1
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Morgan EW, Perdew GH, Patterson AD. Multi-Omics Strategies for Investigating the Microbiome in Toxicology Research. Toxicol Sci 2022; 187:189-213. [PMID: 35285497 PMCID: PMC9154275 DOI: 10.1093/toxsci/kfac029] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Microbial communities on and within the host contact environmental pollutants, toxic compounds, and other xenobiotic compounds. These communities of bacteria, fungi, viruses, and archaea possess diverse metabolic potential to catabolize compounds and produce new metabolites. Microbes alter chemical disposition thus making the microbiome a natural subject of interest for toxicology. Sequencing and metabolomics technologies permit the study of microbiomes altered by acute or long-term exposure to xenobiotics. These investigations have already contributed to and are helping to re-interpret traditional understandings of toxicology. The purpose of this review is to provide a survey of the current methods used to characterize microbes within the context of toxicology. This will include discussion of commonly used techniques for conducting omic-based experiments, their respective strengths and deficiencies, and how forward-looking techniques may address present shortcomings. Finally, a perspective will be provided regarding common assumptions that currently impede microbiome studies from producing causal explanations of toxicologic mechanisms.
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Affiliation(s)
- Ethan W Morgan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Gary H Perdew
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Andrew D Patterson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.,Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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2
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Li XV, Leonardi I, Putzel GG, Semon A, Fiers WD, Kusakabe T, Lin WY, Gao IH, Doron I, Gutierrez-Guerrero A, DeCelie MB, Carriche GM, Mesko M, Yang C, Naglik JR, Hube B, Scherl EJ, Iliev ID. Immune regulation by fungal strain diversity in inflammatory bowel disease. Nature 2022; 603:672-678. [PMID: 35296857 PMCID: PMC9166917 DOI: 10.1038/s41586-022-04502-w] [Citation(s) in RCA: 104] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 02/02/2022] [Indexed: 12/21/2022]
Abstract
The fungal microbiota (mycobiota) is an integral part of the complex multikingdom microbial community colonizing the mammalian gastrointestinal tract and has an important role in immune regulation1-6. Although aberrant changes in the mycobiota have been linked to several diseases, including inflammatory bowel disease3-9, it is currently unknown whether fungal species captured by deep sequencing represent living organisms and whether specific fungi have functional consequences for disease development in affected individuals. Here we developed a translational platform for the functional analysis of the mycobiome at the fungal-strain- and patient-specific level. Combining high-resolution mycobiota sequencing, fungal culturomics and genomics, a CRISPR-Cas9-based fungal strain editing system, in vitro functional immunoreactivity assays and in vivo models, this platform enables the examination of host-fungal crosstalk in the human gut. We discovered a rich genetic diversity of opportunistic Candida albicans strains that dominate the colonic mucosa of patients with inflammatory bowel disease. Among these human-gut-derived isolates, strains with high immune-cell-damaging capacity (HD strains) reflect the disease features of individual patients with ulcerative colitis and aggravated intestinal inflammation in vivo through IL-1β-dependent mechanisms. Niche-specific inflammatory immunity and interleukin-17A-producing T helper cell (TH17 cell) antifungal responses by HD strains in the gut were dependent on the C. albicans-secreted peptide toxin candidalysin during the transition from a benign commensal to a pathobiont state. These findings reveal the strain-specific nature of host-fungal interactions in the human gut and highlight new diagnostic and therapeutic targets for diseases of inflammatory origin.
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Affiliation(s)
- Xin V Li
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Irina Leonardi
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Gregory G Putzel
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Alexa Semon
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - William D Fiers
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Takato Kusakabe
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Woan-Yu Lin
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Iris H Gao
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Itai Doron
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Alejandra Gutierrez-Guerrero
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Meghan B DeCelie
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Guilhermina M Carriche
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Marissa Mesko
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Chen Yang
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Julian R Naglik
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Bernhard Hube
- Department of Microbial Pathogenicity Mechanisms, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
- Institute of Microbiology, FriedrichSchiller University, Jena, Germany
| | - Ellen J Scherl
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA
- The Jill Roberts Center for Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, USA
| | - Iliyan D Iliev
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- The Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, Cornell University, New York, NY, USA.
- Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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3
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Ahmed I, Yusuf K, Roy BC, Stubbs J, Anant S, Attard TM, Sampath V, Umar S. Dietary Interventions Ameliorate Infectious Colitis by Restoring the Microbiome and Promoting Stem Cell Proliferation in Mice. Int J Mol Sci 2021; 23:339. [PMID: 35008767 PMCID: PMC8745185 DOI: 10.3390/ijms23010339] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/21/2021] [Accepted: 12/25/2021] [Indexed: 12/15/2022] Open
Abstract
Decreases in short-chain-fatty-acids (SCFAs) are linked to inflammatory bowel disease (IBD). Yet, the mechanisms through which SCFAs promote wound healing, orchestrated by intestinal stem cells, are poorly understood. We discovered that, in mice with Citrobacter rodentium (CR)-induced infectious colitis, treatment with Pectin and Tributyrin diets reduced the severity of colitis by restoring Firmicutes and Bacteroidetes and by increasing mucus production. RNA-seq in young adult mouse colon (YAMC) cells identified higher expression of Lgr4, Lgr6, DCLK1, Muc2, and SIGGIR after Butyrate treatment. Lineage tracing in CR-infected Lgr5-EGFP-IRES-CreERT2/ROSA26-LacZ (Lgr5-R) mice also revealed an expansion of LacZ-labeled Lgr5(+) stem cells in the colons of both Pectin and Tributyrin-treated mice compared to control. Interestingly, gut microbiota was required for Pectin but not Tributyrin-induced Lgr5(+) stem cell expansion. YAMC cells treated with sodium butyrate exhibited increased Lgr5 promoter reporter activity due to direct Butyrate binding with Lgr5 at -4.0 Kcal/mol, leading to thermal stabilization. Upon ChIP-seq, H3K4me3 increased near Lgr5 transcription start site that contained the consensus binding motif for a transcriptional activator of Lgr5 (SPIB). Thus, a multitude of effects on gut microbiome, differential gene expression, and/or expansion of Lgr5(+) stem cells seem to underlie amelioration of colitis following dietary intervention.
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Affiliation(s)
- Ishfaq Ahmed
- Department of Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA; (I.A.); (K.Y.); (B.C.R.)
| | - Kafayat Yusuf
- Department of Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA; (I.A.); (K.Y.); (B.C.R.)
| | - Badal C. Roy
- Department of Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA; (I.A.); (K.Y.); (B.C.R.)
| | - Jason Stubbs
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Shrikant Anant
- Cancer Biology Department, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Thomas M. Attard
- Department of Pediatrics and Gastroenterology, Children’s Mercy Hospital, Kansas City, KS 66160, USA; (T.M.A.); (V.S.)
| | - Venkatesh Sampath
- Department of Pediatrics and Gastroenterology, Children’s Mercy Hospital, Kansas City, KS 66160, USA; (T.M.A.); (V.S.)
| | - Shahid Umar
- Department of Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA; (I.A.); (K.Y.); (B.C.R.)
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4
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Wang C, Yan D, Huang J, Li Y. Impacts of changes in intestinal flora on the metabolism of Sprague-Dawley rats. Bioengineered 2021; 12:10603-10611. [PMID: 34852718 PMCID: PMC8809924 DOI: 10.1080/21655979.2021.2000242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/26/2021] [Accepted: 10/27/2021] [Indexed: 11/10/2022] Open
Abstract
Changes in intestinal flora affect the health and cause metabolic diseases of the host. The extent to which the impact of different changes in intestinal flora would have on the metabolism of an individual has not been reported. This study aims to investigate the effect of different changes in intestinal flora on the metabolism of Sprague-Dawley (SD) normal rats' individuals. Forty-eight SD rats were randomly divided into 6 groups (8 rats per group), which were treated with normal saline, probiotics, nonpathogenic Escherichia coli, Salmonella enteritidis, gentamicin, and magnesium sulfate, respectively. After 7 days, the ileum of each group of rats was collected and real-time polymerase chain reaction was used to analyze the composition of intestinal flora. And gas chromatography/mass spectrometry (GC/MS) was used to analyze plasma metabolic profile. The results revealed that the decrease in alanine content in the probiotics group was statistically significant, while the alanine content in the nonpathogenic Escherichia group increased significantly. Alanine, leucine, isoleucine, and serine decreased significantly in the Salmonella group. Proline and butyric acid decreased significantly in the gentamicin group. The principal component analysis showed significant differences in the Salmonella group compared with other test groups. Overall, the most significant metabolic changes were observed in SD rats in the Salmonella group, while a great similarity was observed in the probiotics, Escherichia group, and gentamicin groups compared with the normal group. Changes in intestinal flora had a certain impact on the metabolism in SD rats, especially on amino acid levels.
