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Oldereid TS, Jiang X, Øgaard J, Schrumpf E, Bjørnholt JV, Rasmussen H, Melum E. Microbial exposure during early life regulates development of bile duct inflammation. Scand J Gastroenterol 2024; 59:192-201. [PMID: 37997753 DOI: 10.1080/00365521.2023.2278423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/29/2023] [Indexed: 11/25/2023]
Abstract
OBJECTIVES The early life microbiome has been linked to inflammatory diseases in adulthood and a role for the microbiome in bile duct inflammation is supported by both human and murine studies. We utilized the NOD.c3c4 mouse model that develops a spontaneous immune-driven biliary disease with a known contribution of the microbiome to evaluate the temporal effects of the early life microbiome. MATERIALS AND METHODS Germ-free (GF) NOD.c3c4 mice were conventionalized into a specific pathogen free environment at birth (conventionally raised, CONV-R) or at weaning (germ-free raised, GF-R) and compared with age and gender-matched GF and conventional (CONV) NOD.c3c4 mice. At 9 weeks of age, liver pathology was assessed by conventional histology and flow cytometry immunophenotyping. RESULTS Neonatal exposure to microbes (CONV-R) increased biliary inflammation to similar levels as regular conventional NOD.c3c4 mice, while delayed exposure to microbes (GF-R) restrained the biliary inflammation. Neutrophil infiltration was increased in all conventionalized mice compared to GF. An immunophenotype in the liver similar to CONV was restored in both CONV-R and GF-R compared to GF mice displaying a proportional increase of B cells and reduction of T cells in the liver. CONCLUSIONS Microbial exposure during early life has a temporal impact on biliary tract inflammation in the NOD.c3c4 mouse model suggesting that age-sensitive interaction with commensal microbes have long-lasting effects on biliary immunity that can be of importance for human cholangiopathies.
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Affiliation(s)
- Tine S Oldereid
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Xiaojun Jiang
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Jonas Øgaard
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Elisabeth Schrumpf
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Dermatology, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Jørgen V Bjørnholt
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Microbiology, Division of Laboratory Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Henrik Rasmussen
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Comparative Medicine, Division of Oslo Hospital Services, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Espen Melum
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Section of Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Hybrid Technology Hub - Centre of Excellence, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
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2
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Zhang ZW, Han P, Fu J, Yu H, Xu H, Hu JC, Lu JY, Yang XY, Zhang HJ, Bu MM, Jiang JD, Wang Y. Gut microbiota-based metabolites of Xiaoyao Pills (a typical Traditional Chinese medicine) ameliorate depression by inhibiting fatty acid amide hydrolase levels in brain. JOURNAL OF ETHNOPHARMACOLOGY 2023; 313:116555. [PMID: 37100263 DOI: 10.1016/j.jep.2023.116555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 05/09/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Traditional Chinese medicines (TCMs) are often prepared in oral dosage forms, making TCMs interact with gut microbiota after oral administration, which could affect the therapeutic effect of TCM. Xiaoyao Pills (XYPs) are a commonly used TCM in China to treat depression. The biological underpinnings, however, are still in its infancy due to its complex chemical composition. AIM OF THE STUDY The study aims to explore XYPs' underlying antidepressant mechanism from both in vivo and in vitro. MATERIALS AND METHODS XYPs were composed of 8 herbs, including the root of Bupleurum chinense DC., the root of Angelica sinensis (Oliv.) Diels, the root of Paeonia lactiflora Pall., the sclerotia of Poria cocos (Schw.) Wolf, the rhizome of Glycyrrhiza uralensis Fisch., the leaves of Mentha haplocalyx Briq., the rhizome of Atractylis lancea var. chinensis (Bunge) Kitam., and the rhizome of Zingiber officinale Roscoe, in a ratio of 5:5:5:5:4:1:5:5. The chronic unpredictable mild stress (CUMS) rat models were established. After that, the sucrose preference test (SPT) was carried out to evaluate if the rats were depressed. After 28 days of treatment, the forced swimming test and SPT were carried out to evaluate the antidepressant efficacy of XYPs. The feces, brain and plasma were taken out for 16SrRNA gene sequencing analysis, untargeted metabolomics and gut microbiota transformation analysis. RESULTS The results revealed multiple pathways affected by XYPs. Among them, the hydrolysis of fatty acids amide in brain decreased most significant via XYPs treatment. Moreover, the XYPs' metabolites which mainly derived from gut microbiota (benzoic acid, liquiritigenin, glycyrrhetinic acid and saikogenin D) were found in plasma and brain of CUMS rats and could inhibit the levels of FAAH in brain, which contributed to XYPs' antidepressant effect. CONCLUSIONS The potential antidepressant mechanism of XYPs by untargeted metabolomics combined with gut microbiota-transformation analysis was revealed, which further support the theory of gut-brain axis and provide valuable evidence of the drug discovery.
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Affiliation(s)
- Zheng-Wei Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China.
| | - Pei Han
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China.
| | - Jie Fu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China.
| | - Hang Yu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China.
| | - Hui Xu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China.
| | - Jia-Chun Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China.
| | - Jin-Yue Lu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China.
| | - Xin-Yu Yang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China.
| | - Hao-Jian Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China.
| | - Meng-Meng Bu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China.
| | - Jian-Dong Jiang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China.
| | - Yan Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences/Peking Union Medical College, Beijing, 100050, China.
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3
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Roman LJ, Snijders AM, Chang H, Mao JH, Jones KJA, Lawson GW. Effect of Husbandry Practices on the Fecal Microbiota of C57BL/6J Breeding Colonies Housed in 2 Different Barrier Facilities in the Same Institution. JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2023; 62:26-37. [PMID: 36755206 PMCID: PMC9936858 DOI: 10.30802/aalas-jaalas-22-000068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Evidence showing a relationship between the mouse gut microbiome and properties such as phenotype and reaction to therapeutic agents and other treatments has increased significantly over the past 20 to 30 y. Recent concerns regarding the reproducibility of animal experiments have underscored the importance of understanding this relationship and how differences in husbandry practices can affect the gut microbiome. The current study focuses on effects of different barrier practices in 2 barrier facilities at the same institution on the fecal microbiome of breeding C57Bl/6J mice. Ten female and 10 male C57Bl/6J mice were obtained in one shipment from Jackson Laboratories and were housed under different barrier conditions upon arrival. Fecal samples were collected on arrival and periodically thereafter and were sent to TransnetYX for microbiome analysis. Mice used for collection of feces were housed as breeding pairs, with a total of 5 breeding pairs per barrier. An additional fecal sample was collected from these mice at 8 wk after arrival. One F1 female and one F1 male from each breeding cage were housed as brother-sister breeding pairs and a fecal sample was collected from them at 8 wk of age. Brother-sister breeding colonies were continued through F3, with fecal samples for microbiome analysis were collected from each generation at 8 wk of age. Breeding colonies in the 2 barriers showed differences in relative abundance, α -diversity, and β -diversity. Our data indicate that differences in barrier husbandry practices, including the use of autoclaved cages, the degree of restricted access, feed treatment practices, and water provision practices, can affect fecal microbiome divergence in both the parental and filial generations of different breeding colonies. To our knowledge, this is the first study to examine the effect of barrier husbandry practices on the microbiome of breeding colonies through the F3 generation.
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Affiliation(s)
- Libette J Roman
- Office of Laboratory Animal Care, University of California Berkeley, Berkeley, California,,Corresponding author.
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Kristina JA Jones
- Office of Laboratory Animal Care, University of California Berkeley, Berkeley, California
| | - Gregory W Lawson
- Office of Laboratory Animal Care, University of California Berkeley, Berkeley, California
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4
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Xia H, Chen H, Cheng X, Yin M, Yao X, Ma J, Huang M, Chen G, Liu H. Zebrafish: an efficient vertebrate model for understanding role of gut microbiota. Mol Med 2022; 28:161. [PMID: 36564702 PMCID: PMC9789649 DOI: 10.1186/s10020-022-00579-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Gut microbiota plays a critical role in the maintenance of host health. As a low-cost and genetically tractable vertebrate model, zebrafish have been widely used for biological research. Zebrafish and humans share some similarities in intestinal physiology and function, and this allows zebrafish to be a surrogate model for investigating the crosstalk between the gut microbiota and host. Especially, zebrafish have features such as high fecundity, external fertilization, and early optical transparency. These enable the researchers to employ the fish to address questions not easily addressed in other animal models. In this review, we described the intestine structure of zebrafish. Also, we summarized the methods of generating a gnotobiotic zebrafish model, the factors affecting its intestinal flora, and the study progress of gut microbiota functions in zebrafish. Finally, we discussed the limitations and challenges of the zebrafish model for gut microbiota studies. In summary, this review established that zebrafish is an attractive research tool to understand mechanistic insights into host-microbe interaction.
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Affiliation(s)
- Hui Xia
- College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065, China
| | - Huimin Chen
- College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065, China
| | - Xue Cheng
- College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065, China
| | - Mingzhu Yin
- College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065, China
| | - Xiaowei Yao
- College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065, China
| | - Jun Ma
- College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065, China
| | - Mengzhen Huang
- College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065, China
| | - Gang Chen
- Hubei Provincial Hospital of Traditional Chinese Medicine, Wuhan, 430061, China.
| | - Hongtao Liu
- College of Basic Medicine, Hubei University of Chinese Medicine, Huangjiahu West Road 16, Hongshan Disctrict, Wuhan, 430065, China.
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5
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Cage Environment Regulates Gut Microbiota Independent of Toll-Like Receptors. Infect Immun 2021; 89:e0018721. [PMID: 33941577 DOI: 10.1128/iai.00187-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome orchestrates epithelial homeostasis and both local and remote immunological responses. Critical to these regulatory interactions are innate immune receptors termed Toll-like receptors (TLRs). Studies to date have implicated innate immunity and Toll-like receptors in shaping key features of the gut microbiome. However, a variety of biological and environmental variables are also implicated in determining gut microbiota composition. In this report, we hypothesized that cohousing and environment dominated the regulation of the gut microbiota in animal models independent of innate immunity. To determine the importance of these variables, innate immunity, or environment in shaping gut microbiota, we used a randomized cohousing strategy and transgenic TLR-deficient mice. We have found that mice cohoused together by genotype exhibited limited changes over time in the composition of the gut microbiota. However, for mice randomized to cage, we report extensive changes in the gut microbiota, independent of TLR function, whereby the fecal microbiota of TLR-deficient mice converges with that of wild-type mice. TLR5-deficient mice in these experiments exhibit greater susceptibility to comparative changes in the microbiota than other TLR-deficient mice and wild-type mice. Our work has broad implications for the study of innate immunity and host-microbiota interactions. Given the profound impact that gut dysbiosis may have on immunity, this report highlights the potential impact of cohousing on the gut microbiota and indices of inflammation as outcomes in biological models of infectious or inflammatory disease.
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6
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Long LL, Svenson KL, Mourino AJ, Michaud M, Fahey JR, Waterman L, Vandegrift KL, Adams MD. Shared and distinctive features of the gut microbiome of C57BL/6 mice from different vendors and production sites, and in response to a new vivarium. Lab Anim (NY) 2021; 50:185-195. [PMID: 34127866 DOI: 10.1038/s41684-021-00777-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 05/07/2021] [Indexed: 02/08/2023]
Abstract
Animal models play a critical role in establishing causal relationships between gut microbiota and disease. The laboratory mouse is widely used to study the role of microbes in various disorders; however, differences between mouse vendors, genetic lineages and husbandry protocols have been shown to contribute to variation in phenotypes and to non-reproducibility of experimental results. We sought to understand how gut microbiome profiles of mice vary by vendor, vendor production facility and health status upon receipt into an academic facility and how they change over 12 weeks in the new environment. C57BL/6 mice were sourced from two different production sites for each of three different vendors. Mice were shipped to an academic research vivarium, and fresh-catch stool samples were collected from mice immediately from the shipping box upon receipt, and again after 2, 6 and 12 weeks in the new facility. Substantial variation in bacterial proportional abundance was observed among mice from each vendor at the time of receipt, but shared microbes accounted for most sequence reads. Vendor-specific microbes were generally of low abundance. Microbial profiles of mice from all vendors exhibited shifts over time, highlighting the importance of environmental conditions on microbial dynamics. Our results emphasize the need for continued efforts to account for sources of variation in animal models and understand how they contribute to experimental reproducibility.
