251
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Taguer M, Maurice CF. The complex interplay of diet, xenobiotics, and microbial metabolism in the gut: Implications for clinical outcomes. Clin Pharmacol Ther 2016; 99:588-99. [PMID: 26950037 DOI: 10.1002/cpt.366] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 03/01/2016] [Accepted: 03/02/2016] [Indexed: 12/14/2022]
Abstract
From digestion to pathogen resistance and immune system development, the gut microbiota and its collection of microbial genes are redefining what it means to be human. Despite tremendous advances in this field, there is still a limited understanding of how microbial metabolism in the gut impacts human health, which precludes the development of microbiota-targeted therapies. In this article, we discuss the increasing evidence emphasizing the importance of bacterial metabolism in the gut and discuss its intricate links with diet and pharmaceutical compounds leading to altered therapeutic outcomes. We also detail how applying and testing microbial ecology hypotheses will be crucial to fully understand the therapeutic potential of this host-associated community. Going forward, functional and mechanistic studies combining biomedical research, ecology, bioinformatics, statistical modeling, and engineering will be key in our pursuit of personalized medicine.
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Affiliation(s)
- M Taguer
- Department of Microbiology and Immunology, Microbiome and Disease Tolerance Centre, McGill University, Montreal, Quebec, Canada
| | - C F Maurice
- Department of Microbiology and Immunology, Microbiome and Disease Tolerance Centre, McGill University, Montreal, Quebec, Canada
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252
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Bomhof MR, Paul HA, Geuking MB, Eller LK, Reimer RA. Improvement in adiposity with oligofructose is modified by antibiotics in obese rats. FASEB J 2016; 30:2720-32. [PMID: 27059718 DOI: 10.1096/fj.201600151r] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/05/2016] [Indexed: 12/21/2022]
Abstract
Given the intimate link between gut microbiota and host physiology, there is growing interest in understanding the mechanisms by which diet influences gut microbiota and affects human metabolic health. Using antibiotics and the prebiotic oligofructose, which has been shown to counteract excess fat mass, we explored the gut microbiota-dependent effects of oligofructose on body composition and host metabolism. Diet-induced obese male Sprague Dawley rats, fed a background high-fat/sucrose diet, were randomized to one of the following diets for 6 wk: 1) high-energy control; 2) 10% oligofructose; 3) ampicillin; 4) ampicillin + 10% oligofructose; 5) ampicillin/neomycin; or 6) ampicillin/neomycin + 10% oligofructose. Combining oligofructose with ampicillin treatment blunted the decrease in adiposity seen with oligofructose. Although ampicillin did not affect total bacteria, ampicillin impeded oligofructose-induced increases in Bifidobacterium and Lactobacillus In contrast, the combination of ampicillin and neomycin reduced total bacteria but did not abrogate the oligofructose-induced decrease in adiposity. Oligofructose-mediated effects on host adiposity and metabolic health appear to be in part dependent on the presence of specific microbial species within the gut.-Bomhof, M. R., Paul, H. A., Geuking, M. B., Eller, L. K., Reimer, R. A. Improvement in adiposity with oligofructose is modified by antibiotics in obese rats.