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Affiliation(s)
- Chengfei Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, HangzhouZhejiang Province, China
| | - Dong Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, HangzhouZhejiang Province, China
| | - Jianrong Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, HangzhouZhejiang Province, China
| | - Yongtao Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, HangzhouZhejiang Province, China
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5
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Ericsson AC, Franklin CL. The gut microbiome of laboratory mice: considerations and best practices for translational research. Mamm Genome 2021; 32:239-250. [PMID: 33689000 PMCID: PMC8295156 DOI: 10.1007/s00335-021-09863-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/18/2021] [Indexed: 12/14/2022]
Abstract
Just as the gut microbiota (GM) is now recognized as an integral mediator of environmental influences on human physiology, susceptibility to disease, and response to pharmacological intervention, so too does the GM of laboratory mice affect the phenotype of research using mouse models. Multiple experimental factors have been shown to affect the composition of the GM in research mice, as well as the model phenotype, suggesting that the GM represents a major component in experimental reproducibility. Moreover, several recent studies suggest that manipulation of the GM of laboratory mice can substantially improve the predictive power or translatability of data generated in mouse models to the human conditions under investigation. This review provides readers with information related to these various factors and practices, and recommendations regarding methods by which issues with poor reproducibility or translatability can be transformed into discoveries.
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Affiliation(s)
- Aaron C Ericsson
- University of Missouri Metagenomics Center (MUMC), MU Mutant Mouse Resource and Research Center (MU MMRRC), Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA.
| | - Craig L Franklin
- University of Missouri Metagenomics Center (MUMC), MU Mutant Mouse Resource and Research Center (MU MMRRC), Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
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6
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Niu J, Xie SW, Fang HH, Xie JJ, Guo TY, Zhang YM, Liu ZL, Liao SY, He JY, Tian LX, Liu YJ. Dietary values of macroalgae Porphyra haitanensis in Litopenaeus vannamei under normal rearing and WSSV challenge conditions: Effect on growth, immune response and intestinal microbiota. FISH & SHELLFISH IMMUNOLOGY 2018; 81:135-149. [PMID: 30017927 DOI: 10.1016/j.fsi.2018.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 05/30/2018] [Accepted: 06/06/2018] [Indexed: 06/08/2023]
Abstract
Two trials were conducted to determine the effects of dietary macroalgae Porphyra haitanensis on growth, immunity and intestinal microbiota of Litopenaeus vannamei. In trial 1, shrimp (mean initial wet weight about 0.64 g) were fed with seven diets (P0, P1, P2, P3, P4, P5 and P6) containing 0% (basal diet), 1%, 2%, 3%, 4%, 5% and 6% P. haitanensis in triplicate for 60 days. Growth performance (weight gain, WG; specific growth rate, SGR) of shrimp fed the P4 diet were significantly higher than that of shrimp fed P0, P5 and P6 diets (P < 0.05) but without significant differences with shrimp fed P1-P3 diets (P > 0.05). Hepatopancreas phenoloxidase (PO) activity of shrimp fed the P. haitanensis containing diets was significantly higher than that of shrimp fed the basal diet (P0) (P < 0.05). Total haemocyte count (THC) of shrimp fed basal diet (P0) was significantly lower than that of shrimp fed diets containing P. haitanensis. Our results declared that dietary P. haitanensis supplementation increases the abundance of beneficial bacterials such as Nitrosopumilus, Marinobacter or Bifidobacterium and reduces the abundance of harmful bacterias such as Vibrio, and especially pronounced in P4 diet treatment. In trial 2, a WSSV injection challenge test was conducted for 7-day after the rearing trial and shrimp survival was also compared among treatments. A sudden shrimp death was found from the 4th day, and values of survival of shrimp fed the P3-P4 diets were higher than that of shrimp fed other diets during 4-7 days challenge test. The immune response in trial 2 were characterized by higher superoxide dismutase activity (SOD) and PO activities, lower THC and higher HCT compared to levels found in trial 1. In conclusion, suitable dietary P. haitanensis could enhance the growth performance, antioxidant capacity and alter total bacterial numbers or microbial diversity of L. vannamei and furthermore reduce oxidative stress and immune depression challenged by WSSV injection stress, and the level of P. haitanensis supplemented in the diet should be between 2.51% and 3.14%.
