotic-treated children was less diverse in terms of both bacterial species and strains, with some species often dominated by single strains. In addition, we observed short-term composition changes between consecutive samples from children treated with antibiotics. Antibiotic resistance genes carried on microbial chromosomes showed a peak in abundance after antibiotic treatment followed by a sharp decline, whereas some genes carried on mobile elements persisted longer after antibiotic therapy ended. Our results highlight the value of high-density longitudinal sampling studies with high-resolution strain profiling for studying the establishment and response to perturbation of the infant gut microbiome.
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Affiliation(s)
- Moran Yassour
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA. Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Tommi Vatanen
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA. Department of Computer Science, Aalto University School of Science, 02150 Espoo, Finland
| | - Heli Siljander
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland. Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland. Department of Pediatrics, Tampere University Hospital, 33521 Tampere, Finland
| | - Anu-Maaria Hämäläinen
- Department of Pediatrics, Jorvi Hospital, Helsinki University Hospital, 02740 Espoo, Finland
| | - Taina Härkönen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland. Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland
| | - Samppa J Ryhänen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland. Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland
| | - Eric A Franzosa
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Hera Vlamakis
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA
| | - Curtis Huttenhower
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA. Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA
| | - Dirk Gevers
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA
| | - Eric S Lander
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA. Department of Biology, MIT, Cambridge, MA 02139, USA. Department of Systems Biology, Harvard Medical School, Boston, MA 02114, USA
| | - Mikael Knip
- Children's Hospital, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland. Research Programs Unit, Diabetes and Obesity, University of Helsinki, 00290 Helsinki, Finland. Department of Pediatrics, Tampere University Hospital, 33521 Tampere, Finland. Folkhälsan Research Center, 00290 Helsinki, Finland
| | | | - Ramnik J Xavier
- Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, MA 02142, USA. Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Center for Microbiome Informatics and Therapeutics, MIT, Cambridge, MA 02139, USA.
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189
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Iizumi T, Battaglia T, Ruiz V, Perez Perez GI. Gut Microbiome and Antibiotics. Arch Med Res 2017; 48:727-734. [PMID: 29221800 DOI: 10.1016/j.arcmed.2017.11.004] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 11/15/2017] [Indexed: 12/12/2022]
Abstract
Despite that the human gastrointestinal tract is the most populated ecological niche by bacteria in the human body, much is still unknown about its characteristics. This site is highly susceptible to the effects of many external factors that may affect in the quality and the quantity of the microbiome. Specific factors such as diet, personal hygiene, pharmacological drugs and the use of antibiotics can produce a significant impact on the gut microbiota. The effect of these factors is more relevant early in life, when the gut microbiota has not yet fully established. In this review, we discussed the effect of type and doses of the antibiotics on the gut microbiota and what the major consequences in the use and abuse of these antimicrobial agents.
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Affiliation(s)
- Tadasu Iizumi
- Department of Medicine, New York University School of Medicine NYU Langone Health, New York, NY, USA.
| | - Thomas Battaglia
- Department of Medicine, New York University School of Medicine NYU Langone Health, New York, NY, USA
| | - Victoria Ruiz
- Department of Medicine, New York University School of Medicine NYU Langone Health, New York, NY, USA
| | - Guillermo I Perez Perez
- Department of Medicine, New York University School of Medicine NYU Langone Health, New York, NY, USA
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190
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Lien entre les probiotiques et le microbiote : vision du clinicien. CAHIERS DE NUTRITION ET DE DIÉTÉTIQUE 2017. [DOI: 10.1016/s0007-9960(17)30193-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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191
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Action and function of Akkermansia muciniphila in microbiome ecology, health and disease. Best Pract Res Clin Gastroenterol 2017; 31:637-642. [PMID: 29566906 DOI: 10.1016/j.bpg.2017.10.001] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 09/22/2017] [Accepted: 10/10/2017] [Indexed: 01/31/2023]
Abstract
The discovery of Akkermansia muciniphila has opened new avenues for the use of this abundant intestinal symbiont in next generation therapeutic products, as well as targeting microbiota dynamics. A. muciniphila is known to colonize the mucosal layer of the human intestine where it triggers both host metabolic and immune responses. A. muciniphila is particularly effective in increasing mucus thickness and increasing gut barrier function. As a result host metabolic markers ameliorate. The mechanism of host regulation is thought to involve the outer membrane composition, including the type IV pili of A. muciniphila, that directly signal to host immune receptors. At the same time the metabolic activity of A. muciniphila leads to the production of short chain fatty acids that are beneficial to the host and microbiota members. This contributes to host-microbiota and microbe-microbe syntrophy The mucolytic activity and metabolite production make A. muciniphila a key species in the mucus layer, stimulating beneficial mucosal microbial networks. This well studied member of the microbiota has been studied in three aspects that will be further described in this review: i) A. muciniphila characteristics and mucin adaptation, ii) its role as key species in the mucosal microbiome, and iii) its role in host health.