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Affiliation(s)
- Marc R Bomhof
- Faculty of Kinesiology, University of Calgary, Calgary, Alberta Canada
| | - Heather A Paul
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta Canada; and
| | - Markus B Geuking
- Division of Gastroenterology, Department of Clinical Research, University Clinic for Visceral Surgery and Medicine, University of Bern, Bern, Switzerland
| | - Lindsay K Eller
- Faculty of Kinesiology, University of Calgary, Calgary, Alberta Canada
| | - Raylene A Reimer
- Faculty of Kinesiology, University of Calgary, Calgary, Alberta Canada; Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta Canada; and
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253
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Laubitz D, Harrison CA, Midura-Kiela MT, Ramalingam R, Larmonier CB, Chase JH, Caporaso JG, Besselsen DG, Ghishan FK, Kiela PR. Reduced Epithelial Na+/H+ Exchange Drives Gut Microbial Dysbiosis and Promotes Inflammatory Response in T Cell-Mediated Murine Colitis. PLoS One 2016; 11:e0152044. [PMID: 27050757 PMCID: PMC4822813 DOI: 10.1371/journal.pone.0152044] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 02/16/2016] [Indexed: 12/26/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are associated with functional inhibition of epithelial Na+/H+ exchange. In mice, a selective disruption of NHE3 (Slc9a3), a major apical Na+/H+ exchanger, also promotes IBD-like symptoms and gut microbial dysbiosis. We hypothesized that disruption of Na+/H+ exchange is necessary for the development of dysbiosis, which promotes an exacerbated mucosal inflammatory response. Therefore, we performed a temporal analysis of gut microbiota composition, and mucosal immune response to adoptive T cell transfer was evaluated in Rag2-/- and NHE3-/-/Rag2-/- (DKO) mice with and without broad-spectrum antibiotics. Microbiome (16S profiling), colonic histology, T cell and neutrophil infiltration, mucosal inflammatory tone, and epithelial permeability were analyzed. In adoptive T cell transfer colitis model, Slc9a3 status was the most significant determinant of gut microbial community. In DKO mice, NHE3-deficiency and dysbiosis were associated with dramatically accelerated and exacerbated disease, with rapid body weight loss, increased mucosal T cell and neutrophil influx, increased mucosal cytokine expression, increased permeability, and expansion of CD25-FoxP3+ Tregs; this enhanced susceptibility was alleviated by oral broad-spectrum antibiotics. Based on these results and our previous work, we postulate that epithelial electrolyte homeostasis is an important modulator in the progression of colitis, acting through remodeling of the gut microbial community.
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Affiliation(s)
- Daniel Laubitz
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Christy A. Harrison
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Monica T. Midura-Kiela
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Rajalakshmy Ramalingam
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Claire B. Larmonier
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - John H. Chase
- Department of Biological Sciences, Center for Microbial Genetics and Genomics at Northern Arizona University, Flagstaff, Arizona, United States of America
| | - J. Gregory Caporaso
- Department of Biological Sciences, Center for Microbial Genetics and Genomics at Northern Arizona University, Flagstaff, Arizona, United States of America
| | - David G. Besselsen
- University Animal Care, University of Arizona, Tucson, Arizona, United States of America
| | - Fayez K. Ghishan
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
| | - Pawel R. Kiela
- Department of Pediatrics—Steele Children’s Research Center, University of Arizona, Tucson, Arizona, United States of America
- Department of Immunobiology, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
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254
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Gomez de Aguero M, Ganal-Vonarburg SC, Fuhrer T, Rupp S, Uchimura Y, Li H, Steinert A, Heikenwalder M, Hapfelmeier S, Sauer U, McCoy KD, Macpherson AJ. The maternal microbiota drives early postnatal innate immune development. Science 2016; 351:1296-302. [DOI: 10.1126/science.aad2571] [Citation(s) in RCA: 696] [Impact Index Per Article: 87.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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255
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Crosstalk between microbiota, pathogens and the innate immune responses. Int J Med Microbiol 2016; 306:257-265. [PMID: 26996809 DOI: 10.1016/j.ijmm.2016.03.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 02/07/2023] Open
Abstract
Research in the last decade has convincingly demonstrated that the microbiota is crucial in order to prime and orchestrate innate and adaptive immune responses of their host and influence barrier function as well as multiple developmental and metabolic parameters of the host. Reciprocally, host reactions and immune responses instruct the composition of the microbiota. This review summarizes recent evidence from experimental and human studies which supports these arms of mutual relationship and crosstalk between host and resident microbiota, with a focus on innate immune responses in the gut, the role of cell death pathways and antimicrobial peptides. We also provide some recent examples on how dysbiosis and pathogens can act in concert to promote intestinal infection, inflammatory pathologies and cancer. The future perspectives of these combined research efforts include the discovery of protective species within the microbiota and specific traits and factors of microbes that weaken or enforce host intestinal homeostasis.