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Affiliation(s)
- Lauren L Long
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Karen L Svenson
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | | | - Michael Michaud
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - James R Fahey
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Linda Waterman
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Mark D Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
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7
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Avery EG, Bartolomaeus H, Maifeld A, Marko L, Wiig H, Wilck N, Rosshart SP, Forslund SK, Müller DN. The Gut Microbiome in Hypertension: Recent Advances and Future Perspectives. Circ Res 2021; 128:934-950. [PMID: 33793332 DOI: 10.1161/circresaha.121.318065] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The pathogenesis of hypertension is known to involve a diverse range of contributing factors including genetic, environmental, hormonal, hemodynamic and inflammatory forces, to name a few. There is mounting evidence to suggest that the gut microbiome plays an important role in the development and pathogenesis of hypertension. The gastrointestinal tract, which houses the largest compartment of immune cells in the body, represents the intersection of the environment and the host. Accordingly, lifestyle factors shape and are modulated by the microbiome, modifying the risk for hypertensive disease. One well-studied example is the consumption of dietary fibers, which leads to the production of short-chain fatty acids and can contribute to the expansion of anti-inflammatory immune cells, consequently protecting against the progression of hypertension. Dietary interventions such as fasting have also been shown to impact hypertension via the microbiome. Studying the microbiome in hypertensive disease presents a variety of unique challenges to the use of traditional model systems. Integrating microbiome considerations into preclinical research is crucial, and novel strategies to account for reciprocal host-microbiome interactions, such as the wildling mouse model, may provide new opportunities for translation. The intricacies of the role of the microbiome in hypertensive disease is a matter of ongoing research, and there are several technical considerations which should be accounted for moving forward. In this review we provide insights into the host-microbiome interaction and summarize the evidence of its importance in the regulation of blood pressure. Additionally, we provide recommendations for ongoing and future research, such that important insights from the microbiome field at large can be readily integrated in the context of hypertension.
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Affiliation(s)
- Ellen G Avery
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,For Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.G.A.,H.B., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,Freie Universität Berlin, Department of Biology, Chemistry, Pharmacy, Berlin, Germany (E.G.A.)
| | - Hendrik Bartolomaeus
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany (H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,For Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.G.A.,H.B., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.)
| | - Andras Maifeld
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany (H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.)
| | - Lajos Marko
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany (H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.)
| | - Helge Wiig
- Department of Biomedicine, University of Bergen, Norway (H.W.)
| | - Nicola Wilck
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany (H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,For Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.G.A.,H.B., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,For Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany (N.W.)
| | - Stephan P Rosshart
- Medical Center-University of Freiburg, Department of Medicine II, Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases, Freiburg, Germany (S.P.R.)
| | - Sofia K Forslund
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany (H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,For Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.G.A.,H.B., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.)
| | - Dominik N Müller
- Experimental and Clinical Research Center, a cooperation of Charité-Universitätsmedizin Berlin and Max Delbruck Center for Molecular Medicine, Berlin, Germany (E.G.A.,H.B.,A.M.,L.M.,N.W.,S.K.F.,D.N.M.).,Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany (H.B., A.M., L.M., N.W., S.K.F., D.N.M.).,For Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany (E.G.A.,H.B., N.W., S.K.F., D.N.M.).,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany (E.G.A., H.B., A.M., L.M., N.W., S.K.F., D.N.M.)
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8
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Guo H, Gibson SA, Ting JPY. Gut microbiota, NLR proteins, and intestinal homeostasis. J Exp Med 2021; 217:152098. [PMID: 32941596 PMCID: PMC7537383 DOI: 10.1084/jem.20181832] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 08/10/2020] [Accepted: 08/14/2020] [Indexed: 12/21/2022] Open
Abstract
The gastrointestinal tract harbors a highly complex microbial community, which is referred to as gut microbiota. With increasing evidence suggesting that the imbalance of gut microbiota plays a significant role in the pathogenesis of multiple diseases, interactions between the host immune system and the gut microbiota are now attracting emerging interest. Nucleotide-binding and leucine-rich repeat–containing receptors (NLRs) encompass a large number of innate immune sensors and receptors, which mediate the activation of Caspase-1 and the subsequent release of mature interleukin-1β and interleukin-18. Several family members have been found to restrain rather than activate inflammatory cytokines and immune signaling. NLR family members are central regulators of pathogen recognition, host immunity, and inflammation with utmost importance in human diseases. In this review, we focus on the potential roles played by NLRs in controlling and shaping the microbiota community and discuss how the functional axes interconnecting gut microbiota with NLRs impact the modulation of colitis, inflammatory bowel diseases, and colorectal cancer.
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Affiliation(s)
- Hao Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Sara A Gibson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jenny P Y Ting
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC.,Department of Microbiology-Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC
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9
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Unger AL, Eckstrom K, Jetton TL, Kraft J. Facility-dependent metabolic phenotype and gut bacterial composition in CD-1 mice from a single vendor: A brief report. PLoS One 2020; 15:e0238893. [PMID: 32956361 PMCID: PMC7505418 DOI: 10.1371/journal.pone.0238893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 08/25/2020] [Indexed: 12/16/2022] Open
Abstract
Utilization of murine models remains a valuable tool in biomedical research, yet, disease phenotype of mice across studies can vary considerably. With advances in next generation sequencing, it is increasingly recognized that inconsistencies in host phenotype can be attributed, at least in part, to differences in gut bacterial composition. Research with inbred murine strains demonstrates that housing conditions play a significant role in variations of gut bacterial composition, however, few studies have assessed whether observed variation influences host phenotype in response to an intervention. Our study initially sought to examine the effects of a long-term (9-months) dietary intervention (i.e., diets with distinct fatty acid compositions) on the metabolic health, in particular glucose homeostasis, of genetically-outbred male and female CD-1 mice. Yet, mice were shipped from two different husbandry facilities of the same commercial vendor (Cohort A and B, respectively), and we observed throughout the study that diet, sex, and aging differentially influenced the metabolic phenotype of mice depending on their husbandry facility of origin. Examination of the colonic bacteria of mice revealed distinct bacterial compositions, including 23 differentially abundant genera and an enhanced alpha diversity in mice of Cohort B compared to Cohort A. We also observed that a distinct metabolic phenotype was linked with these differentially abundant bacteria and indices of alpha diversity. Our findings support that metabolic phenotypic variation of mice of the same strain but shipped from different husbandry facilities may be influenced by their colonic bacterial community structure. Our work is an important precautionary note for future research of metabolic diseases via mouse models, particularly those that seek to examine factors such diet, sex, and aging.
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Affiliation(s)
- Allison L. Unger
- Department of Animal and Veterinary Sciences, The University of Vermont, Burlington, Vermont, United States of America
| | - Korin Eckstrom
- Department of Microbiology and Molecular Genetics, The University of Vermont, Burlington, Vermont, United States of America
| | - Thomas L. Jetton
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, The University of Vermont, Colchester, Vermont, United States of America
| | - Jana Kraft
- Department of Animal and Veterinary Sciences, The University of Vermont, Burlington, Vermont, United States of America
- Division of Endocrinology, Metabolism and Diabetes, Department of Medicine, The University of Vermont, Colchester, Vermont, United States of America
- * E-mail:
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10
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Dynamic and Asymmetric Changes of the Microbial Communities after Cohousing in Laboratory Mice. Cell Rep 2020; 27:3401-3412.e3. [PMID: 31189120 DOI: 10.1016/j.celrep.2019.05.042] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/08/2018] [Accepted: 05/10/2019] [Indexed: 12/17/2022] Open
Abstract
Horizontal transmission of the microbiota between different individuals is widely used to normalize the microbiota in laboratory mice. However, little is known about the dynamics of microbial communities and the level of microbiota transmission after cohousing. We extensively analyzed the fecal microbiota in Jackson and Taconic C57BL/6 mice to study horizontal transmission after weaning. Changes in the microbiota were clearly detected on day 3, almost plateaued on day 7, and resulted in near-comparable composition by day 28 after cohousing. Notably, the transmission of bacterial species was asymmetric in kinetics and abundance, resulting in a microbiota that is more similar to that of Jackson mice than Taconic. Several operational taxonomic units (OTUs) increased their abundance rapidly after cohousing in Taconic mice whereas several OTUs including two mucus-associated bacteria increased their abundance with delayed kinetics in Jackson mice. These studies provide insight into the dynamics and normalization of the microbiota during horizontal transmission.
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11
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Mandal RK, Denny JE, Waide ML, Li Q, Bhutiani N, Anderson CD, Baby BV, Jala VR, Egilmez NK, Schmidt NW. Temporospatial shifts within commercial laboratory mouse gut microbiota impact experimental reproducibility. BMC Biol 2020; 18:83. [PMID: 32620114 PMCID: PMC7334859 DOI: 10.1186/s12915-020-00810-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 06/16/2020] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Experimental reproducibility in mouse models is impacted by both genetics and environment. The generation of reproducible data is critical for the biomedical enterprise and has become a major concern for the scientific community and funding agencies alike. Among the factors that impact reproducibility in experimental mouse models is the variable composition of the microbiota in mice supplied by different commercial vendors. Less attention has been paid to how the microbiota of mice supplied by a particular vendor might change over time. RESULTS In the course of conducting a series of experiments in a mouse model of malaria, we observed a profound and lasting change in the severity of malaria in mice infected with Plasmodium yoelii; while for several years mice obtained from a specific production suite of a specific commercial vendor were able to clear the parasites effectively in a relatively short time, mice subsequently shipped from the same unit suffered much more severe disease. Gut microbiota analysis of frozen cecal samples identified a distinct and lasting shift in bacteria populations that coincided with the altered response of the later shipments of mice to infection with malaria parasites. Germ-free mice colonized with cecal microbiota from mice within the same production suite before and after this change followed by Plasmodium infection provided a direct demonstration that the change in gut microbiota profoundly impacted the severity of malaria. Moreover, spatial changes in gut microbiota composition were also shown to alter the acute bacterial burden following Salmonella infection, and tumor burden in a lung tumorigenesis model. CONCLUSION These changes in gut bacteria may have impacted the experimental reproducibility of diverse research groups and highlight the need for both laboratory animal providers and researchers to collaborate in determining the methods and criteria needed to stabilize the gut microbiota of animal breeding colonies and research cohorts, and to develop a microbiota solution to increase experimental rigor and reproducibility.
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Affiliation(s)
- Rabindra K Mandal
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, USA
- Present Address: Ryan White Center for Pediatric Infectious Diseases and Global Health, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202, USA
| | - Joshua E Denny
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, USA
| | - Morgan L Waide
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, USA
| | - Qingsheng Li
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, USA
| | - Neal Bhutiani
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, USA
| | - Charles D Anderson
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, USA
| | - Becca V Baby
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, USA
| | - Venkatakrishna R Jala
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, USA
| | - Nejat K Egilmez
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, USA
| | - Nathan W Schmidt
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, USA.
- Present Address: Ryan White Center for Pediatric Infectious Diseases and Global Health, Department of Pediatrics, Indiana University School of Medicine, 1044 W. Walnut St., Indianapolis, IN, 46202, USA.
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12
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Walters AW, Hughes RC, Call TB, Walker CJ, Wilcox H, Petersen SC, Rudman SM, Newell PD, Douglas AE, Schmidt PS, Chaston JM. The microbiota influences the Drosophila melanogaster life history strategy. Mol Ecol 2020; 29:639-653. [PMID: 31863671 DOI: 10.1111/mec.15344] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 12/03/2019] [Accepted: 12/16/2019] [Indexed: 12/17/2022]
Abstract
Organisms are locally adapted when members of a population have a fitness advantage in one location relative to conspecifics in other geographies. For example, across latitudinal gradients, some organisms may trade off between traits that maximize fitness components in one, but not both, of somatic maintenance or reproductive output. Latitudinal gradients in life history strategies are traditionally attributed to environmental selection on an animal's genotype, without any consideration of the possible impact of associated microorganisms ("microbiota") on life history traits. Here, we show in Drosophila melanogaster, a key model for studying local adaptation and life history strategy, that excluding the microbiota from definitions of local adaptation is a major shortfall. First, we reveal that an isogenic fly line reared with different bacteria varies the investment in early reproduction versus somatic maintenance. Next, we show that in wild fruit flies, the abundance of these same bacteria was correlated with the latitude and life history strategy of the flies, suggesting geographic specificity of the microbiota composition. Variation in microbiota composition of locally adapted D. melanogaster could be attributed to both the wild environment and host genetic selection. Finally, by eliminating or manipulating the microbiota of fly lines collected across a latitudinal gradient, we reveal that host genotype contributes to latitude-specific life history traits independent of the microbiota and that variation in the microbiota can suppress or reverse the differences between locally adapted fly lines. Together, these findings establish the microbiota composition of a model animal as an essential consideration in local adaptation.