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192
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Milani C, Duranti S, Bottacini F, Casey E, Turroni F, Mahony J, Belzer C, Delgado Palacio S, Arboleya Montes S, Mancabelli L, Lugli GA, Rodriguez JM, Bode L, de Vos W, Gueimonde M, Margolles A, van Sinderen D, Ventura M. The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota. Microbiol Mol Biol Rev 2017; 81:e00036-17. [PMID: 29118049 PMCID: PMC5706746 DOI: 10.1128/mmbr.00036-17] [Citation(s) in RCA: 976] [Impact Index Per Article: 139.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Eoghan Casey
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Jennifer Mahony
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Susana Delgado Palacio
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Silvia Arboleya Montes
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Juan Miguel Rodriguez
- Department of Nutrition, Food Science and Food Technology, Complutense University of Madrid, Madrid, Spain
| | - Lars Bode
- Department of Pediatrics and Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence, University of California-San Diego, La Jolla, California, USA
| | - Willem de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Department of Bacteriology & Immunology, RPU Immunobiology, University of Helsinki, Helsinki, Finland
| | - Miguel Gueimonde
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Abelardo Margolles
- Departamento de Microbiologia y Bioquimica de Productos Lacteos, IPLA-CSIC, Villaviciosa, Asturias, Spain
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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193
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Abstract
PURPOSE OF REVIEW Changes in the constituents and activity of the microbiome have been associated with a number of conditions linked to bone and joint disease. This review concentrates on ways in which the microbiome is known to influence osteoarthritis and osteoporosis. RECENT FINDINGS Animal studies have demonstrated that changes in the microbiome can mediate the effects of obesity on cartilage degeneration. Additionally, the microbiome influences the amount of the bone (bone quantity), as well as bone tissue material properties (bone quality). Early clinical findings support the effects of the microbiome on osteoporosis and osteoarthritis. Although animal studies implicate the microbiome in the development of bone and joint disease, available results are limited and can be conflicting. Further investigation of the mechanisms linking from changes in the microbiome to alterations in the bones and joints are necessary.
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Affiliation(s)
- Christopher J Hernandez
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, NY, 14853, USA. .,Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA. .,Hospital for Special Surgery, New York, NY, USA.
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194
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Hernandez CJ. Bone Mechanical Function and the Gut Microbiota. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1033:249-270. [DOI: 10.1007/978-3-319-66653-2_12] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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195
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Chen YC, Greenbaum J, Shen H, Deng HW. Association Between Gut Microbiota and Bone Health: Potential Mechanisms and Prospective. J Clin Endocrinol Metab 2017; 102:3635-3646. [PMID: 28973392 PMCID: PMC5630250 DOI: 10.1210/jc.2017-00513] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 07/18/2017] [Indexed: 12/12/2022]
Abstract
CONTEXT It has been well established that the human gut microbiome plays a critical role in the regulation of important biological processes and the mechanisms underlying numerous complex diseases. Although researchers have only recently begun to study the relationship between the gut microbiota and bone metabolism, early efforts have provided increased evidence to suggest an important association. EVIDENCE ACQUISITION In this study, we attempt to comprehensively summarize the relationship between the gut microbiota and bone metabolism by detailing the regulatory effects of the microbiome on various biological processes, including nutrient absorption and the intestinal mucosal barrier, immune system functionality, the gut-brain axis, and excretion of functional byproducts. In this review, we incorporate evidence from various types of studies, including observational, in vitro and in vivo animal experiments, as well as small efficacy clinic trails. EVIDENCE SYNTHESIS We review the various potential mechanisms of influence for the gut microbiota on the regulation of bone metabolism and discuss the importance of further examining the potential effects of the gut microbiota on the risk of osteoporosis in humans. Furthermore, we outline some useful tools/approaches for metagenomics research and present some prominent examples of metagenomics association studies in humans. CONCLUSION Current research efforts, although limited, clearly indicate that the gut microbiota may be implicated in bone metabolism, and therefore, further exploration of this relationship is a promising area of focus in bone health and osteoporosis research. Although most existing studies investigate this relationship using animal models, human studies are both needed and on the horizon.