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Affiliation(s)
- Jin Niu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China.
| | - Shi-Wei Xie
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Hao-Hang Fang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Jia-Jun Xie
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Tian-Yu Guo
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Yan-Mei Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Zhen-Lu Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Shi-Yu Liao
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
| | - Ju-Yun He
- Health & Nutrition, Evonik Degussa (China) Co., Ltd., Chaoyang, Beijing, China
| | - Li-Xia Tian
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China.
| | - Yong-Jian Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animal and Guangdong Province Key Laboratory for Aquatic Economic Animals, School of Life Science, Sun Yat-sen University, Guangzhou, 510275, PR China
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7
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Selber-Hnatiw S, Rukundo B, Ahmadi M, Akoubi H, Al-Bizri H, Aliu AF, Ambeaghen TU, Avetisyan L, Bahar I, Baird A, Begum F, Ben Soussan H, Blondeau-Éthier V, Bordaries R, Bramwell H, Briggs A, Bui R, Carnevale M, Chancharoen M, Chevassus T, Choi JH, Coulombe K, Couvrette F, D'Abreau S, Davies M, Desbiens MP, Di Maulo T, Di Paolo SA, Do Ponte S, Dos Santos Ribeiro P, Dubuc-Kanary LA, Duncan PK, Dupuis F, El-Nounou S, Eyangos CN, Ferguson NK, Flores-Chinchilla NR, Fotakis T, Gado Oumarou H D M, Georgiev M, Ghiassy S, Glibetic N, Grégoire Bouchard J, Hassan T, Huseen I, Ibuna Quilatan MF, Iozzo T, Islam S, Jaunky DB, Jeyasegaram A, Johnston MA, Kahler MR, Kaler K, Kamani C, Karimian Rad H, Konidis E, Konieczny F, Kurianowicz S, Lamothe P, Legros K, Leroux S, Li J, Lozano Rodriguez ME, Luponio-Yoffe S, Maalouf Y, Mantha J, McCormick M, Mondragon P, Narayana T, Neretin E, Nguyen TTT, Niu I, Nkemazem RB, O'Donovan M, Oueis M, Paquette S, Patel N, Pecsi E, Peters J, Pettorelli A, Poirier C, Pompa VR, Rajen H, Ralph RO, Rosales-Vasquez J, Rubinshtein D, Sakr S, Sebai MS, Serravalle L, Sidibe F, Sinnathurai A, Soho D, Sundarakrishnan A, Svistkova V, Ugbeye TE, Vasconcelos MS, Vincelli M, Voitovich O, Vrabel P, Wang L, Wasfi M, Zha CY, Gamberi C. Human Gut Microbiota: Toward an Ecology of Disease. Front Microbiol 2017; 8:1265. [PMID: 28769880 PMCID: PMC5511848 DOI: 10.3389/fmicb.2017.01265] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 06/23/2017] [Indexed: 12/17/2022] Open
Abstract
Composed of trillions of individual microbes, the human gut microbiota has adapted to the uniquely diverse environments found in the human intestine. Quickly responding to the variances in the ingested food, the microbiota interacts with the host via reciprocal biochemical signaling to coordinate the exchange of nutrients and proper immune function. Host and microbiota function as a unit which guards its balance against invasion by potential pathogens and which undergoes natural selection. Disturbance of the microbiota composition, or dysbiosis, is often associated with human disease, indicating that, while there seems to be no unique optimal composition of the gut microbiota, a balanced community is crucial for human health. Emerging knowledge of the ecology of the microbiota-host synergy will have an impact on how we implement antibiotic treatment in therapeutics and prophylaxis and how we will consider alternative strategies of global remodeling of the microbiota such as fecal transplants. Here we examine the microbiota-human host relationship from the perspective of the microbial community dynamics.