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Affiliation(s)
- Amber W Walters
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Rachel C Hughes
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Tanner B Call
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Carson J Walker
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Hailey Wilcox
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Samara C Petersen
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | - Seth M Rudman
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Peter D Newell
- Department of Biological Sciences, SUNY Oswego, Oswego, NY, USA
| | - Angela E Douglas
- Department of Entomology and Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Paul S Schmidt
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - John M Chaston
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
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13
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Fang S, Chen X, Zhou L, Wang C, Chen Q, Lin R, Xiao T, Gan Q. Faecal microbiota and functional capacity associated with weaning weight in meat rabbits. Microb Biotechnol 2019; 12:1441-1452. [PMID: 31571427 PMCID: PMC6801154 DOI: 10.1111/1751-7915.13485] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/15/2019] [Accepted: 08/15/2019] [Indexed: 12/18/2022] Open
Abstract
Weaning weight is an important economic trait in the meat rabbit industry. Evidence has linked the gut microbiota to health and production performance in rabbits. However, the effect of gut microbiota on meat rabbit weaning weight remains unclear. In this study, we performed 16S rRNA gene sequencing analysis of 135 faecal samples from commercial Ira rabbits. We detected 50 OTUs significantly associated with weaning weight. OTUs that showed positive associations with weaning weight were mostly members of the family Ruminococcaceae which are important in degrading dietary fibres and producing butyrate. On the contrary, OTUs annotated to genera Blautia, Lachnoclostridium and Butyricicoccus correlated with fat deposition were negatively associated with weaning weight. Predicted functional capacity analysis revealed that 91 KOs and 26 KEGG pathways exhibited potential correlations with weaning weight. We found that gut microbiota involved in the metabolism of amino acids, butanoate, energy and monosaccharides affected weaning weight. Additionally, cross-validation analysis indicated that 16.16% of the variation in weaning weight was explained by the gut microbiome. Our findings provide important information to improve weaning weight of meat rabbits by modulating their gut microbiome.
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Affiliation(s)
- Shaoming Fang
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xuan Chen
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liwen Zhou
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Chongchong Wang
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Qiaohui Chen
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ruiyi Lin
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Tianfang Xiao
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - QianFu Gan
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
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14
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Goertz S, de Menezes AB, Birtles RJ, Fenn J, Lowe AE, MacColl ADC, Poulin B, Young S, Bradley JE, Taylor CH. Geographical location influences the composition of the gut microbiota in wild house mice (Mus musculus domesticus) at a fine spatial scale. PLoS One 2019; 14:e0222501. [PMID: 31557179 PMCID: PMC6767902 DOI: 10.1371/journal.pone.0222501] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/02/2019] [Indexed: 02/07/2023] Open
Abstract
The composition of the mammalian gut microbiota can be influenced by a multitude of environmental variables such as diet and infections. Studies investigating the effect of these variables on gut microbiota composition often sample across multiple separate populations and habitat types. In this study we explore how variation in the gut microbiota of the house mouse (Mus musculus domesticus) on the Isle of May, a small island off the east coast of Scotland, is associated with environmental and biological factors. Our study focuses on the effects of environmental variables, specifically trapping location and surrounding vegetation, as well as the host variables sex, age, body weight and endoparasite infection, on the gut microbiota composition across a fine spatial scale in a freely interbreeding population. We found that differences in gut microbiota composition were significantly associated with the trapping location of the host, even across this small spatial scale. Sex of the host showed a weak association with microbiota composition. Whilst sex and location could be identified as playing an important role in the compositional variation of the gut microbiota, 75% of the variation remains unexplained. Whereas other rodent studies have found associations between gut microbiota composition and age of the host or parasite infections, the present study could not clearly establish these associations. We conclude that fine spatial scales are important when considering gut microbiota composition and investigating differences among individuals.
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Affiliation(s)
- Sarah Goertz
- School of Life Sciences, University of Nottingham, Nottingham, United
Kingdom
| | | | - Richard J. Birtles
- School of Environment and Life Sciences, University of Salford,
Manchester, United Kingdom
| | - Jonathan Fenn
- School of Life Sciences, University of Nottingham, Nottingham, United
Kingdom
| | - Ann E. Lowe
- School of Life Sciences, University of Nottingham, Nottingham, United
Kingdom
| | | | - Benoit Poulin
- School of Life Sciences, University of Nottingham, Nottingham, United
Kingdom
| | - Stuart Young
- IUCN SSC Asian Wild Cattle Specialist Group, c/o Chester Zoo, Chester,
United Kingdom
| | - Janette E. Bradley
- School of Life Sciences, University of Nottingham, Nottingham, United
Kingdom
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15
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Hosie S, Ellis M, Swaminathan M, Ramalhosa F, Seger GO, Balasuriya GK, Gillberg C, Råstam M, Churilov L, McKeown SJ, Yalcinkaya N, Urvil P, Savidge T, Bell CA, Bodin O, Wood J, Franks AE, Bornstein JC, Hill-Yardin EL. Gastrointestinal dysfunction in patients and mice expressing the autism-associated R451C mutation in neuroligin-3. Autism Res 2019; 12:1043-1056. [PMID: 31119867 PMCID: PMC6606367 DOI: 10.1002/aur.2127] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Revised: 04/11/2019] [Accepted: 04/21/2019] [Indexed: 02/06/2023]
Abstract
Gastrointestinal (GI) problems constitute an important comorbidity in many patients with autism. Multiple mutations in the neuroligin family of synaptic adhesion molecules are implicated in autism, however whether they are expressed and impact GI function via changes in the enteric nervous system is unknown. We report the GI symptoms of two brothers with autism and an R451C mutation in Nlgn3 encoding the synaptic adhesion protein, neuroligin-3. We confirm the presence of an array of synaptic genes in the murine GI tract and investigate the impact of impaired synaptic protein expression in mice carrying the human neuroligin-3 R451C missense mutation (NL3R451C ). Assessing in vivo gut dysfunction, we report faster small intestinal transit in NL3R451C compared to wild-type mice. Using an ex vivo colonic motility assay, we show increased sensitivity to GABAA receptor modulation in NL3R451C mice, a well-established Central Nervous System (CNS) feature associated with this mutation. We further show increased numbers of small intestine myenteric neurons in NL3R451C mice. Although we observed altered sensitivity to GABAA receptor modulators in the colon, there was no change in colonic neuronal numbers including the number of GABA-immunoreactive myenteric neurons. We further identified altered fecal microbial communities in NL3R451C mice. These results suggest that the R451C mutation affects small intestinal and colonic function and alter neuronal numbers in the small intestine as well as impact fecal microbes. Our findings identify a novel GI phenotype associated with the R451C mutation and highlight NL3R451C mice as a useful preclinical model of GI dysfunction in autism. Autism Res 2019, 12: 1043-1056. © 2019 International Society for Autism Research, Wiley Periodicals, Inc. LAY SUMMARY: People with autism commonly experience gastrointestinal problems, however the cause is unknown. We report gut symptoms in patients with the autism-associated R451C mutation encoding the neuroligin-3 protein. We show that many of the genes implicated in autism are expressed in mouse gut. The neuroligin-3 R451C mutation alters the enteric nervous system, causes gastrointestinal dysfunction, and disrupts gut microbe populations in mice. Gut dysfunction in autism could be due to mutations that affect neuronal communication.
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Affiliation(s)
- Suzanne Hosie
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia
| | - Melina Ellis
- Department of Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Mathusi Swaminathan
- Department of Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Fatima Ramalhosa
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal
| | - Gracia O Seger
- Department of Physiology, The University of Melbourne, Parkville, VIC, Australia
| | | | - Christopher Gillberg
- Gillberg Neuropsychiatry Centre, Institute of Neuroscience and Physiology, University of Gothenburg, Göteborg, Sweden
| | - Maria Råstam
- Gillberg Neuropsychiatry Centre, Institute of Neuroscience and Physiology, University of Gothenburg, Göteborg, Sweden.,Department of Clinical Sciences Lund, Child and Adolescent Psychiatry, Lund University, Lund, Sweden
| | - Leonid Churilov
- School of Science Cluster, RMIT University, Melbourne City Campus, Melbourne, VIC, Australia.,Florey Institute of Neuroscience and Mental Health, Heidelberg, VIC, Australia
| | - Sonja J McKeown
- Cancer Program, Monash Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC, Australia
| | - Nalzi Yalcinkaya
- Texas Children's Microbiome Center, Texas Children's Hospital and Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Petri Urvil
- Texas Children's Microbiome Center, Texas Children's Hospital and Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Tor Savidge
- Texas Children's Microbiome Center, Texas Children's Hospital and Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Carolyn A Bell
- La Trobe University, Department of Physiology, Anatomy & Microbiology, School of Life Sciences, Bundoora, VIC, Australia
| | - Oonagh Bodin
- La Trobe University, Department of Physiology, Anatomy & Microbiology, School of Life Sciences, Bundoora, VIC, Australia
| | - Jen Wood
- La Trobe University, Department of Physiology, Anatomy & Microbiology, School of Life Sciences, Bundoora, VIC, Australia
| | - Ashley E Franks
- La Trobe University, Department of Physiology, Anatomy & Microbiology, School of Life Sciences, Bundoora, VIC, Australia
| | - Joel C Bornstein
- Department of Physiology, The University of Melbourne, Parkville, VIC, Australia
| | - Elisa L Hill-Yardin
- School of Health and Biomedical Sciences, RMIT University, Bundoora, VIC, Australia.,Department of Physiology, The University of Melbourne, Parkville, VIC, Australia
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16
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Dalby MJ, Aviello G, Ross AW, Walker AW, Barrett P, Morgan PJ. Diet induced obesity is independent of metabolic endotoxemia and TLR4 signalling, but markedly increases hypothalamic expression of the acute phase protein, SerpinA3N. Sci Rep 2018; 8:15648. [PMID: 30353127 PMCID: PMC6199263 DOI: 10.1038/s41598-018-33928-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/08/2018] [Indexed: 01/17/2023] Open
Abstract
Hypothalamic inflammation is thought to contribute to obesity. One potential mechanism is via gut microbiota derived bacterial lipopolysaccharide (LPS) entering into the circulation and activation of Toll-like receptor-4. This is called metabolic endotoxemia. Another potential mechanism is systemic inflammation arising from sustained exposure to high-fat diet (HFD) over more than 12 weeks. In this study we show that mice fed HFD over 8 weeks become obese and show elevated plasma LPS binding protein, yet body weight gain and adiposity is not attenuated in mice lacking Tlr4 or its co-receptor Cd14. In addition, caecal microbiota composition remained unchanged by diet. Exposure of mice to HFD over a more prolonged period (20 weeks) to drive systemic inflammation also caused obesity. RNAseq used to assess hypothalamic inflammation in these mice showed increased hypothalamic expression of Serpina3n and Socs3 in response to HFD, with few other genes altered. In situ hybridisation confirmed increased Serpina3n and Socs3 expression in the ARC and DMH at 20-weeks, but also at 8-weeks and increased SerpinA3N protein could be detected as early as 1 week on HFD. Overall these data show lack of hypothalamic inflammation in response to HFD and that metabolic endotoxemia does not link HFD to obesity.
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Affiliation(s)
- Matthew J Dalby
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Gabriella Aviello
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Alexander W Ross
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Alan W Walker
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Perry Barrett
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom
| | - Peter J Morgan
- Rowett Institute, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom.