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Affiliation(s)
- Yuan-Cheng Chen
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, PR China
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, Louisiana 70112
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana 70112
| | - Jonathan Greenbaum
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, Louisiana 70112
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana 70112
| | - Hui Shen
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, Louisiana 70112
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana 70112
| | - Hong-Wen Deng
- Department of Endocrinology and Metabolism, The Third Affiliated Hospital of Southern Medical University, Guangzhou 510630, PR China
- Center of Bioinformatics and Genomics, Tulane University, New Orleans, Louisiana 70112
- Department of Global Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, Louisiana 70112
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196
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Ruiz VE, Battaglia T, Kurtz ZD, Bijnens L, Ou A, Engstrand I, Zheng X, Iizumi T, Mullins BJ, Müller CL, Cadwell K, Bonneau R, Perez-Perez GI, Blaser MJ. A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity. Nat Commun 2017; 8:518. [PMID: 28894149 PMCID: PMC5593929 DOI: 10.1038/s41467-017-00531-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 07/05/2017] [Indexed: 12/17/2022] Open
Abstract
Broad-spectrum antibiotics are frequently prescribed to children. Early childhood represents a dynamic period for the intestinal microbial ecosystem, which is readily shaped by environmental cues; antibiotic-induced disruption of this sensitive community may have long-lasting host consequences. Here we demonstrate that a single pulsed macrolide antibiotic treatment (PAT) course early in life is sufficient to lead to durable alterations to the murine intestinal microbiota, ileal gene expression, specific intestinal T-cell populations, and secretory IgA expression. A PAT-perturbed microbial community is necessary for host effects and sufficient to transfer delayed secretory IgA expression. Additionally, early-life antibiotic exposure has lasting and transferable effects on microbial community network topology. Our results indicate that a single early-life macrolide course can alter the microbiota and modulate host immune phenotypes that persist long after exposure has ceased.High or multiple doses of macrolide antibiotics, when given early in life, can perturb the metabolic and immunological development of lab mice. Here, Ruiz et al. show that even a single macrolide course, given early in life, leads to long-lasting changes in the gut microbiota and immune system of mice.
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Affiliation(s)
- Victoria E Ruiz
- Departments of Medicine and Microbiology, New York University School of Medicine (NYUSM), New York, NY, 10016, USA
| | - Thomas Battaglia
- Departments of Medicine and Microbiology, New York University School of Medicine (NYUSM), New York, NY, 10016, USA
| | - Zachary D Kurtz
- Departments of Medicine and Microbiology, New York University School of Medicine (NYUSM), New York, NY, 10016, USA
| | - Luc Bijnens
- Janssen R&D, Janssen Pharmaceutical Companies of J&J, Turnhoutseweg 30, Beerse, 2340, Belgium
| | - Amy Ou
- Departments of Medicine and Microbiology, New York University School of Medicine (NYUSM), New York, NY, 10016, USA
| | - Isak Engstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Xuhui Zheng
- Departments of Medicine and Microbiology, New York University School of Medicine (NYUSM), New York, NY, 10016, USA
| | - Tadasu Iizumi
- Departments of Medicine and Microbiology, New York University School of Medicine (NYUSM), New York, NY, 10016, USA
| | - Briana J Mullins
- Departments of Medicine and Microbiology, New York University School of Medicine (NYUSM), New York, NY, 10016, USA
| | - Christian L Müller
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA
| | - Ken Cadwell
- Kimmel Center for Biology and Medicine at the Skirball Institute, NYUSM, New York, NY, 10016, USA
| | - Richard Bonneau
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, 10010, USA.,Department of Biology, Center for Genomics and Systems Biology, NYU, New York, NY, 10003, USA.,Courant Institute of Mathematical Sciences, NYU, New York, NY, 10012, USA
| | - Guillermo I Perez-Perez
- Departments of Medicine and Microbiology, New York University School of Medicine (NYUSM), New York, NY, 10016, USA
| | - Martin J Blaser
- Departments of Medicine and Microbiology, New York University School of Medicine (NYUSM), New York, NY, 10016, USA. .,New York Harbor Department of Veterans Affairs Medical Center, New York, NY, 10010, USA.