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256
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Derrien M, Belzer C, de Vos WM. Akkermansia muciniphila and its role in regulating host functions. Microb Pathog 2016; 106:171-181. [PMID: 26875998 DOI: 10.1016/j.micpath.2016.02.005] [Citation(s) in RCA: 624] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 02/07/2016] [Accepted: 02/09/2016] [Indexed: 02/08/2023]
Abstract
Akkermansia muciniphila is an intestinal bacterium that was isolated a decade ago from a human fecal sample. Its specialization in mucin degradation makes it a key organism at the mucosal interface between the lumen and host cells. Although it was isolated quite recently, it has rapidly raised significant interest as A. muciniphila is the only cultivated intestinal representative of the Verrucomicrobia, one of the few phyla in the human gut that can be easily detected in phylogenetic and metagenome analyses. There has also been a growing interest in A. muciniphila, due to its association with health in animals and humans. Notably, reduced levels of A. muciniphila have been observed in patients with inflammatory bowel diseases (mainly ulcerative colitis) and metabolic disorders, which suggests it may have potential anti-inflammatory properties. The aims of this review are to summarize the existing data on the intestinal distribution of A. muciniphila in health and disease, to provide insight into its ecology and its role in founding microbial networks at the mucosal interface, as well as to discuss recent research on its role in regulating host functions that are disturbed in various diseases, with a specific focus on metabolic disorders in both animals and humans.
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Affiliation(s)
- Muriel Derrien
- Danone Nutricia Research, Avenue de la Vauve, 91767 Palaiseau, France.
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands; Immunobiology Research Program, Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Helsinki, Finland.
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257
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Bauer PV, Hamr SC, Duca FA. Regulation of energy balance by a gut-brain axis and involvement of the gut microbiota. Cell Mol Life Sci 2016; 73:737-55. [PMID: 26542800 PMCID: PMC11108299 DOI: 10.1007/s00018-015-2083-z] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 12/11/2022]
Abstract
Despite significant progress in understanding the homeostatic regulation of energy balance, successful therapeutic options for curbing obesity remain elusive. One potential target for the treatment of obesity is via manipulation of the gut-brain axis, a complex bidirectional communication system that is crucial in maintaining energy homeostasis. Indeed, ingested nutrients induce secretion of gut peptides that act either via paracrine signaling through vagal and non-vagal neuronal relays, or in an endocrine fashion via entry into circulation, to ultimately signal to the central nervous system where appropriate responses are generated. We review here the current hypotheses of nutrient sensing mechanisms of enteroendocrine cells, including the release of gut peptides, mainly cholecystokinin, glucagon-like peptide-1, and peptide YY, and subsequent gut-to-brain signaling pathways promoting a reduction of food intake and an increase in energy expenditure. Furthermore, this review highlights recent research suggesting this energy regulating gut-brain axis can be influenced by gut microbiota, potentially contributing to the development of obesity.
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Affiliation(s)
- Paige V Bauer
- Department of Medicine, Toronto General Research Institute, UHN, Toronto, ON, M5G 1L7, Canada
- Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Sophie C Hamr
- Department of Medicine, Toronto General Research Institute, UHN, Toronto, ON, M5G 1L7, Canada
- Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Frank A Duca
- Department of Medicine, Toronto General Research Institute, UHN, Toronto, ON, M5G 1L7, Canada.
- MaRS Centre, Toronto Medical Discovery Tower, Room 10-701H, 101 College Street, Toronto, ON, M5G 1L7, Canada.