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17
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Bacterial Methionine Metabolism Genes Influence Drosophila melanogaster Starvation Resistance. Appl Environ Microbiol 2018; 84:AEM.00662-18. [PMID: 29934334 DOI: 10.1128/aem.00662-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/25/2018] [Indexed: 11/20/2022] Open
Abstract
Animal-associated microorganisms (microbiota) dramatically influence the nutritional and physiological traits of their hosts. To expand our understanding of such influences, we predicted bacterial genes that influence a quantitative animal trait by a comparative genomic approach, and we extended these predictions via mutant analysis. We focused on Drosophila melanogaster starvation resistance (SR). We first confirmed that D. melanogaster SR responds to the microbiota by demonstrating that bacterium-free flies have greater SR than flies bearing a standard 5-species microbial community, and we extended this analysis by revealing the species-specific influences of 38 genome-sequenced bacterial species on D. melanogaster SR. A subsequent metagenome-wide association analysis predicted bacterial genes with potential influence on D. melanogaster SR, among which were significant enrichments in bacterial genes for the metabolism of sulfur-containing amino acids and B vitamins. Dietary supplementation experiments established that the addition of methionine, but not B vitamins, to the diets significantly lowered D. melanogaster SR in a way that was additive, but not interactive, with the microbiota. A direct role for bacterial methionine metabolism genes in D. melanogaster SR was subsequently confirmed by analysis of flies that were reared individually with distinct methionine cycle Escherichia coli mutants. The correlated responses of D. melanogaster SR to bacterial methionine metabolism mutants and dietary modification are consistent with the established finding that bacteria can influence fly phenotypes through dietary modification, although we do not provide explicit evidence of this conclusion. Taken together, this work reveals that D. melanogaster SR is a microbiota-responsive trait, and specific bacterial genes underlie these influences.IMPORTANCE Extending descriptive studies of animal-associated microorganisms (microbiota) to define causal mechanistic bases for their influence on animal traits is an emerging imperative. In this study, we reveal that D. melanogaster starvation resistance (SR), a model quantitative trait in animal genetics, responds to the presence and identity of the microbiota. Using a predictive analysis, we reveal that the amino acid methionine has a key influence on D. melanogaster SR and show that bacterial methionine metabolism mutants alter normal patterns of SR in flies bearing the bacteria. Our data further suggest that these effects are additive, and we propose the untested hypothesis that, similar to bacterial effects on fruit fly triacylglyceride deposition, the bacterial influence may be through dietary modification. Together, these findings expand our understanding of the bacterial genetic basis for influence on a nutritionally relevant trait of a model animal host.
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18
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Miyoshi J, Leone V, Nobutani K, Musch MW, Martinez-Guryn K, Wang Y, Miyoshi S, Bobe AM, Eren AM, Chang EB. Minimizing confounders and increasing data quality in murine models for studies of the gut microbiome. PeerJ 2018; 6:e5166. [PMID: 30013837 PMCID: PMC6046200 DOI: 10.7717/peerj.5166] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 06/15/2018] [Indexed: 12/28/2022] Open
Abstract
Murine models are widely used to explore host-microbe interactions because of the challenges and limitations inherent to human studies. However, microbiome studies in murine models are not without their nuances. Inter-individual variations in gut microbiota are frequent even in animals housed within the same room. We therefore sought to find an efficient and effective standard operating procedure (SOP) to minimize these effects to improve consistency and reproducibility in murine microbiota studies. Mice were housed in a single room under specific-pathogen free conditions. Soiled cage bedding was routinely mixed weekly and distributed among all cages from weaning (three weeks old) until the onset of the study. Females and males were separated by sex and group-housed (up to five mice/cage) at weaning. 16S rRNA gene analyses of fecal samples showed that this protocol significantly reduced pre-study variability of gut microbiota amongst animals compared to other conventional measures used to normalize microbiota when large experimental cohorts have been required. A significant and consistent effect size was observed in gut microbiota when mice were switched from regular chow to purified diet in both sexes. However, sex and aging appeared to be independent drivers of gut microbial assemblage and should be taken into account in studies of this nature. In summary, we report a practical and effective pre-study SOP for normalizing the gut microbiome of murine cohorts that minimizes inter-individual variability and resolves co-housing problems inherent to male mice. This SOP may increase quality, rigor, and reproducibility of data acquisition and analysis.
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Affiliation(s)
- Jun Miyoshi
- Department of Medicine, The University of Chicago, Chicago, IL, United States of America
| | - Vanessa Leone
- Department of Medicine, The University of Chicago, Chicago, IL, United States of America
| | - Kentaro Nobutani
- Department of Medicine, The University of Chicago, Chicago, IL, United States of America
| | - Mark W Musch
- Department of Medicine, The University of Chicago, Chicago, IL, United States of America
| | - Kristina Martinez-Guryn
- Department of Medicine, The University of Chicago, Chicago, IL, United States of America.,Biomedical Sciences Program, Midwestern University, Downers Grove, IL, United States of America
| | - Yunwei Wang
- Department of Medicine, The University of Chicago, Chicago, IL, United States of America
| | - Sawako Miyoshi
- Department of Medicine, The University of Chicago, Chicago, IL, United States of America
| | - Alexandria M Bobe
- Department of Medicine, The University of Chicago, Chicago, IL, United States of America
| | - A Murat Eren
- Department of Medicine, The University of Chicago, Chicago, IL, United States of America
| | - Eugene B Chang
- Department of Medicine, The University of Chicago, Chicago, IL, United States of America
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19
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Turner PV. The role of the gut microbiota on animal model reproducibility. Animal Model Exp Med 2018; 1:109-115. [PMID: 30891555 PMCID: PMC6388061 DOI: 10.1002/ame2.12022] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/08/2018] [Indexed: 12/24/2022] Open
Abstract
The gut microbiota is composed of approximately 1010-1014 cells, including fungi, bacteria, archaea, protozoa, viruses, and bacteriophages; their genes and their various metabolites were found throughout the gastrointestinal tract. It has co-evolved with each species to assist with day to day bodily functions, such as digestion, metabolism of xenobiotics, development of mucosal immunity and immunomodulation, and protection against invading pathogens. Because of the significant beneficial impact that gut microbiota may have, there is interest in learning more about it and translating these findings into clinical therapies. Results from recent studies characterizing the gut microbiota of various species have demonstrated the range of influences that may affect gut microbiota diversity, including animal strain, obesity, types of enrichment used, bedding and housing methods, treatment with antimicrobials, vendor source, specific animal housing, diet, and intercurrent disease. Relatively little is known about the functional consequences of alterations of the gut microbiota and exactly how changes in richness and diversity of the microbiota translate into changes in health and susceptibility to disease. Furthermore, questions have been raised as to whether germ-free or even ultraclean, barrier-raised mice are relevant models of human disease, given their significantly reduced gut microbiota diversity and complexity compared with conventionally housed mice. In addition, evidence suggests that the specific anatomical location selected for assessing the gut microbiota has a highly significant effect on study outcomes, in that bacterial phyla change significantly along the gastrointestinal tract. This paper will explore animal model reproducibility in light of this information about the gut microbiota.
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Mamantopoulos M, Ronchi F, McCoy KD, Wullaert A. Inflammasomes make the case for littermate-controlled experimental design in studying host-microbiota interactions. Gut Microbes 2018; 9:374-381. [PMID: 29672197 PMCID: PMC6219641 DOI: 10.1080/19490976.2017.1421888] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Several human diseases are thought to evolve due to a combination of host genetic mutations and environmental factors that include alterations in intestinal microbiota composition termed dysbiosis. Although in some cases, host genetics may shape the gut microbiota and enable it to provoke disease, experimentally disentangling cause and consequence in such host-microbe interactions requires strict control over non-genetic confounding factors. Mouse genetic studies previously proposed Nlrp6/ASC inflammasomes as innate immunity regulators of the intestinal ecosystem. In contrast, using littermate-controlled experimental setups, we recently showed that Nlrp6/ASC inflammasomes do not alter the gut microbiota composition. Our analyses indicated that maternal inheritance and long-term separate housing are non-genetic confounders that preclude the use of non-littermate mice when analyzing host genetic effects on intestinal ecology. Here, we summarize and discuss our gut microbiota analyses in inflammasome-deficient mice for illustrating the importance of littermate experimental design in studying host-microbiota interactions.
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Affiliation(s)
- Michail Mamantopoulos
- Department of Internal Medicine, Ghent University, Ghent, Belgium,VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium,Ghent Gut Inflammation Group (GGIG), Ghent University, Ghent, Belgium
| | - Francesca Ronchi
- Department for BioMedical Research (DBMR), University of Bern, Inselspital, 3012 Bern, Switzerland
| | - Kathy D. McCoy
- Department of Physiology and Pharmacology and Gastrointestinal Research Group, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary AB T2N 4N1, Canada
| | - Andy Wullaert
- Department of Internal Medicine, Ghent University, Ghent, Belgium,VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium,Ghent Gut Inflammation Group (GGIG), Ghent University, Ghent, Belgium,CONTACT Andy Wullaert
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21
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Mamantopoulos M, Ronchi F, Van Hauwermeiren F, Vieira-Silva S, Yilmaz B, Martens L, Saeys Y, Drexler SK, Yazdi AS, Raes J, Lamkanfi M, McCoy KD, Wullaert A. Nlrp6- and ASC-Dependent Inflammasomes Do Not Shape the Commensal Gut Microbiota Composition. Immunity 2017; 47:339-348.e4. [PMID: 28801232 DOI: 10.1016/j.immuni.2017.07.011] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/27/2017] [Accepted: 07/18/2017] [Indexed: 01/16/2023]
Abstract
The gut microbiota regulate susceptibility to multiple human diseases. The Nlrp6-ASC inflammasome is widely regarded as a hallmark host innate immune axis that shapes the gut microbiota composition. This notion stems from studies reporting dysbiosis in mice lacking these inflammasome components when compared with non-littermate wild-type animals. Here, we describe microbial analyses in inflammasome-deficient mice while minimizing non-genetic confounders using littermate-controlled Nlrp6-deficient mice and ex-germ-free littermate-controlled ASC-deficient mice that were all allowed to shape their gut microbiota naturally after birth. Careful microbial phylogenetic analyses of these cohorts failed to reveal regulation of the gut microbiota composition by the Nlrp6- and ASC-dependent inflammasomes. Our results obtained in two geographically separated animal facilities dismiss a generalizable impact of Nlrp6- and ASC-dependent inflammasomes on the composition of the commensal gut microbiota and highlight the necessity for littermate-controlled experimental design in assessing the influence of host immunity on gut microbial ecology.
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Affiliation(s)
- Michail Mamantopoulos
- Department of Internal Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
| | - Francesca Ronchi
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland
| | - Filip Van Hauwermeiren
- Department of Internal Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, KU Leuven, Rega Institute, Leuven, Belgium; VIB-KU Leuven Center for Microbiology, VIB, Leuven, Belgium
| | - Bahtiyar Yilmaz
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland
| | - Liesbet Martens
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Yvan Saeys
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium; Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | | | - Amir S Yazdi
- Department of Dermatology, University of Tübingen, Tübingen, Germany
| | - Jeroen Raes
- Department of Microbiology and Immunology, KU Leuven, Rega Institute, Leuven, Belgium; VIB-KU Leuven Center for Microbiology, VIB, Leuven, Belgium
| | - Mohamed Lamkanfi
- Department of Internal Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium
| | - Kathy D McCoy
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern, Bern, Switzerland; Department of Physiology and Pharmacology and Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - Andy Wullaert
- Department of Internal Medicine, Ghent University, Ghent, Belgium; VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium.