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Affiliation(s)
| | - Belise Rukundo
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Masoumeh Ahmadi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Hayfa Akoubi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Hend Al-Bizri
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Adelekan F Aliu
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Lilit Avetisyan
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Irmak Bahar
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Alexandra Baird
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Fatema Begum
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | - Helene Bramwell
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Alicia Briggs
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Richard Bui
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Talia Chevassus
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Jin H Choi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Karyne Coulombe
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Meghan Davies
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Tamara Di Maulo
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | - Paola K Duncan
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Sara El-Nounou
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | - Tanya Fotakis
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Metodi Georgiev
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | - Tazkia Hassan
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Iman Huseen
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Tania Iozzo
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Safina Islam
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Dilan B Jaunky
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | - Cedric Kamani
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Filip Konieczny
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Karina Legros
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Jun Li
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Yara Maalouf
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Jessica Mantha
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | - Thi T T Nguyen
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Ian Niu
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | - Matthew Oueis
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Nehal Patel
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Emily Pecsi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Jackie Peters
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | | | | | | | - Surya Sakr
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Lisa Serravalle
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Fily Sidibe
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | - Dominique Soho
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | | | | | | | | | | | - Olga Voitovich
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Pamela Vrabel
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Lu Wang
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Maryse Wasfi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Cong Y Zha
- Department of Biology, Concordia UniversityMontréal, QC, Canada
| | - Chiara Gamberi
- Department of Biology, Concordia UniversityMontréal, QC, Canada
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8
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Microbiota and reproducibility of rodent models. Lab Anim (NY) 2017; 46:114-122. [PMID: 28328896 DOI: 10.1038/laban.1222] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 01/27/2017] [Indexed: 02/07/2023]
Abstract
The gut microbiota (GM) plays a critical role in human health and disease. Likewise, it is becoming increasingly evident that changes or disruptions to the GM can have significant effects on animal models and their expressed phenotypes, adding a complex and important variable into basic research and preclinical studies. In this article, we review some of the most common sources of GM variability in rodent models, and discuss measures to address this variability for improved reproducibility.
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Abstract
Eukaryotic organisms are colonized by rich and dynamic communities of microbes, both internally (e.g., in the gastrointestinal and respiratory tracts) and externally (e.g., on skin and external mucosal surfaces). The vast majority of bacterial microbes reside in the lower gastrointestinal (GI) tract, and it is estimated that the gut of a healthy human is home to some 100 trillion bacteria, roughly an order of magnitude greater than the number of host somatic cells. The development of culture-independent methods to characterize the gut microbiota (GM) has spurred a renewed interest in its role in host health and disease. Indeed, associations have been identified between various changes in the composition of the GM and an extensive list of diseases, both enteric and systemic. Animal models provide a means whereby causal relationships between characteristic differences in the GM and diseases or conditions can be formally tested using genetically identical animals in highly controlled environments. Clearly, the GM and its interactions with the host and myriad environmental factors are exceedingly complex, and it is rare that a single microbial taxon associates with, much less causes, a phenotype with perfect sensitivity and specificity. Moreover, while the exact numbers are the subject of debate, it is well recognized that only a minority of gut bacteria can be successfully cultured ex vivo. Thus, to perform studies investigating causal roles of the GM in animal model phenotypes, researchers need clever techniques to experimentally manipulate the GM of animals, and several ingenious methods of doing so have been developed, each providing its own type of information and with its own set of advantages and drawbacks. The current review will focus on the various means of experimentally manipulating the GM of research animals, drawing attention to the factors that would aid a researcher in selecting an experimental approach, and with an emphasis on mice and rats, the primary model species used to evaluate the contribution of the GM to a disease phenotype.
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Affiliation(s)
- Aaron C Ericsson
- Aaron C. Ericsson, DVM, PhD, is a research assistant professor and Craig L. Franklin, DVM, PhD, DACLAM, is a professor in the Department of Veterinary Pathobiology at the University of Missouri in Columbia, Missouri
| | - Craig L Franklin
- Aaron C. Ericsson, DVM, PhD, is a research assistant professor and Craig L. Franklin, DVM, PhD, DACLAM, is a professor in the Department of Veterinary Pathobiology at the University of Missouri in Columbia, Missouri
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11
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Kato T, Fukuda S, Fujiwara A, Suda W, Hattori M, Kikuchi J, Ohno H. Multiple omics uncovers host-gut microbial mutualism during prebiotic fructooligosaccharide supplementation. DNA Res 2014; 21:469-80. [PMID: 24848698 PMCID: PMC4195493 DOI: 10.1093/dnares/dsu013] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fructooligosaccharide (FOS), a prebiotic well known for its health-promoting properties, can improve the human gut ecosystem most likely through changes in its microbial composition. However, the detailed mechanism(s) of action of FOS in the modulation of the gut ecosystem remain(s) obscure. Traditional methods of profiling microbes and metabolites could barely show any significant features due to the existence of large interindividual differences, but our novel microbe–metabolite correlation approach, combined with faecal immunoglobulin A (IgA) measurements, has revealed that the induction of mucosal IgA by FOS supplementation correlated with the presence of specific bacteria. Furthermore, the metabolic dynamics of butyrate, l-phenylalanine, l-lysine and tyramine were positively correlated with that of these bacteria and IgA production, whereas p-cresol was negatively correlated. Taken together, our focused intraindividual analysis with omics approaches is a powerful strategy for uncovering the gut molecular network and could provide a new vista for understanding the human gut ecosystem.
