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Singh V, West G, Fiocchi C, Good CE, Katz J, Jacobs MR, Dichosa AEK, Flask C, Wesolowski M, McColl C, Grubb B, Ahmed S, Bank NC, Thamma K, Bederman I, Erokwu B, Yang X, Sundrud MS, Menghini P, Basson AR, Ezeji J, Viswanath SE, Veloo A, Sykes DB, Cominelli F, Rodriguez-Palacios A. Clonal Parabacteroides from Gut Microfistulous Tracts as Transmissible Cytotoxic Succinate-Commensal Model of Crohn's Disease Complications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574896. [PMID: 38260564 PMCID: PMC10802508 DOI: 10.1101/2024.01.09.574896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Crohn's disease (CD) has been traditionally viewed as a chronic inflammatory disease that cause gut wall thickening and complications, including fistulas, by mechanisms not understood. By focusing on Parabacteroides distasonis (presumed modern succinate-producing commensal probiotic), recovered from intestinal microfistulous tracts (cavernous fistulous micropathologies CavFT proposed as intermediate between 'mucosal fissures' and 'fistulas') in two patients that required surgery to remove CD-damaged ilea, we demonstrate that such isolates exert pathogenic/pathobiont roles in mouse models of CD. Our isolates are clonally-related; potentially emerging as transmissible in the community and mice; proinflammatory and adapted to the ileum of germ-free mice prone to CD-like ileitis (SAMP1/YitFc) but not healthy mice (C57BL/6J), and cytotoxic/ATP-depleting to HoxB8-immortalized bone marrow derived myeloid cells from SAMP1/YitFc mice when concurrently exposed to succinate and extracts from CavFT-derived E. coli , but not to cells from healthy mice. With unique genomic features supporting recent genetic exchange with Bacteroides fragilis -BGF539, evidence of international presence in primarily human metagenome databases, these CavFT Pdis isolates could represent to a new opportunistic Parabacteroides species, or subspecies (' cavitamuralis' ) adapted to microfistulous niches in CD.
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2
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Muralitharan RR, Snelson M, Meric G, Coughlan MT, Marques FZ. Guidelines for microbiome studies in renal physiology. Am J Physiol Renal Physiol 2023; 325:F345-F362. [PMID: 37440367 DOI: 10.1152/ajprenal.00072.2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/28/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023] Open
Abstract
Gut microbiome research has increased dramatically in the last decade, including in renal health and disease. The field is moving from experiments showing mere association to causation using both forward and reverse microbiome approaches, leveraging tools such as germ-free animals, treatment with antibiotics, and fecal microbiota transplantations. However, we are still seeing a gap between discovery and translation that needs to be addressed, so that patients can benefit from microbiome-based therapies. In this guideline paper, we discuss the key considerations that affect the gut microbiome of animals and clinical studies assessing renal function, many of which are often overlooked, resulting in false-positive results. For animal studies, these include suppliers, acclimatization, baseline microbiota and its normalization, littermates and cohort/cage effects, diet, sex differences, age, circadian differences, antibiotics and sweeteners, and models used. Clinical studies have some unique considerations, which include sampling, gut transit time, dietary records, medication, and renal phenotypes. We provide best-practice guidance on sampling, storage, DNA extraction, and methods for microbial DNA sequencing (both 16S rRNA and shotgun metagenome). Finally, we discuss follow-up analyses, including tools available, metrics, and their interpretation, and the key challenges ahead in the microbiome field. By standardizing study designs, methods, and reporting, we will accelerate the findings from discovery to translation and result in new microbiome-based therapies that may improve renal health.