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22
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Ehret T, Torelli F, Klotz C, Pedersen AB, Seeber F. Translational Rodent Models for Research on Parasitic Protozoa-A Review of Confounders and Possibilities. Front Cell Infect Microbiol 2017. [PMID: 28638807 PMCID: PMC5461347 DOI: 10.3389/fcimb.2017.00238] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Rodents, in particular Mus musculus, have a long and invaluable history as models for human diseases in biomedical research, although their translational value has been challenged in a number of cases. We provide some examples in which rodents have been suboptimal as models for human biology and discuss confounders which influence experiments and may explain some of the misleading results. Infections of rodents with protozoan parasites are no exception in requiring close consideration upon model choice. We focus on the significant differences between inbred, outbred and wild animals, and the importance of factors such as microbiota, which are gaining attention as crucial variables in infection experiments. Frequently, mouse or rat models are chosen for convenience, e.g., availability in the institution rather than on an unbiased evaluation of whether they provide the answer to a given question. Apart from a general discussion on translational success or failure, we provide examples where infections with single-celled parasites in a chosen lab rodent gave contradictory or misleading results, and when possible discuss the reason for this. We present emerging alternatives to traditional rodent models, such as humanized mice and organoid primary cell cultures. So-called recombinant inbred strains such as the Collaborative Cross collection are also a potential solution for certain challenges. In addition, we emphasize the advantages of using wild rodents for certain immunological, ecological, and/or behavioral questions. The experimental challenges (e.g., availability of species-specific reagents) that come with the use of such non-model systems are also discussed. Our intention is to foster critical judgment of both traditional and newly available translational rodent models for research on parasitic protozoa that can complement the existing mouse and rat models.
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Affiliation(s)
- Totta Ehret
- FG16 - Mycotic and Parasitic Agents and Mycobacteria, Robert Koch InstituteBerlin, Germany.,Department of Molecular Parasitology, Humboldt-Universität zu BerlinBerlin, Germany
| | - Francesca Torelli
- FG16 - Mycotic and Parasitic Agents and Mycobacteria, Robert Koch InstituteBerlin, Germany
| | - Christian Klotz
- FG16 - Mycotic and Parasitic Agents and Mycobacteria, Robert Koch InstituteBerlin, Germany
| | - Amy B Pedersen
- School of Biological Sciences, University of EdinburghEdinburgh, United Kingdom
| | - Frank Seeber
- FG16 - Mycotic and Parasitic Agents and Mycobacteria, Robert Koch InstituteBerlin, Germany
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23
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Choo JM, Trim PJ, Leong LEX, Abell GCJ, Brune C, Jeffries N, Wesselingh S, Dear TN, Snel MF, Rogers GB. Inbred Mouse Populations Exhibit Intergenerational Changes in Intestinal Microbiota Composition and Function Following Introduction to a Facility. Front Microbiol 2017; 8:608. [PMID: 28443082 PMCID: PMC5387074 DOI: 10.3389/fmicb.2017.00608] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/24/2017] [Indexed: 12/31/2022] Open
Abstract
Inbred mice are used to investigate many aspects of human physiology, including susceptibility to disease and response to therapies. Despite increasing evidence that the composition and function of the murine intestinal microbiota can substantially influence a broad range of experimental outcomes, relatively little is known about microbiome dynamics within experimental mouse populations. We investigated changes in the intestinal microbiome between C57BL/6J mice spanning six generations (assessed at generations 1, 2, 3, and 6), following their introduction to a stringently controlled facility. Fecal microbiota composition and function were assessed by 16S rRNA gene amplicon sequencing and liquid chromatography mass spectrometry, respectively. Significant divergence of the intestinal microbiota between founder and second generation mice, as well as continuing inter-generational variance, was observed. Bacterial taxa whose relative abundance changed significantly through time included Akkermansia, Turicibacter, and Bifidobacterium (p < 0.05), all of which are recognized as having the potential to substantially influence host physiology. Shifts in microbiota composition were mirrored by corresponding differences in the fecal metabolome (r = 0.57, p = 0.0001), with notable differences in levels of tryptophan pathway metabolites and amino acids, including glutamine, glutamate and aspartate. We related the magnitude of changes in the intestinal microbiota and metabolome characteristics during acclimation to those observed between populations housed in separate facilities, which differed in regards to husbandry, barrier conditions and dietary intake. The microbiome variance reported here has implications for experimental reproducibility, and as a consequence, experimental design and the interpretation of research outcomes across wide range of contexts.
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Affiliation(s)
- Jocelyn M Choo
- Infection and Immunity Theme, South Australian Health and Medical Research Institute, AdelaideSA, Australia
| | - Paul J Trim
- Lysosomal Diseases Research Unit, Nutrition and Metabolism Theme, South Australia Health and Medical Research Institute, AdelaideSA, Australia
| | - Lex E X Leong
- Infection and Immunity Theme, South Australian Health and Medical Research Institute, AdelaideSA, Australia
| | - Guy C J Abell
- School of Medicine, Flinders University, AdelaideSA, Australia
| | - Carly Brune
- Bioresources facility, South Australia Health and Medical Research Institute, AdelaideSA, Australia
| | - Nicole Jeffries
- Bioresources facility, South Australia Health and Medical Research Institute, AdelaideSA, Australia
| | - Steve Wesselingh
- Infection and Immunity Theme, South Australian Health and Medical Research Institute, AdelaideSA, Australia
| | - T N Dear
- Infection and Immunity Theme, South Australian Health and Medical Research Institute, AdelaideSA, Australia
| | - Marten F Snel
- Lysosomal Diseases Research Unit, Nutrition and Metabolism Theme, South Australia Health and Medical Research Institute, AdelaideSA, Australia
| | - Geraint B Rogers
- Infection and Immunity Theme, South Australian Health and Medical Research Institute, AdelaideSA, Australia.,School of Medicine, Flinders University, AdelaideSA, Australia
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24
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Divergent Relationships between Fecal Microbiota and Metabolome following Distinct Antibiotic-Induced Disruptions. mSphere 2017; 2:mSphere00005-17. [PMID: 28194448 PMCID: PMC5299068 DOI: 10.1128/msphere.00005-17] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 01/13/2017] [Indexed: 12/11/2022] Open
Abstract
Despite the fundamental importance of antibiotic therapies to human health, their functional impact on the intestinal microbiome and its subsequent ability to recover are poorly understood. Much research in this area has focused on changes in microbiota composition, despite the interdependency and overlapping functions of many members of the microbial community. These relationships make prediction of the functional impact of microbiota-level changes difficult, while analyses based on the metabolome alone provide relatively little insight into the taxon-level changes that underpin changes in metabolite levels. Here, we used combined microbiota and metabolome profiling to characterize changes associated with clinically important antibiotic combinations with distinct effects on the gut. Correlation analysis of changes in the metabolome and microbiota indicate that a combined approach will be essential for a mechanistic understanding of the functional impact of distinct antibiotic classes. The intestinal microbiome plays an essential role in regulating many aspects of host physiology, and its disruption through antibiotic exposure has been implicated in the development of a range of serious pathologies. The complex metabolic relationships that exist between members of the intestinal microbiota and the potential redundancy in functional pathways mean that an integrative analysis of changes in both structure and function are needed to understand the impact of antibiotic exposure. We used a combination of next-generation sequencing and nuclear magnetic resonance (NMR) metabolomics to characterize the effects of two clinically important antibiotic treatments, ciprofloxacin and vancomycin-imipenem, on the intestinal microbiomes of female C57BL/6 mice. This assessment was performed longitudinally and encompassed both antibiotic challenge and subsequent microbiome reestablishment. Both antibiotic treatments significantly altered the microbiota and metabolite compositions of fecal pellets during challenge and recovery. Spearman’s correlation analysis of microbiota and NMR data revealed that, while some metabolites could be correlated with individual operational taxonomic units (OTUs), frequently multiple OTUs were associated with a significant change in a given metabolite. Furthermore, one metabolite, arginine, can be associated with increases/decreases in different sets of OTUs under differing conditions. Taken together, these findings indicate that reliance on shifts in one data set alone will generate an incomplete picture of the functional effect of antibiotic intervention. A full mechanistic understanding will require knowledge of the baseline microbiota composition, combined with both a comparison and an integration of microbiota, metabolomics, and phenotypic data. IMPORTANCE Despite the fundamental importance of antibiotic therapies to human health, their functional impact on the intestinal microbiome and its subsequent ability to recover are poorly understood. Much research in this area has focused on changes in microbiota composition, despite the interdependency and overlapping functions of many members of the microbial community. These relationships make prediction of the functional impact of microbiota-level changes difficult, while analyses based on the metabolome alone provide relatively little insight into the taxon-level changes that underpin changes in metabolite levels. Here, we used combined microbiota and metabolome profiling to characterize changes associated with clinically important antibiotic combinations with distinct effects on the gut. Correlation analysis of changes in the metabolome and microbiota indicate that a combined approach will be essential for a mechanistic understanding of the functional impact of distinct antibiotic classes.
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25
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Stahl M, Graef FA, Vallance BA. Mouse Models for Campylobacter jejuni Colonization and Infection. Methods Mol Biol 2017; 1512:171-188. [PMID: 27885607 DOI: 10.1007/978-1-4939-6536-6_15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Relevant animal models for Campylobacter jejuni infection have been difficult to establish due to C. jejuni's inability to cause disease in many common animal research models. Fortunately, recent work has proven successful in developing several new and relevant mouse models of C. jejuni infection, including the SIGIRR-deficient mouse strain that develops acute enterocolitis in response to C. jejuni. Here we describe how to properly infect mice with C. jejuni, as well as a number of accompanying histological techniques to aid in studying C. jejuni colonization and infection in mice.
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Affiliation(s)
- Martin Stahl
- Division of Gastroenterology, Department of Pediatrics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, V6H 3V4, Canada
| | - Franziska A Graef
- Division of Gastroenterology, Department of Pediatrics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, V6H 3V4, Canada
| | - Bruce A Vallance
- Division of Gastroenterology, Department of Pediatrics, Child and Family Research Institute, University of British Columbia, Vancouver, BC, V6H 3V4, Canada.
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26
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Studer N, Desharnais L, Beutler M, Brugiroux S, Terrazos MA, Menin L, Schürch CM, McCoy KD, Kuehne SA, Minton NP, Stecher B, Bernier-Latmani R, Hapfelmeier S. Functional Intestinal Bile Acid 7α-Dehydroxylation by Clostridium scindens Associated with Protection from Clostridium difficile Infection in a Gnotobiotic Mouse Model. Front Cell Infect Microbiol 2016; 6:191. [PMID: 28066726 PMCID: PMC5168579 DOI: 10.3389/fcimb.2016.00191] [Citation(s) in RCA: 129] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/05/2016] [Indexed: 12/26/2022] Open
Abstract
Bile acids, important mediators of lipid absorption, also act as hormone-like regulators and as antimicrobial molecules. In all these functions their potency is modulated by a variety of chemical modifications catalyzed by bacteria of the healthy gut microbiota, generating a complex variety of secondary bile acids. Intestinal commensal organisms are well-adapted to normal concentrations of bile acids in the gut. In contrast, physiological concentrations of the various intestinal bile acid species play an important role in the resistance to intestinal colonization by pathogens such as Clostridium difficile. Antibiotic therapy can perturb the gut microbiota and thereby impair the production of protective secondary bile acids. The most important bile acid transformation is 7α-dehydroxylation, producing deoxycholic acid (DCA) and lithocholic acid (LCA). The enzymatic pathway carrying out 7α-dehydroxylation is restricted to a narrow phylogenetic group of commensal bacteria, the best-characterized of which is Clostridium scindens. Like many other intestinal commensal species, 7-dehydroxylating bacteria are understudied in vivo. Conventional animals contain variable and uncharacterized indigenous 7α-dehydroxylating organisms that cannot be selectively removed, making controlled colonization with a specific strain in the context of an undisturbed microbiota unfeasible. In the present study, we used a recently established, standardized gnotobiotic mouse model that is stably associated with a simplified murine 12-species “oligo-mouse microbiota” (Oligo-MM12). It is representative of the major murine intestinal bacterial phyla, but is deficient for 7α-dehydroxylation. We find that the Oligo-MM12 consortium carries out bile acid deconjugation, a prerequisite for 7α-dehydroxylation, and confers no resistance to C. difficile infection (CDI). Amendment of Oligo-MM12 with C. scindens normalized the large intestinal bile acid composition by reconstituting 7α-dehydroxylation. These changes had only minor effects on the composition of the native Oligo-MM12, but significantly decreased early large intestinal C. difficile colonization and pathogenesis. The delayed pathogenesis of C. difficile in C. scindens-colonized mice was associated with breakdown of cecal microbial bile acid transformation.