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258
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Korpela K, Salonen A, Virta LJ, Kekkonen RA, Forslund K, Bork P, de Vos WM. Intestinal microbiome is related to lifetime antibiotic use in Finnish pre-school children. Nat Commun 2016; 7:10410. [PMID: 26811868 PMCID: PMC4737757 DOI: 10.1038/ncomms10410] [Citation(s) in RCA: 444] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 12/03/2015] [Indexed: 12/14/2022] Open
Abstract
Early-life antibiotic use is associated with increased risk for metabolic and immunological diseases, and mouse studies indicate a causal role of the disrupted microbiome. However, little is known about the impacts of antibiotics on the developing microbiome of children. Here we use phylogenetics, metagenomics and individual antibiotic purchase records to show that macrolide use in 2–7 year-old Finnish children (N=142; sampled at two time points) is associated with a long-lasting shift in microbiota composition and metabolism. The shift includes depletion of Actinobacteria, increase in Bacteroidetes and Proteobacteria, decrease in bile-salt hydrolase and increase in macrolide resistance. Furthermore, macrolide use in early life is associated with increased risk of asthma and predisposes to antibiotic-associated weight gain. Overweight and asthmatic children have distinct microbiota compositions. Penicillins leave a weaker mark on the microbiota than macrolides. Our results support the idea that, without compromising clinical practice, the impact on the intestinal microbiota should be considered when prescribing antibiotics. The impact of antibiotics on the microbiome and health of children is poorly understood. Here, Korpela et al. study the gut microbiome of 142 children and show that the use of macrolides, but not penicillins, is associated with long-lasting shifts in microbiota composition and increased risk of asthma and overweight.
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Affiliation(s)
- Katri Korpela
- Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Haartmaninkatu 3, PO Box 21, 00014 Helsinki, Finland
| | - Anne Salonen
- Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Haartmaninkatu 3, PO Box 21, 00014 Helsinki, Finland
| | - Lauri J Virta
- Research Department, Social Insurance Institution, Turku, Peltolantie 3, 20720, Finland
| | | | - Kristoffer Forslund
- European Molecular Biology Laboratory, PO Box 1022.40, 69012 Heidelberg, Germany
| | - Peer Bork
- European Molecular Biology Laboratory, PO Box 1022.40, 69012 Heidelberg, Germany
| | - Willem M de Vos
- Immunobiology Research Program, Department of Bacteriology and Immunology, University of Helsinki, Haartmaninkatu 3, PO Box 21, 00014 Helsinki, Finland.,Department of Veterinary Biosciences, University of Helsinki, PO Box 66, 00014 Helsinki, Finland.,Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands
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259
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Ballou AL, Ali RA, Mendoza MA, Ellis JC, Hassan HM, Croom WJ, Koci MD. Development of the Chick Microbiome: How Early Exposure Influences Future Microbial Diversity. Front Vet Sci 2016; 3:2. [PMID: 26835461 PMCID: PMC4718982 DOI: 10.3389/fvets.2016.00002] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 01/05/2016] [Indexed: 12/22/2022] Open
Abstract
The concept of improving animal health through improved gut health has existed in food animal production for decades; however, only recently have we had the tools to identify microbes in the intestine associated with improved performance. Currently, little is known about how the avian microbiome develops or the factors that affect its composition. To begin to address this knowledge gap, the present study assessed the development of the cecal microbiome in chicks from hatch to 28 days of age with and without a live Salmonella vaccine and/or probiotic supplement; both are products intended to promote gut health. The microbiome of growing chicks develops rapidly from days 1–3, and the microbiome is primarily Enterobacteriaceae, but Firmicutes increase in abundance and taxonomic diversity starting around day 7. As the microbiome continues to develop, the influence of the treatments becomes stronger. Predicted metagenomic content suggests that, functionally, treatment may stimulate more differences at day 14, despite the strong taxonomic differences at day 28. These results demonstrate that these live microbial treatments do impact the development of the bacterial taxa found in the growing chicks; however, additional experiments are needed to understand the biochemical and functional consequences of these alterations.