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197
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Yu K, Mu C, Yang Y, Su Y, Zhu W. Segment-specific responses of intestinal epithelium transcriptome to in-feed antibiotics in pigs. Physiol Genomics 2017; 49:582-591. [PMID: 28887368 DOI: 10.1152/physiolgenomics.00020.2017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/10/2017] [Accepted: 08/28/2017] [Indexed: 11/22/2022] Open
Abstract
Despite widespread use of antibiotics for treatment of human diseases and promotion of growth of agricultural animals, our understanding of their effects on the host is still very limited. We used a model in which pigs were fed with or without a cocktail of antibiotics and found, based on the denaturing gradient gel electrophoresis (DGGE) patterns, that the fecal bacteria from the treatment and control animals were distinct. Furthermore, the total bacterial population in the feces tended to be decreased by the antibiotic treatment (P = 0.07), and the counts of Lactobacillus and Clostridium XIVa were significantly reduced (P < 0.05). To explore the effects of antibiotics on host intestinal epithelium, we assessed gene expression profiles of the jejunum and ileum and their response to antibiotic administration. The results indicate that in-feed antibiotics increased expression of genes involved in immune functions in both the jejunum and ileum, some of which were clustered in the coexpression network. Gene ontology terms of metabolic processes were altered predominantly in the jejunum but not in the ileum. Notably, antibiotics diminished intestinal segment-specific transcriptional changes, especially for genes associated with metabolic functions. This study reveals segment-specific responses of host intestinal epithelium to in-feed antibiotics, which can be a valuable resource for deciphering antibiotic-microbiota-host interactions.
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Affiliation(s)
- Kaifan Yu
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Chunlong Mu
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuxiang Yang
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yong Su
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Weiyun Zhu
- Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal Health, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
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198
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Zhang Y, Han SW, Cox LM, Li H. A multivariate distance-based analytic framework for microbial interdependence association test in longitudinal study. Genet Epidemiol 2017; 41:769-778. [PMID: 28872698 DOI: 10.1002/gepi.22065] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 05/30/2017] [Accepted: 07/10/2017] [Indexed: 12/31/2022]
Abstract
Human microbiome is the collection of microbes living in and on the various parts of our body. The microbes living on our body in nature do not live alone. They act as integrated microbial community with massive competing and cooperating and contribute to our human health in a very important way. Most current analyses focus on examining microbial differences at a single time point, which do not adequately capture the dynamic nature of the microbiome data. With the advent of high-throughput sequencing and analytical tools, we are able to probe the interdependent relationship among microbial species through longitudinal study. Here, we propose a multivariate distance-based test to evaluate the association between key phenotypic variables and microbial interdependence utilizing the repeatedly measured microbiome data. Extensive simulations were performed to evaluate the validity and efficiency of the proposed method. We also demonstrate the utility of the proposed test using a well-designed longitudinal murine experiment and a longitudinal human study. The proposed methodology has been implemented in the freely distributed open-source R package and Python code.
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Affiliation(s)
- Yilong Zhang
- Merck Research Laboratories, Rahway, New Jersey, United States of America
| | - Sung Won Han
- Fusion Data Analytics Lab, School of Industrial Management Engineering, Korea University, Seoul, South Korea
| | - Laura M Cox
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Huilin Li
- Department of Population Health (Biostatistics), NYU Langone Medical Center, New York, NY, United States of America.,Department of Environmental Medicine, NYU Langone Medical Center, New York, NY, United States of America
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199
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Minter MR, Hinterleitner R, Meisel M, Zhang C, Leone V, Zhang X, Oyler-Castrillo P, Zhang X, Musch MW, Shen X, Jabri B, Chang EB, Tanzi RE, Sisodia SS. Antibiotic-induced perturbations in microbial diversity during post-natal development alters amyloid pathology in an aged APP SWE/PS1 ΔE9 murine model of Alzheimer's disease. Sci Rep 2017; 7:10411. [PMID: 28874832 PMCID: PMC5585265 DOI: 10.1038/s41598-017-11047-w] [Citation(s) in RCA: 193] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/18/2017] [Indexed: 02/06/2023] Open
Abstract
Recent evidence suggests the commensal microbiome regulates host immunity and influences brain function; findings that have ramifications for neurodegenerative diseases. In the context of Alzheimer’s disease (AD), we previously reported that perturbations in microbial diversity induced by life-long combinatorial antibiotic (ABX) selection pressure in the APPSWE/PS1ΔE9 mouse model of amyloidosis is commensurate with reductions in amyloid-β (Aβ) plaque pathology and plaque-localised gliosis. Considering microbiota-host interactions, specifically during early post-natal development, are critical for immune- and neuro-development we now examine the impact of microbial community perturbations induced by acute ABX exposure exclusively during this period in APPSWE/PS1ΔE9 mice. We show that early post-natal (P) ABX treatment (P14-P21) results in long-term alterations of gut microbial genera (predominantly Lachnospiraceae and S24-7) and reduction in brain Aβ deposition in aged APPSWE/PS1ΔE9 mice. These mice exhibit elevated levels of blood- and brain-resident Foxp3+ T-regulatory cells and display an alteration in the inflammatory milieu of the serum and cerebrospinal fluid. Finally, we confirm that plaque-localised microglia and astrocytes are reduced in ABX-exposed mice. These findings suggest that ABX-induced microbial diversity perturbations during post-natal stages of development coincide with altered host immunity mechanisms and amyloidosis in a murine model of AD.