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Affiliation(s)
- Tamotsu Kato
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Graduate School of Nanobioscience, Yokohama City University, Kanagawa 230-0045, Japan
| | - Shinji Fukuda
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Institute for Advanced Biosciences, Keio University, Yamagata 997-0052, Japan
| | - Akemi Fujiwara
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Graduate School of Nanobioscience, Yokohama City University, Kanagawa 230-0045, Japan
| | - Wataru Suda
- Center for Omics and Bioinformatics, Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8561, Japan
| | - Masahira Hattori
- Center for Omics and Bioinformatics, Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8561, Japan
| | - Jun Kikuchi
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa 230-0045, Japan Environmental Metabolic Analysis Research Team, RIKEN Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences (IMS), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan Graduate School of Medical Life Science, Yokohama City University, Kanagawa 230-0045, Japan
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The intestinal microbiota in the rat model: major breakthroughs from new technologies. Anim Health Res Rev 2013; 13:54-63. [PMID: 22853927 DOI: 10.1017/s1466252312000072] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The mammalian intestine harbors a large and diverse community of micro-organisms, known as the intestinal microbiota. Recent developments in molecular profiling methods, mainly based on microbial 16S ribosomal RNA gene sequencing, have provided unprecedented insights into the make-up and diversity of intestinal microbial communities. Using these culture-independent analyses, gut microbiota of several mammals including laboratory rodents, have been revisited. The laboratory rat is one of the major species bred and kept for scientific research. Although this animal is bred in confined environments and subjected to procedures for satisfying health requirements that hamper natural colonization, some major features of mammalian gut microbiota are conserved. However, the gut microbiota varies according to the breeding conditions of the rats and this could impact reproducibility of the experimental models. Determining the non-pathogenic microbial community might be relevant in standards of quality control of laboratory animals. Molecular profiling techniques could be applied to document this information.
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Bibiloni R. Rodent models to study the relationships between mammals and their bacterial inhabitants. Gut Microbes 2012; 3:536-43. [PMID: 22918304 PMCID: PMC3495791 DOI: 10.4161/gmic.21905] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Laboratory rodents have been instrumental in helping researchers to unravel the complex interactions that mammals have with their microbial commensals. Progress in defining these interactions has also been possible thanks to the development of culture-independent methods for describing the microbiota associated to body surfaces. Understanding the mechanisms that govern this relationship at the molecular, cellular, and ecological levels is central to both health and disease. The present review of rodent models commonly used to investigate microbial-host "conversations" is focused on those complex bacterial communities residing in the lower gut. Although many types of pathology have been studied using gnotobiotic animals, only the models relevant to commensal bacteria will be described.
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Kuang H, Li Z, Peng C, Liu L, Xu L, Zhu Y, Wang L, Xu C. Metabonomics Approaches and the Potential Application in Foodsafety Evaluation. Crit Rev Food Sci Nutr 2012; 52:761-74. [DOI: 10.1080/10408398.2010.508345] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Clayton TA. Metabolic differences underlying two distinct rat urinary phenotypes, a suggested role for gut microbial metabolism of phenylalanine and a possible connection to autism. FEBS Lett 2012; 586:956-61. [DOI: 10.1016/j.febslet.2012.01.049] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 01/08/2012] [Accepted: 01/23/2012] [Indexed: 11/25/2022]
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Bleich A, Hansen AK. Time to include the gut microbiota in the hygienic standardisation of laboratory rodents. Comp Immunol Microbiol Infect Dis 2012; 35:81-92. [PMID: 22257867 DOI: 10.1016/j.cimid.2011.12.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 11/17/2011] [Accepted: 12/19/2011] [Indexed: 02/06/2023]
Abstract
The gut microbiota (GM) composition and its impact on animal experiments has become currently dramatically relevant in our days: (1) recent progress in metagenomic technologies, (2) the availability of large scale quantitative analyses to characterize even subtle phenotypes, (3) the limited diversity of laboratory rodent GM due to strict barriers at laboratory animal vendors, and (4) the availability of up to 300.000 different transgenic mouse strains from different sources displaying a huge variety in their GM composition. In this review the GM is described as a variable in animal experiments which need to be reduced for scientific as well as ethical reasons, and strategies how to implement this in routine diagnostic procedures are proposed. We conclude that we have both enough information available to state that the GM has an essential impact on animal models, as well as the methods available to start dealing with these impacts.