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Affiliation(s)
- Rikeish R Muralitharan
- Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Melbourne, Victoria, Australia
- Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | - Matthew Snelson
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Guillaume Meric
- Cambridge-Baker Systems Genomics Initiative, Baker Heart & Diabetes Institute, Melbourne, Victoria, Australia
- Department of Cardiometabolic Health, University of Melbourne, Melbourne, Victoria, Australia
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Cardiovascular Research Translation and Implementation, La Trobe University, Melbourne, Victoria, Australia
| | - Melinda T Coughlan
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Victoria, Australia
| | - Francine Z Marques
- Hypertension Research Laboratory, School of Biological Sciences, Faculty of Science, Monash University, Melbourne, Victoria, Australia
- Heart Failure Research Group, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Victorian Heart Institute, Monash University, Melbourne, Victoria, Australia
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3
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Verderio P, Lecchi M, Ciniselli CM, Shishmani B, Apolone G, Manenti G. 3Rs Principle and Legislative Decrees to Achieve High Standard of Animal Research. Animals (Basel) 2023; 13:ani13020277. [PMID: 36670818 PMCID: PMC9854901 DOI: 10.3390/ani13020277] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/15/2023] Open
Abstract
Animal experimentation is a vast ecosystem that tries to make different issues such as legislative, ethical and scientific coexist. Research in animal experimentation has made many strides thanks to the 3Rs principle and the attached legislative decrees, but for this very reason, it needs to be evenly implemented both among the countries that have adhered to the decrees and among the team members who design and execute the experimental practice. In this article, we emphasize the importance of the 3Rs principle's application, with a particular focus on the concept of Reduction and related key aspects that can best be handled with the contribution of experts from different fields.
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Affiliation(s)
- Paolo Verderio
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
- Correspondence: ; Tel.: +39-02-2390-3201
| | - Mara Lecchi
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Chiara Maura Ciniselli
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Bjorn Shishmani
- Unit of Bioinformatics and Biostatistics, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Giovanni Apolone
- Scientific Directorate, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
| | - Giacomo Manenti
- Unit of Animal Health and Welfare, Fondazione IRCCS Istituto Nazionale dei Tumori, 20133 Milan, Italy
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4
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Re-Analysis and Additional Information Needed to Inform Conclusions. Comment on Halenova et al. Deuterium-Depleted Water as Adjuvant Therapeutic Agent for Treatment of Diet-Induced Obesity in Rats. Molecules 2020, 25, 23. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165186. [PMID: 36014426 PMCID: PMC9414091 DOI: 10.3390/molecules27165186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/26/2022] [Accepted: 08/11/2022] [Indexed: 02/02/2023]
Abstract
We were interested to read the report by Halenova et al. [...].
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Moysidou CM, Withers AM, Nisbet AJ, Price DRG, Bryant CE, Cantacessi C, Owens RM. Investigation of Host-Microbe-Parasite Interactions in an In Vitro 3D Model of the Vertebrate Gut. Adv Biol (Weinh) 2022; 6:e2200015. [PMID: 35652159 DOI: 10.1002/adbi.202200015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/23/2022] [Indexed: 01/28/2023]
Abstract
In vitro models of the gut-microbiome axis are in high demand. Conventionally, intestinal monolayers grown on Transwell setups are used to test the effects of commensals/pathogens on the barrier integrity, both under homeostatic and pathophysiological conditions. While such models remain valuable for deepening the understanding of host-microbe interactions, often, they lack key biological components that mediate this intricate crosstalk. Here, a 3D in vitro model of the vertebrate intestinal epithelium, interfaced with immune cells surviving in culture for over 3 weeks, is developed and applied to proof-of-concept studies of host-microbe interactions. More specifically, the establishment of stable host-microbe cocultures is described and functional and morphological changes in the intestinal barrier induced by the presence of commensal bacteria are shown. Finally, evidence is provided that the 3D vertebrate gut models can be used as platforms to test host-microbe-parasite interactions. Exposure of gut-immune-bacteria cocultures to helminth "excretory/secretory products" induces in vivo-like up-/down-regulation of certain cytokines. These findings support the robustness of the modular in vitro cell systems for investigating the dynamics of host-microbe crosstalk and pave the way toward new approaches for systems biology studies of pathogens that cannot be maintained in vitro, including parasitic helminths.