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Affiliation(s)
- Myles R Minter
- Department of Neurobiology, The University of Chicago, Chicago, IL, 60637, USA.,The Microbiome Center, The University of Chicago, Chicago, IL, 60637, USA
| | - Reinhard Hinterleitner
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.,Committee on Immunology, The University of Chicago, Chicago, IL, 60637, USA
| | - Marlies Meisel
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.,Committee on Immunology, The University of Chicago, Chicago, IL, 60637, USA
| | - Can Zhang
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Diseases, Massachusetts General Hospital, Charlestown, MA, 02114, USA
| | - Vanessa Leone
- The Microbiome Center, The University of Chicago, Chicago, IL, 60637, USA.,Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Xiaoqiong Zhang
- Department of Neurobiology, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Xulun Zhang
- Department of Neurobiology, The University of Chicago, Chicago, IL, 60637, USA
| | - Mark W Musch
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Xunuo Shen
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Diseases, Massachusetts General Hospital, Charlestown, MA, 02114, USA
| | - Bana Jabri
- Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA.,Committee on Immunology, The University of Chicago, Chicago, IL, 60637, USA
| | - Eugene B Chang
- The Microbiome Center, The University of Chicago, Chicago, IL, 60637, USA.,Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Rudolph E Tanzi
- Department of Neurology, Genetics and Aging Research Unit, MassGeneral Institute for Neurodegenerative Diseases, Massachusetts General Hospital, Charlestown, MA, 02114, USA
| | - Sangram S Sisodia
- Department of Neurobiology, The University of Chicago, Chicago, IL, 60637, USA. .,The Microbiome Center, The University of Chicago, Chicago, IL, 60637, USA.
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200
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Magne F, Puchi Silva A, Carvajal B, Gotteland M. The Elevated Rate of Cesarean Section and Its Contribution to Non-Communicable Chronic Diseases in Latin America: The Growing Involvement of the Microbiota. Front Pediatr 2017; 5:192. [PMID: 28929093 PMCID: PMC5591430 DOI: 10.3389/fped.2017.00192] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/18/2017] [Indexed: 12/21/2022] Open
Abstract
The current recommendation of the World Health Organization (WHO) regarding cesarean section (C-section) is that this clinical practice should be carried out only under specific conditions, when the health or life of the mother/newborn dyad is threatened, and that its use should not exceed 10-15% of the total deliveries. However, over the last few decades, the frequency of C-section delivery in medium- and high-income countries has rapidly increased worldwide. This review describes the evolution of this procedure in Latin American countries, showing that today more than half of newborns in the region are delivered by C-section. Given that C-section delivery is more expensive than vaginal delivery, its use has increased more rapidly in the private than the public sector; nevertheless, the prevalence of C-section deliveries in the public sector is higher than the WHO's recommendations and continues to increase, representing a growing challenge for Latin America. Although the medium- and long-term consequences of C-section delivery, as opposed to vaginal delivery, on the infant health are unclear, epidemiological studies suggest that it is associated with higher risk of developing asthma, food allergy, type 1 diabetes, and obesity during infancy. These findings are important, as the incidence of these diseases in the Latin American pediatric population is also increasing, particularly obesity. Although the link between these diseases and delivery mode remains controversial, recent studies indicate that the establishment of the gut microbiota is delayed in infants born by C-section during the postnatal period, i.e., during a critical developmental window for the maturation of the newborn's immune system. This delay may favor the subsequent development of inflammatory and metabolic disorders during infancy. Accordingly, from a public health perspective, it is important to slow down and eventually reverse the pattern of increased C-section use in the affected populations.
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Affiliation(s)
- Fabien Magne
- Microbiology and Mycology Program, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
| | - Alexa Puchi Silva
- Faculty of Medicine, Andres Bello University, Vina del Mar, Santiago, Chile
| | - Bielka Carvajal
- Department of Women and Newborn’s Health Promotion, University of Chile, Santiago, Chile
| | - Martin Gotteland
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
- Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile
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