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Affiliation(s)
- Nicolas Studer
- Institute for Infectious Diseases, University of BernBern, Switzerland; Graduate School for Cellular and Biomedical Sciences, University of BernBern, Switzerland
| | - Lyne Desharnais
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne, Switzerland
| | - Markus Beutler
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich (LMU) Munich, Germany
| | - Sandrine Brugiroux
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich (LMU) Munich, Germany
| | - Miguel A Terrazos
- Institute for Infectious Diseases, University of Bern Bern, Switzerland
| | - Laure Menin
- Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne, Switzerland
| | | | - Kathy D McCoy
- Maurice Müller Laboratories (DKF), Universitätsklinik für Viszerale Chirurgie und Medizin Inselspital, University of Bern Bern, Switzerland
| | - Sarah A Kuehne
- Clostridia Research Group, Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC) Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham Nottingham, UK
| | - Nigel P Minton
- Clostridia Research Group, Biotechnology and Biological Sciences Research Council (BBSRC) and the Engineering and Physical Sciences Research Council (EPSRC) Synthetic Biology Research Centre, School of Life Sciences, University of Nottingham Nottingham, UK
| | - Bärbel Stecher
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Ludwig-Maximilians-University of Munich (LMU)Munich, Germany; German Center for Infection Research, Deutsches Zentrum für Infektionsforschung (DZIF), Partner Site Ludwig-Maximilians-University of Munich (LMU)Munich, Germany
| | - Rizlan Bernier-Latmani
- Environmental Microbiology Laboratory, École Polytechnique Fédérale de Lausanne (EPFL) Lausanne, Switzerland
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27
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Rahman K, Desai C, Iyer SS, Thorn NE, Kumar P, Liu Y, Smith T, Neish AS, Li H, Tan S, Wu P, Liu X, Yu Y, Farris AB, Nusrat A, Parkos CA, Anania FA. Loss of Junctional Adhesion Molecule A Promotes Severe Steatohepatitis in Mice on a Diet High in Saturated Fat, Fructose, and Cholesterol. Gastroenterology 2016; 151:733-746.e12. [PMID: 27342212 PMCID: PMC5037035 DOI: 10.1053/j.gastro.2016.06.022] [Citation(s) in RCA: 217] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 05/19/2016] [Accepted: 06/10/2016] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS There is evidence from clinical studies that compromised intestinal epithelial permeability contributes to the development of nonalcoholic steatohepatitis (NASH), but the exact mechanisms are not clear. Mice with disruption of the gene (F11r) encoding junctional adhesion molecule A (JAM-A) have defects in intestinal epithelial permeability. We used these mice to study how disruption of the intestinal epithelial barrier contributes to NASH. METHODS Male C57BL/6 (control) or F11r(-/-) mice were fed a normal diet or a diet high in saturated fat, fructose, and cholesterol (HFCD) for 8 weeks. Liver and intestinal tissues were collected and analyzed by histology, quantitative reverse-transcription polymerase chain reaction, and flow cytometry. Intestinal epithelial permeability was assessed in mice by measuring permeability to fluorescently labeled dextran. The intestinal microbiota were analyzed using 16S ribosomal RNA sequencing. We also analyzed biopsy specimens from proximal colons of 30 patients with nonalcoholic fatty liver disease (NAFLD) and 19 subjects without NAFLD (controls) undergoing surveillance colonoscopy. RESULTS F11r(-/-) mice fed a HFCD, but not a normal diet, developed histologic and pathologic features of severe NASH including steatosis, lobular inflammation, hepatocellular ballooning, and fibrosis, whereas control mice fed a HFCD developed only modest steatosis. Interestingly, there were no differences in body weight, ratio of liver weight:body weight, or glucose homeostasis between control and F11r(-/-) mice fed a HFCD. In these mice, liver injury was associated with significant increases in mucosal inflammation, tight junction disruption, and intestinal epithelial permeability to bacterial endotoxins, compared with control mice or F11r(-/-) mice fed a normal diet. The HFCD led to a significant increase in inflammatory microbial taxa in F11r(-/-) mice, compared with control mice. Administration of oral antibiotics or sequestration of bacterial endotoxins with sevelamer hydrochloride reduced mucosal inflammation and restored normal liver histology in F11r(-/-) mice fed a HFCD. Protein and transcript levels of JAM-A were significantly lower in the intestinal mucosa of patients with NAFLD than without NAFLD; decreased expression of JAM-A correlated with increased mucosal inflammation. CONCLUSIONS Mice with defects in intestinal epithelial permeability develop more severe steatohepatitis after a HFCD than control mice, and colon tissues from patients with NAFLD have lower levels of JAM-A and higher levels of inflammation than subjects without NAFLD. These findings indicate that intestinal epithelial barrier function and microbial dysbiosis contribute to the development of NASH. Restoration of intestinal barrier integrity and manipulation of gut microbiota might be developed as therapeutic strategies for patients with NASH.
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Affiliation(s)
- Khalidur Rahman
- Division of Digestive Diseases, Department of Medicine, Yerkes National Primate Center, Emory University, Atlanta, Georgia; Atlanta VA Medical Center, Decatur, Georgia.
| | - Chirayu Desai
- P.D. Patel Institute of Applied Sciences, Charotar University of Science and Technology, Gujarat, India
| | - Smita S Iyer
- Microbiology and Immunology, Yerkes National Primate Center, Emory University, Atlanta, Georgia
| | - Natalie E Thorn
- Division of Digestive Diseases, Department of Medicine, Yerkes National Primate Center, Emory University, Atlanta, Georgia
| | - Pradeep Kumar
- Division of Digestive Diseases, Department of Medicine, Yerkes National Primate Center, Emory University, Atlanta, Georgia
| | | | - Tekla Smith
- Division of Digestive Diseases, Department of Medicine, Yerkes National Primate Center, Emory University, Atlanta, Georgia; Atlanta VA Medical Center, Decatur, Georgia
| | - Andrew S Neish
- Department of Pathology and Laboratory Medicine, Yerkes National Primate Center, Emory University, Atlanta, Georgia
| | - Hongliang Li
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China; Cardiovascular Research Institute, Renmin Hospital of Wuhan University, Wuhan, China
| | - Shiyun Tan
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Pengbo Wu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Xiaoxiong Liu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China; Cardiovascular Research Institute, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yuanjie Yu
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Alton B Farris
- Department of Pathology and Laboratory Medicine, Yerkes National Primate Center, Emory University, Atlanta, Georgia
| | - Asma Nusrat
- Department of Pathology, The University of Michigan, Ann Arbor, Michigan
| | - Charles A Parkos
- Department of Pathology, The University of Michigan, Ann Arbor, Michigan
| | - Frank A Anania
- Division of Digestive Diseases, Department of Medicine, Yerkes National Primate Center, Emory University, Atlanta, Georgia; Atlanta VA Medical Center, Decatur, Georgia.
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28
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Koyle ML, Veloz M, Judd AM, Wong ACN, Newell PD, Douglas AE, Chaston JM. Rearing the Fruit Fly Drosophila melanogaster Under Axenic and Gnotobiotic Conditions. J Vis Exp 2016. [PMID: 27500374 DOI: 10.3791/54219] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The influence of microbes on myriad animal traits and behaviors has been increasingly recognized in recent years. The fruit fly Drosophila melanogaster is a model for understanding microbial interactions with animal hosts, facilitated by approaches to rear large sample sizes of Drosophila under microorganism-free (axenic) conditions, or with defined microbial communities (gnotobiotic). This work outlines a method for collection of Drosophila embryos, hypochlorite dechorionation and sterilization, and transfer to sterile diet. Sterilized embryos are transferred to sterile diet in 50 ml centrifuge tubes, and developing larvae and adults remain free of any exogenous microbes until the vials are opened. Alternatively, flies with a defined microbiota can be reared by inoculating sterile diet and embryos with microbial species of interest. We describe the introduction of 4 bacterial species to establish a representative gnotobiotic microbiota in Drosophila. Finally, we describe approaches for confirming bacterial community composition, including testing if axenic Drosophila remain bacteria-free into adulthood.
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Affiliation(s)
- Melinda L Koyle
- Department of Plant and Wildlife Sciences, Brigham Young University
| | - Madeline Veloz
- Department of Plant and Wildlife Sciences, Brigham Young University
| | - Alec M Judd
- Department of Plant and Wildlife Sciences, Brigham Young University
| | - Adam C-N Wong
- Department of Entomology, Cornell University; Division of Infectious Diseases, Boston Children's Hospital, Harvard Medical School
| | - Peter D Newell
- Department of Entomology, Cornell University; Biological Sciences, SUNY Oswego
| | - Angela E Douglas
- Department of Entomology, Cornell University; Department of Molecular Biology and Genetics, Cornell University
| | - John M Chaston
- Department of Plant and Wildlife Sciences, Brigham Young University; Department of Entomology, Cornell University;
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Hedin C, van der Gast CJ, Rogers GB, Cuthbertson L, McCartney S, Stagg AJ, Lindsay JO, Whelan K. Siblings of patients with Crohn's disease exhibit a biologically relevant dysbiosis in mucosal microbial metacommunities. Gut 2016; 65:944-53. [PMID: 25856344 DOI: 10.1136/gutjnl-2014-308896] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 03/11/2015] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To determine the existence of mucosal dysbiosis in siblings of patients with Crohn's disease (CD) using 454 pyrosequencing and to comprehensively characterise and determine the influence of genotypical and phenotypical factors, on that dysbiosis. Siblings of patients with CD have elevated risk of developing CD and display aspects of disease phenotype, including faecal dysbiosis. Whether the mucosal microbiota is disrupted in these at-risk individuals is unknown. DESIGN Rectal biopsy DNA was extracted from 21 patients with quiescent CD, 17 of their healthy siblings and 19 unrelated healthy controls. Mucosal microbiota was analysed by 16S rRNA gene pyrosequencing and were classified into core and rare species. Genotypical risk was determined using Illumina Immuno BeadChip, faecal calprotectin by ELISA and blood T-cell phenotype by flow cytometry. RESULTS Core microbiota of both patients with CD and healthy siblings was significantly less diverse than controls. Metacommunity profiling (Bray-Curtis (SBC) index) showed the sibling core microbial composition to be more similar to CD (SBC=0.70) than to healthy controls, whereas the sibling rare microbiota was more similar to healthy controls (SBC=0.42). Faecalibacterium prausnitzii contributed most to core metacommunity dissimilarity both between siblings and controls, and between patients and controls. Phenotype/genotype markers of CD risk significantly influenced microbiota variation between and within groups, of which genotype had the largest effect. CONCLUSIONS Individuals with elevated CD-risk display mucosal dysbiosis characterised by reduced diversity of core microbiota and lower abundance of F. prausnitzii. This dysbiosis in healthy people at risk of CD implicates microbiological processes in CD pathogenesis.