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Affiliation(s)
- Anne L Ballou
- Prestage Department of Poultry Science, North Carolina State University , Raleigh, NC , USA
| | - Rizwana A Ali
- Prestage Department of Poultry Science, North Carolina State University , Raleigh, NC , USA
| | - Mary A Mendoza
- Prestage Department of Poultry Science, North Carolina State University , Raleigh, NC , USA
| | - J C Ellis
- In Silico LLC , Fuquay-Varina, NC , USA
| | - Hosni M Hassan
- Prestage Department of Poultry Science, North Carolina State University , Raleigh, NC , USA
| | - W J Croom
- Prestage Department of Poultry Science, North Carolina State University , Raleigh, NC , USA
| | - Matthew D Koci
- Prestage Department of Poultry Science, North Carolina State University , Raleigh, NC , USA
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260
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Abstract
Probiotics are live microorganisms, mainly belonging to the genera Lactobacillus and Bifidobacterium, although also strain of other species are commercialized, that have a beneficial effect on the host. From the perspective of antibiotic use, probiotics have been observed to reduce the risk of certain infectious disease such as certain types of diarrhea and respiratory tract infection. This may be accompanied with a reduced need of antibiotics for secondary infections. Antibiotics tend to be effective against most common diseases, but increasingly resistance is being observed among pathogens. Probiotics are specifically selected to not contribute to the spread of antibiotic resistance and not carry transferable antibiotic resistance. Concomitant use of probiotics with antibiotics has been observed to reduce the incidence, duration and/or severity of antibiotic-associated diarrhea. This contributes to better adherence to the antibiotic prescription and thereby reduces the evolution of resistance. To what extent probiotics directly reduce the spread of antibiotic resistance is still much under investigation; but maintaining a balanced microbiota during antibiotic use may certainly provide opportunities for reducing the spread of resistances. Key messages Probiotics may reduce the risk for certain infectious diseases and thereby reduce the need for antibiotics. Probiotics may reduce the risk for antibiotic-associated diarrhea Probiotics do not contribute to the spread of antibiotic resistance and may even reduce it.
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Affiliation(s)
| | - Sofia Forssten
- a Active Nutrition, DuPont Nutrition and Health , Kantvik , Finland
| | | | - Anna Lyra
- a Active Nutrition, DuPont Nutrition and Health , Kantvik , Finland
| | - Buffy Stahl
- c DuPont Health and Nutrition , Madison , WI , USA
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261
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Clemente Actis G. The Changing Face of Inflammatory Bowel Disease: Etiology, Physiopathology, Epidemiology. ACTA ACUST UNITED AC 2016. [DOI: 10.17795/acr-32942] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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262
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van Best N, Hornef MW, Savelkoul PHM, Penders J. On the origin of species: Factors shaping the establishment of infant's gut microbiota. ACTA ACUST UNITED AC 2015; 105:240-51. [DOI: 10.1002/bdrc.21113] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/03/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Niels van Best
- Institute of Medical Microbiology, RWTH University Hospital Aachen; Aachen Germany
- Department of Medical Microbiology; NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+; Maastricht The Netherlands
| | - Mathias W. Hornef
- Institute of Medical Microbiology, RWTH University Hospital Aachen; Aachen Germany
| | - Paul H. M. Savelkoul
- Department of Medical Microbiology; NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+; Maastricht The Netherlands
- Department of Medical Microbiology and Infection Control; VU University Medical Center Amsterdam; The Netherlands
- Department of Medical Microbiology; Caphri School for Public Health and Primary Care, Maastricht University Medical Centre+; Maastricht The Netherlands
| | - John Penders
- Department of Medical Microbiology; NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Centre+; Maastricht The Netherlands
- Department of Medical Microbiology; Caphri School for Public Health and Primary Care, Maastricht University Medical Centre+; Maastricht The Netherlands
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