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Affiliation(s)
- André Bleich
- Institute for Laboratory Animal Science, Hannover Medical School, Hannover, Germany, Hannover, Germany.
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Gong L, Aranibar N, Han YH, Zhang Y, Lecureux L, Bhaskaran V, Khandelwal P, Klaassen CD, Lehman-McKeeman LD. Characterization of organic anion-transporting polypeptide (Oatp) 1a1 and 1a4 null mice reveals altered transport function and urinary metabolomic profiles. Toxicol Sci 2011; 122:587-97. [PMID: 21561886 DOI: 10.1093/toxsci/kfr114] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Organic anion-transporting polypeptides (Oatp) 1a1 and 1a4 were deleted by homologous recombination, and mice were characterized for Oatp expression in liver and kidney, transport in isolated hepatocytes, in vivo disposition of substrates, and urinary metabolomic profiles. Oatp1a1 and Oatp1a4 proteins were undetected in liver, and both lines were viable and fertile. Hepatic constitutive messenger RNAs (mRNAs) for Oatp1a4, 1b2, or 2b1 were unchanged in Oatp1a1⁻/⁻ mice, whereas renal Oatp1a4 mRNA decreased approximately 50% (both sexes). In Oatp1a4⁻/⁻ mice, no changes in constitutive mRNAs for other Oatps were observed. Uptake of estradiol-17β-D-glucuronide and estrone-3-sulfate in primary hepatocytes decreased 95 and 75%, respectively, in Oatp1a1⁻/⁻ mice and by 60 and 30%, respectively, in Oatp1a4⁻/⁻ mice. Taurocholate uptake decreased by 20 and 50% in Oatp1a1⁻/⁻ and Oatp1a4⁻/⁻ mice, respectively, whereas digoxin was unaffected. Plasma area under the curve (AUC) for estradiol-17β-D-glucuronide increased 35 and 55% in male and female Oatp1a1⁻/⁻ mice, respectively, with a concurrent 50% reduction in liver-to-plasma ratios. In contrast, plasma AUC or tissue concentrations of estradiol-17β-D-glucuronide were unchanged in Oatp1a4⁻/⁻ mice. Plasma AUCs for dibromosulfophthalein increased nearly threefold in male Oatp1a1⁻/⁻ and Oatp1a4⁻/⁻ mice, increased by 40% in female Oatp1a4⁻/⁻ mice, and were unchanged in female Oatp1a1⁻/⁻ mice. In both lines, no changes in serum ALT, bilirubin, and cholesterol were noted. NMR analyses showed no generalized increase in urinary excretion of organic anions. However, urinary excretion of taurine decreased by 30-40% and was accompanied by increased excretion of isethionic acid, a taurine metabolite generated by intestinal bacteria, suggesting some perturbations in intestinal bacteria distribution.
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Affiliation(s)
- Lei Gong
- Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Co., Princeton, New Jersey 08543, USA
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Robertson DG, Watkins PB, Reily MD. Metabolomics in toxicology: preclinical and clinical applications. Toxicol Sci 2010; 120 Suppl 1:S146-70. [PMID: 21127352 DOI: 10.1093/toxsci/kfq358] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Donald G Robertson
- Applied and Investigative Metabolomics, Bristol-Myers Squibb Co., Princeton, New Jersey 08543, USA.