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Affiliation(s)
- Charlotte Hedin
- Faculty of Life Sciences & Medicine, Diabetes and Nutritional Sciences Division, King's College London, London, UK Centre for Immunology and Infectious Disease, Blizard Institute, Queen Mary University of London, London, UK
| | | | - Geraint B Rogers
- South Australian Health and Medical Research Institute, Infection and Immunity Theme, Flinders University, Adelaide, Australia
| | - Leah Cuthbertson
- NERC Centre for Ecology & Hydrology, Wallingford, Oxfordshire, UK
| | - Sara McCartney
- Centre for Gastroenterology and Nutrition, University College London, London, UK
| | - Andrew J Stagg
- Centre for Immunology and Infectious Disease, Blizard Institute, Queen Mary University of London, London, UK
| | - James O Lindsay
- Centre for Digestive Diseases, Blizard Institute, Queen Mary University of London, London, UK Department of Gastroenterology, Barts Health NHS Trust, London, UK
| | - Kevin Whelan
- Faculty of Life Sciences & Medicine, Diabetes and Nutritional Sciences Division, King's College London, London, UK
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Rausch P, Basic M, Batra A, Bischoff SC, Blaut M, Clavel T, Gläsner J, Gopalakrishnan S, Grassl GA, Günther C, Haller D, Hirose M, Ibrahim S, Loh G, Mattner J, Nagel S, Pabst O, Schmidt F, Siegmund B, Strowig T, Volynets V, Wirtz S, Zeissig S, Zeissig Y, Bleich A, Baines JF. Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities. Int J Med Microbiol 2016; 306:343-355. [PMID: 27053239 DOI: 10.1016/j.ijmm.2016.03.004] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/04/2016] [Accepted: 03/07/2016] [Indexed: 12/18/2022] Open
Abstract
The intestinal microbiota is involved in many physiological processes and it is increasingly recognized that differences in community composition can influence the outcome of a variety of murine models used in biomedical research. In an effort to describe and account for the variation in intestinal microbiota composition across the animal facilities of participating members of the DFG Priority Program 1656 "Intestinal Microbiota", we performed a survey of C57BL/6J mice from 21 different mouse rooms/facilities located at 13 different institutions across Germany. Fresh feces was sampled from five mice per room/facility using standardized procedures, followed by extraction and 16S rRNA gene profiling (V1-V2 region, Illumina MiSeq) at both the DNA and RNA (reverse transcribed to cDNA) level. In order to determine the variables contributing to bacterial community differences, we collected detailed questionnaires of animal husbandry practices and incorporated this information into our analyses. We identified considerable variation in a number of descriptive aspects including the proportions of major phyla, alpha- and beta diversity, all of which displayed significant associations to specific aspects of husbandry. Salient findings include a reduction in alpha diversity with the use of irradiated chow, an increase in inter-individual variability (beta diversity) with respect to barrier access and open cages and an increase in bacterial community divergence with time since importing from a vendor. We further observe a high degree of facility-level individuality, which is likely due to each facility harboring its own unique combination of multiple varying attributes of animal husbandry. While it is important to account and control for such differences between facilities, the documentation of such diversity may also serve as a valuable future resource for investigating the origins of microbial-driven host phenotypes.
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Affiliation(s)
- Philipp Rausch
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, August-Thienemann-Str. 2, 24306, Plön, Germany; Institute for Experimental Medicine, Evolutionary Genomics, Christian-Albrechts-University of Kiel, Arnold-Heller-Str. 3, Haus 17, 24105 Kiel, Germany
| | - Marijana Basic
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany
| | - Arvind Batra
- Charité-Universitätsklinikum Berlin, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Stephan C Bischoff
- Department of Nutritional Medicine, University of Hohenheim, Fruwirthstr. 12, 70593 Stuttgart, Germany
| | - Michael Blaut
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
| | - Thomas Clavel
- ZIEL Institute for Food and Health, Technische Universität München, Gregor-Mendel-Str. 2, 85354, Freising-Weihenstephan, Germany
| | - Joachim Gläsner
- Institute for Medical Microbiology and Hygiene, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Shreya Gopalakrishnan
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Arnold-Heller-Str. 3, 24105 Kiel, Germany
| | - Guntram A Grassl
- German Center for Infection Research (DZIF), Hannover-Braunschweig Site, Carl-Neuberg-Str. 1, 30625 Hannover, Germany; Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany; Research Center Borstel, Parkallee 1-40, 23845, Borstel, Germany
| | - Claudia Günther
- Medical Clinic 1, Friedrich Alexander University, Ulmenweg 18, 91054 Erlangen, Germany
| | - Dirk Haller
- ZIEL Institute for Food and Health, Technische Universität München, Gregor-Mendel-Str. 2, 85354, Freising-Weihenstephan, Germany; Chair of Nutrition and Immunology, Technische Universität München, Gregor-Mendel-Str. 2, 85354 Freising-Weihenstephan, Germany
| | - Misa Hirose
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Saleh Ibrahim
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Gunnar Loh
- Department of Gastrointestinal Microbiology, German Institute of Human Nutrition Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany
| | - Jochen Mattner
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie und Hygiene, Lehrstuhl für Mikrobiologie und Infektionsimmunologie, Wasserturmstr. 3/5, 91054 Erlangen, Germany
| | - Stefan Nagel
- Charité - Universitätsklinikum Berlin, Research Institutes for Experimental Medicine, Krahmerstr. 6-10, 12207 Berlin, Germany
| | - Oliver Pabst
- Institute of Molecular Medicine, RWTH University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Franziska Schmidt
- Charité-Universitätsklinikum Berlin, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Britta Siegmund
- Charité-Universitätsklinikum Berlin, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Hindenburgdamm 30, 12203 Berlin, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Valentina Volynets
- Department of Nutritional Medicine, University of Hohenheim, Fruwirthstr. 12, 70593 Stuttgart, Germany
| | - Stefan Wirtz
- Medical Clinic 1, Friedrich Alexander University, Ulmenweg 18, 91054 Erlangen, Germany
| | - Sebastian Zeissig
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Arnold-Heller-Str. 3, 24105 Kiel, Germany; Department of Medicine I, University Medical Center Dresden and Center for Regenerative Therapies, Technical University Dresden, 01307 Dresden, Germany
| | - Yvonne Zeissig
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Arnold-Heller-Str. 3, 24105 Kiel, Germany; Department of General Pediatrics, University Medical Center Dresden, Technical University Dresden, 01307 Dresden, Germany
| | - André Bleich
- Institute for Laboratory Animal Science and Central Animal Facility, Hannover Medical School, Carl-Neuberg-Str.1, 30625 Hannover, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, Evolutionary Genomics, August-Thienemann-Str. 2, 24306, Plön, Germany; Institute for Experimental Medicine, Evolutionary Genomics, Christian-Albrechts-University of Kiel, Arnold-Heller-Str. 3, Haus 17, 24105 Kiel, Germany.
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Jarvis MF, Williams M. Irreproducibility in Preclinical Biomedical Research: Perceptions, Uncertainties, and Knowledge Gaps. Trends Pharmacol Sci 2016; 37:290-302. [PMID: 26776451 DOI: 10.1016/j.tips.2015.12.001] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 12/03/2015] [Accepted: 12/07/2015] [Indexed: 01/30/2023]
Abstract
Concerns regarding the reliability of biomedical research outcomes were precipitated by two independent reports from the pharmaceutical industry that documented a lack of reproducibility in preclinical research in the areas of oncology, endocrinology, and hematology. Given their potential impact on public health, these concerns have been extensively covered in the media. Assessing the magnitude and scope of irreproducibility is limited by the anecdotal nature of the initial reports and a lack of quantitative data on specific failures to reproduce published research. Nevertheless, remediation activities have focused on needed enhancements in transparency and consistency in the reporting of experimental methodologies and results. While such initiatives can effectively bridge knowledge gaps and facilitate best practices across established and emerging research disciplines and therapeutic areas, concerns remain on how these improve on the historical process of independent replication in validating research findings and their potential to inhibit scientific innovation.
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Affiliation(s)
| | - Michael Williams
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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Hoy YE, Bik EM, Lawley TD, Holmes SP, Monack DM, Theriot JA, Relman DA. Variation in Taxonomic Composition of the Fecal Microbiota in an Inbred Mouse Strain across Individuals and Time. PLoS One 2015; 10:e0142825. [PMID: 26565698 PMCID: PMC4643986 DOI: 10.1371/journal.pone.0142825] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 10/27/2015] [Indexed: 12/20/2022] Open
Abstract
Genetics, diet, and other environmental exposures are thought to be major factors in the development and composition of the intestinal microbiota of animals. However, the relative contributions of these factors in adult animals, as well as variation with time in a variety of important settings, are still not fully understood. We studied a population of inbred, female mice fed the same diet and housed under the same conditions. We collected fecal samples from 46 individual mice over two weeks, sampling four of these mice for periods as long as 236 days for a total of 190 samples, and determined the phylogenetic composition of their microbial communities after analyzing 1,849,990 high-quality pyrosequencing reads of the 16S rRNA gene V3 region. Even under these controlled conditions, we found significant inter-individual variation in community composition, as well as variation within an individual over time, including increases in alpha diversity during the first 2 months of co-habitation. Some variation was explained by mouse membership in different cage and vendor shipment groups. The differences among individual mice from the same shipment group and cage were still significant. Overall, we found that 23% of the variation in intestinal microbiota composition was explained by changes within the fecal microbiota of a mouse over time, 12% was explained by persistent differences among individual mice, 14% by cage, and 18% by shipment group. Our findings suggest that the microbiota of controlled populations of inbred laboratory animals may not be as uniform as previously thought, that animal rearing and handling may account for some variation, and that as yet unidentified factors may explain additional components of variation in the composition of the microbiota within populations and individuals over time. These findings have implications for the design and interpretation of experiments involving laboratory animals.
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Affiliation(s)
- Yana Emmy Hoy
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Elisabeth M. Bik
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Trevor D. Lawley
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Susan P. Holmes
- Department of Statistics, Stanford University, Stanford, California, United States of America
| | - Denise M. Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Julie A. Theriot
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Stanford, California, United States of America
| | - David A. Relman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
- Veterans Affairs Palo Alto Health Care System, Palo Alto, California, United States of America
- * E-mail:
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33
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The composition of the zebrafish intestinal microbial community varies across development. ISME JOURNAL 2015; 10:644-54. [PMID: 26339860 DOI: 10.1038/ismej.2015.140] [Citation(s) in RCA: 344] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 06/19/2015] [Accepted: 07/05/2015] [Indexed: 01/15/2023]
Abstract
The assembly of resident microbial communities is an important event in animal development; however, the extent to which this process mirrors the developmental programs of host tissues is unknown. Here we surveyed the intestinal bacteria at key developmental time points in a sibling group of 135 individuals of a model vertebrate, the zebrafish (Danio rerio). Our survey revealed stage-specific signatures in the intestinal microbiota and extensive interindividual variation, even within the same developmental stage. Microbial community shifts were apparent during periods of constant diet and environmental conditions, as well as in concert with dietary and environmental change. Interindividual variation in the intestinal microbiota increased with age, as did the difference between the intestinal microbiota and microbes in the surrounding environment. Our results indicate that zebrafish intestinal microbiota assemble into distinct communities throughout development, and that these communities are increasingly different from the surrounding environment and from one another.
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34
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Weldon L, Abolins S, Lenzi L, Bourne C, Riley EM, Viney M. The Gut Microbiota of Wild Mice. PLoS One 2015; 10:e0134643. [PMID: 26258484 PMCID: PMC4530874 DOI: 10.1371/journal.pone.0134643] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/11/2015] [Indexed: 12/28/2022] Open
Abstract
The gut microbiota profoundly affects the biology of its host. The composition of the microbiota is dynamic and is affected by both host genetic and many environmental effects. The gut microbiota of laboratory mice has been studied extensively, which has uncovered many of the effects that the microbiota can have. This work has also shown that the environments of different research institutions can affect the mouse microbiota. There has been relatively limited study of the microbiota of wild mice, but this has shown that it typically differs from that of laboratory mice (and that maintaining wild caught mice in the laboratory can quite quickly alter the microbiota). There is also inter-individual variation in the microbiota of wild mice, with this principally explained by geographical location. In this study we have characterised the gut (both the caecum and rectum) microbiota of wild caught Mus musculus domesticus at three UK sites and have investigated how the microbiota varies depending on host location and host characteristics. We find that the microbiota of these mice are generally consistent with those described from other wild mice. The rectal and caecal microbiotas of individual mice are generally more similar to each other, than they are to the microbiota of other individuals. We found significant differences in the diversity of the microbiotas among mice from different sample sites. There were significant correlations of microbiota diversity and body weight, a measure of age, body-mass index, serum concentration of leptin, and virus, nematode and mite infection.