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Rasmussen H, Martínez I, Lee J, Walter J. Alteration of the gastrointestinal microbiota of mice by edible blue-green algae. J Appl Microbiol 2009; 107:1108-18. [DOI: 10.1111/j.1365-2672.2009.04288.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes. Mol Syst Biol 2008; 4:219. [PMID: 18854818 PMCID: PMC2583082 DOI: 10.1038/msb.2008.56] [Citation(s) in RCA: 251] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2008] [Revised: 07/15/2008] [Indexed: 02/08/2023] Open
Abstract
To characterize the impact of gut microbiota on host metabolism, we investigated the multicompartmental metabolic profiles of a conventional mouse strain (C3H/HeJ) (n=5) and its germ-free (GF) equivalent (n=5). We confirm that the microbiome strongly impacts on the metabolism of bile acids through the enterohepatic cycle and gut metabolism (higher levels of phosphocholine and glycine in GF liver and marked higher levels of bile acids in three gut compartments). Furthermore we demonstrate that (1) well-defined metabolic differences exist in all examined compartments between the metabotypes of GF and conventional mice: bacterial co-metabolic products such as hippurate (urine) and 5-aminovalerate (colon epithelium) were found at reduced concentrations, whereas raffinose was only detected in GF colonic profiles. (2) The microbiome also influences kidney homeostasis with elevated levels of key cell volume regulators (betaine, choline, myo-inositol and so on) observed in GF kidneys. (3) Gut microbiota modulate metabotype expression at both local (gut) and global (biofluids, kidney, liver) system levels and hence influence the responses to a variety of dietary modulation and drug exposures relevant to personalized health-care investigations.
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Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat Rev Microbiol 2008; 6:776-88. [PMID: 18794915 PMCID: PMC2664199 DOI: 10.1038/nrmicro1978] [Citation(s) in RCA: 1052] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In this Analysis we use published 16S ribosomal RNA gene sequences to compare the bacterial assemblages that are associated with humans and other mammals, metazoa and free-living microbial communities that span a range of environments. The composition of the vertebrate gut microbiota is influenced by diet, host morphology and phylogeny, and in this respect the human gut bacterial community is typical of an omnivorous primate. However, the vertebrate gut microbiota is different from free-living communities that are not associated with animal body habitats. We propose that the recently initiated international Human Microbiome Project should strive to include a broad representation of humans, as well as other mammalian and environmental samples, as comparative analyses of microbiotas and their microbiomes are a powerful way to explore the evolutionary history of the biosphere.
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Affiliation(s)
- Ruth E Ley
- Center for Genome Sciences, Washington University School of Medicine, St Louis, Missouri 63108, USA
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Robertson DG. The Muddle of Models: What You Donʼt Know Can Hurt You. Chem Res Toxicol 2008; 21:1917-22. [DOI: 10.1021/tx800204g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Donald G. Robertson
- Applied and Investigative Metabonomics, Bristol-Myers Squibb Company, Princeton, New Jersey 08543
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Coen M, Holmes E, Lindon JC, Nicholson JK. NMR-based metabolic profiling and metabonomic approaches to problems in molecular toxicology. Chem Res Toxicol 2008; 21:9-27. [PMID: 18171018 DOI: 10.1021/tx700335d] [Citation(s) in RCA: 225] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have reviewed the main contributions to the development of NMR-based metabonomic and metabolic profiling approaches for toxicological assessment, biomarker discovery, and studies on toxic mechanisms. The metabonomic approach, (defined as the quantitative measurement of the multiparametric metabolic response of living systems to pathophysiological stimuli or genetic modification) was originally developed to assist interpretation in NMR-based toxicological studies. However, in recent years there has been extensive fusion with metabolomic and other metabolic profiling approaches developed in plant biology, and there is much wider coverage of the biomedical and environmental fields. Specifically, metabonomics involves the use of spectroscopic techniques with statistical and mathematical tools to elucidate dominant patterns and trends directly correlated with time-related metabolic fluctuations within spectral data sets usually derived from biofluids or tissue samples. Temporal multivariate metabolic signatures can be used to discover biomarkers of toxic effect, as general toxicity screening aids, or to provide novel mechanistic information. This approach is complementary to proteomics and genomics and is applicable to a wide range of problems, including disease diagnosis, evaluation of xenobiotic toxicity, functional genomics, and nutritional studies. The use of biological fluids as a source of whole organism metabolic information enhances the use of this approach in minimally invasive longitudinal studies.
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Affiliation(s)
- Muireann Coen
- Department of Biomolecular Medicine, Surgery, Oncology, Reproductive Biology and Anesthetics Division, Faculty of Medicine, Imperial College London, London, UK
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