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Affiliation(s)
- Laura Weldon
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Stephen Abolins
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Luca Lenzi
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Christian Bourne
- Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Eleanor M. Riley
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Mark Viney
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
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Abstract
BACKGROUND Current understanding of the onset of inflammatory bowel diseases relies heavily on data derived from animal models of colitis. However, the omission of information concerning the method used makes the interpretation of studies difficult or impossible. We assessed the current quality of methods reporting in 4 animal models of colitis that are used to inform clinical research into inflammatory bowel disease: dextran sulfate sodium, interleukin-10, CD45RB T cell transfer, and 2,4,6-trinitrobenzene sulfonic acid (TNBS). METHODS We performed a systematic review based on PRISMA guidelines, using a PubMed search (2000-2014) to obtain publications that used a microarray to describe gene expression in colitic tissue. Methods reporting quality was scored against a checklist of essential and desirable criteria. RESULTS Fifty-eight articles were identified and included in this review (29 dextran sulfate sodium, 15 interleukin-10, 5 T cell transfer, and 16 TNBS; some articles use more than 1 colitis model). A mean of 81.7% (SD = ±7.038) of criteria were reported across all models. Only 1 of the 58 articles reported all essential criteria on our checklist. Animal age, gender, housing conditions, and mortality/morbidity were all poorly reported. CONCLUSIONS Failure to include all essential criteria is a cause for concern; this failure can have large impact on the quality and replicability of published colitis experiments. We recommend adoption of our checklist as a requirement for publication to improve the quality, comparability, and standardization of colitis studies and will make interpretation and translation of data to human disease more reliable.
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Noncanonical Effects of IRF9 in Intestinal Inflammation: More than Type I and Type III Interferons. Mol Cell Biol 2015; 35:2332-43. [PMID: 25918247 DOI: 10.1128/mcb.01498-14] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/21/2015] [Indexed: 01/03/2023] Open
Abstract
The interferon (IFN)-stimulated gene factor 3 (ISGF3) transcription factor with its Stat1, Stat2, and interferon regulatory factor 9 (IRF9) subunits is employed for transcriptional responses downstream of receptors for type I interferons (IFN-I) that include IFN-α and IFN-β and type III interferons (IFN-III), also called IFN-λ. Here, we show in a murine model of dextran sodium sulfate (DSS)-induced colitis that IRF9 deficiency protects animals, whereas the combined loss of IFN-I and IFN-III receptors worsens their condition. We explain the different phenotypes by demonstrating a function of IRF9 in a noncanonical transcriptional complex with Stat1, apart from IFN-I and IFN-III signaling. Together, Stat1 and IRF9 produce a proinflammatory activity that overrides the benefits of the IFN-III response on intestinal epithelial cells. Our results further suggest that the CXCL10 chemokine gene is an important mediator of this proinflammatory activity. We thus establish IFN-λ as a potentially anticolitogenic cytokine and propose an important role for IRF9 as a component of noncanonical Stat complexes in the development of colitis.
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Steinbach EC, Gipson GR, Sheikh SZ. Induction of Murine Intestinal Inflammation by Adoptive Transfer of Effector CD4+ CD45RB high T Cells into Immunodeficient Mice. J Vis Exp 2015:52533. [PMID: 25938395 PMCID: PMC4541583 DOI: 10.3791/52533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
There are many different animal models available for studying the pathogenesis of human inflammatory bowel diseases (IBD), each with its own advantages and disadvantages. We describe here an experimental colitis model that is initiated by adoptive transfer of syngeneic splenic CD4(+)CD45RB(high) T cells into T and B cell deficient recipient mice. The CD4(+)CD45RB(high) T cell population that largely consists of naïve effector cells is capable of inducing chronic intestinal inflammation, closely resembling key aspects of human IBD. This method can be manipulated to study aspects of disease onset and progression. Additionally it can be used to study the function of innate, adaptive, and regulatory immune cell populations, and the role of environmental exposures, i.e., the microbiota, in intestinal inflammation. In this article we illustrate the methodology for inducing colitis with a step-by-step protocol. This includes a video demonstration of key technical aspects required to successfully develop this murine model of experimental colitis for research purposes.
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Affiliation(s)
- Erin C Steinbach
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill;
| | - Gregory R Gipson
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill
| | - Shehzad Z Sheikh
- Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill; Department of Genetics, University of North Carolina at Chapel Hill; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill
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Shankar J, Solis NV, Mounaud S, Szpakowski S, Liu H, Losada L, Nierman WC, Filler SG. Using Bayesian modelling to investigate factors governing antibiotic-induced Candida albicans colonization of the GI tract. Sci Rep 2015; 5:8131. [PMID: 25644850 PMCID: PMC4314636 DOI: 10.1038/srep08131] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/07/2015] [Indexed: 12/29/2022] Open
Abstract
Receipt of broad-spectrum antibiotics enhances Candida albicans colonization of the GI tract, a risk factor for haematogenously-disseminated candidiasis. To understand how antibiotics influence C. albicans colonization, we treated mice orally with vancomycin or a combination of penicillin, streptomycin, and gentamicin (PSG) and then inoculated them with C. albicans by gavage. Only PSG treatment resulted in sustained, high-level GI colonization with C. albicans. Furthermore, PSG reduced bacterial diversity in the colon much more than vancomycin. Both antibiotic regimens significantly reduced IL-17A, IL-21, IL-22 and IFN-γ mRNA levels in the terminal ileum but had limited effect on the GI fungal microbiome. Through a series of models that employed Bayesian model averaging, we investigated the associations between antibiotic treatment, GI microbiota, and host immune response and their collective impact on C. albicans colonization. Our analysis revealed that bacterial genera were typically associated with either C. albicans colonization or altered cytokine expression but not with both. The only exception was Veillonella, which was associated with both increased C. albicans colonization and reduced IL-21 expression. Overall, antibiotic-induced changes in the bacterial microbiome were much more consistent determinants of C. albicans colonization than either the GI fungal microbiota or the GI immune response.
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Affiliation(s)
| | - Norma V. Solis
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | | | - Hong Liu
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | | | | | - Scott G. Filler
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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Daft JG, Ptacek T, Kumar R, Morrow C, Lorenz RG. Cross-fostering immediately after birth induces a permanent microbiota shift that is shaped by the nursing mother. MICROBIOME 2015; 3:17. [PMID: 25969735 PMCID: PMC4427954 DOI: 10.1186/s40168-015-0080-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/03/2015] [Indexed: 05/15/2023]
Abstract
BACKGROUND Current research has led to the appreciation that there are differences in the commensal microbiota between healthy individuals and individuals that are predisposed to disease. Treatments to reverse disease pathogenesis through the manipulation of the gastrointestinal (GI) microbiota are now being explored. Normalizing microbiota between different strains of mice in the same study is also needed to better understand disease pathogenesis. Current approaches require repeated delivery of bacteria and large numbers of animals and vary in treatment start time. A method is needed that can shift the microbiota of predisposed individuals to a healthy microbiota at an early age and sustain this shift through the lifetime of the individual. RESULTS We tested cross-fostering of pups within 48 h of birth as a means to permanently shift the microbiota from birth. Taxonomical analysis revealed that the nursing mother was the critical factor in determining bacterial colonization, instead of the birth mother. Data was evaluated using bacterial 16S rDNA sequences from fecal pellets and sequencing was performed on an Illumina Miseq using a 251 bp paired-end library. CONCLUSIONS The results show that cross-fostering is an effective means to induce an early and maintained shift in the commensal microbiota. This will allow for the evaluation of a prolonged microbial shift and its effects on disease pathogenesis. Cross-fostering will also eliminate variation within control models by normalizing the commensal microbiota between different strains of mice.
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Affiliation(s)
- Joseph G Daft
- />Department of Pathology, University of Alabama at Birmingham, 1825 University Blvd, SHEL 602, Birmingham, AL USA
- />Comprehensive Diabetes Center, University of Alabama at Birmingham, 1825 University Boulevard, SHEL 1207, Birmingham, AL USA
| | - Travis Ptacek
- />Department of Microbiology, University of Alabama at Birmingham, 3201 1st Avenue North, Birmingham, AL USA
- />Center for Clinical and Translational Science, University of Alabama at Birmingham, 1924 7th Avenue South, Birmingham, AL USA
| | - Ranjit Kumar
- />Center for Clinical and Translational Science, University of Alabama at Birmingham, 1924 7th Avenue South, Birmingham, AL USA
| | - Casey Morrow
- />Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, 1918 University Boulevard, Birmingham, AL USA
| | - Robin G Lorenz
- />Department of Pathology, University of Alabama at Birmingham, 1825 University Blvd, SHEL 602, Birmingham, AL USA
- />Comprehensive Diabetes Center, University of Alabama at Birmingham, 1825 University Boulevard, SHEL 1207, Birmingham, AL USA
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Abstract
Animal-associated bacteria (microbiota) affect host behaviors and physiological traits. To identify bacterial genetic determinants of microbiota-responsive host traits, we employed a metagenome-wide association (MGWA) approach in two steps. First, we measured two microbiota-responsive host traits, development time and triglyceride (TAG) content, in Drosophila melanogaster flies monoassociated with each of 41 bacterial strains. The effects of monoassociation on host traits were not confined to particular taxonomic groups. Second, we clustered protein-coding sequences of the bacteria by sequence similarity de novo and statistically associated the magnitude of the host trait with the bacterial gene contents. The animals had been monoassociated with genome-sequenced bacteria, so the metagenome content was unambiguous. This analysis showed significant effects of pyrroloquinoline quinone biosynthesis genes on development time, confirming the results of a published transposon mutagenesis screen, thereby validating the MGWA; it also identified multiple genes predicted to affect host TAG content, including extracellular glucose oxidation pathway components. To test the validity of the statistical associations, we expressed candidate genes in a strain that lacks them. Monoassociation with bacteria that ectopically expressed a predicted oxidoreductase or gluconate dehydrogenase conferred reduced Drosophila TAG contents relative to the TAG contents in empty vector controls. Consistent with the prediction that glucose oxidation pathway gene expression increased bacterial glucose utilization, the glucose content of the host diet was reduced when flies were exposed to these strains. Our findings indicate that microbiota affect host nutritional status through modulation of nutrient acquisition. Together, these findings demonstrate the utility of MGWA for identifying bacterial determinants of host traits and provide mechanistic insight into how gut microbiota modulate the nutritional status of a model host. To understand how certain gut bacteria promote the health of their animal hosts, we need to identify the bacterial genes that drive these beneficial relationships. This task is challenging because the bacterial communities can vary widely among different host individuals. To overcome this difficulty, we quantified how well each of 41 bacterial species protected Drosophila fruit flies from high fat content. The genomes of the chosen bacterial strains were previously sequenced, so we could statistically associate specific bacterial genes with bacterially mediated reduction in host fat content. Bacterial genes that promote glucose utilization were strongly represented in the association, and introducing these genes into the gut bacteria was sufficient to lower the animal’s fat content. Our method is applicable to the study of many other host-microbe interactions as a way to uncover microbial genes important for host health.
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Kreisinger J, Cížková D, Vohánka J, Piálek J. Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high-throughput parallel pyrosequencing. Mol Ecol 2014; 23:5048-60. [PMID: 25204516 DOI: 10.1111/mec.12909] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Revised: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 12/26/2022]
Abstract
The effects of gastrointestinal tract microbiota (GTM) on host physiology and health have been the subject of considerable interest in recent years. While a variety of captive bred species have been used in experiments, the extent to which GTM of captive and/or inbred individuals resembles natural composition and variation in wild populations is poorly understood. Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain mice belonging to two subspecies (M. m. musculus and M. m. domesticus). Sequenced individuals were selected according to a 2 × 2 experimental design: wild (14) vs. inbred origin (16) and M. m. musculus (15) vs. M. m. domesticus (15). We compared alpha diversity (i.e. number of operational taxonomic units - OTUs), beta diversity (i.e. interindividual variability) and microbiota composition across the four groups. We found no difference between M. m. musculus and M. m. domesticus subspecies, suggesting low effect of genetic differentiation between these two subspecies on GTM structure. Both inbred and wild populations showed the same level of microbial alpha and beta diversity; however, we found strong differentiation in microbiota composition between wild and inbred populations. Relative abundance of ~ 16% of OTUs differed significantly between wild and inbred individuals. As laboratory mice represent the most abundant model for studying the effects of gut microbiota on host metabolism, immunity and neurology, we suggest that the distinctness of laboratory-kept mouse microbiota, which differs from wild mouse microbiota, needs to be considered in future biomedical research.
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Affiliation(s)
- Jakub Kreisinger
- Studenec Research Facility, Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Květná 8, 603 65, Brno, Czech Republic; Department of Zoology, Faculty of Science, Charles University Prague, Viničná 7, 128 44, Prague, Czech Republic; Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, Research and Innovation Centre, I-38010, San Michele all'Adige, TN, Italy
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