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Affiliation(s)
- Chrysanthi-Maria Moysidou
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, West Cambridge Site, CB3 0AS, UK
| | - Aimee M Withers
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, West Cambridge Site, CB3 0AS, UK
| | - Alasdair J Nisbet
- Moredun Research Institute, Pentlands Science Park, Edinburgh, EH26 0PZ, UK
| | - Daniel R G Price
- Moredun Research Institute, Pentlands Science Park, Edinburgh, EH26 0PZ, UK
| | - Clare E Bryant
- Department of Veterinary Medicine, Cambridge Veterinary School, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Cinzia Cantacessi
- Department of Veterinary Medicine, Cambridge Veterinary School, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Róisín M Owens
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, West Cambridge Site, CB3 0AS, UK
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Russell A, Copio JN, Shi Y, Kang S, Franklin CL, Ericsson AC. Reduced housing density improves statistical power of murine gut microbiota studies. Cell Rep 2022; 39:110783. [PMID: 35545042 PMCID: PMC9161176 DOI: 10.1016/j.celrep.2022.110783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 12/28/2021] [Accepted: 04/13/2022] [Indexed: 11/25/2022] Open
Abstract
The gut microbiome of humans and animals is critical to host health. Mice are used to investigate the microbiome and its influences; however, the predictive value of such studies is hindered by cage effects due to coprophagy. Our objectives were to evaluate the influence of cage density on the statistical power to detect treatment-dependent effects of a selective pressure on microbiome composition. C57BL/6 mice were separated into groups of 2 or 4 mice per cage and then assigned to groups receiving enrofloxacin, broad-spectrum antibiotics, or control. Fecal samples were collected at weeks 0, 1, and 4, along with contents of the jejunum and cecum. Bacterial DNA analysis examined microbiome richness, diversity, and variability within and between cages. Statistical analyses reveal that reduced housing density consistently results in comparable susceptibility to antibiotics, reduced cage effects, and increased statistical power to detect treatment-associated effects, justifying the practice of reduced housing density.
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Affiliation(s)
- Amber Russell
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65201, USA
| | - Joanna N Copio
- College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210 USA
| | - Yushu Shi
- Department of Statistics, College of Arts and Sciences, University of Missouri, Columbia, MO 65201 USA
| | - Sumin Kang
- Department of Statistics, College of Arts and Sciences, University of Missouri, Columbia, MO 65201 USA
| | - Craig L Franklin
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65201, USA; University of Missouri Metagenomics Center, University of Missouri, Columbia, MO 65201 USA; Mutant Mouse Resource and Research Center, University of Missouri, Columbia, MO 65201 USA
| | - Aaron C Ericsson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65201, USA; University of Missouri Metagenomics Center, University of Missouri, Columbia, MO 65201 USA; Mutant Mouse Resource and Research Center, University of Missouri, Columbia, MO 65201 USA.
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Rawle DJ, Dumenil T, Tang B, Bishop CR, Yan K, Le TT, Suhrbier A. Microplastic consumption induces inflammatory signatures in the colon and prolongs a viral arthritis. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 809:152212. [PMID: 34890673 DOI: 10.1016/j.scitotenv.2021.152212] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 06/13/2023]
Abstract
Global microplastic (MP) contamination and the effects on the environment are well described. However, the potential for MP consumption to affect human health remains controversial. Mice consuming ≈80 μg/kg/day of 1 μm polystyrene MPs via their drinking water showed no weight loss, nor were MPs detected in internal organs. The microbiome was also not significantly changed. MP consumption did lead to small transcriptional changes in the colon suggesting plasma membrane perturbations and mild inflammation. Mice were challenged with the arthritogenic chikungunya virus, with MP consumption leading to a significantly prolonged arthritic foot swelling that was associated with elevated Th1, NK cell and neutrophil signatures. Immunohistochemistry also showed a significant increase in the ratio of neutrophils to monocyte/macrophages. The picture that emerges is reminiscent of enteropathic arthritis, whereby perturbations in the colon are thought to activate innate lymphoid cells that can inter alia migrate to joint tissues to promote inflammation.
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Affiliation(s)
- Daniel J Rawle
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Troy Dumenil
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Bing Tang
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Cameron R Bishop
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Kexin Yan
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Thuy T Le
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - Andreas Suhrbier
- Immunology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia; Australian Infectious Disease Research Centre, GVN Center of Excellence, Brisbane, Queensland 4029 and 4072, Australia.
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8
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Dimet-Wiley A, Wu Q, Wiley JT, Eswar A, Neelakantan H, Savidge T, Watowich S. Reduced calorie diet combined with NNMT inhibition establishes a distinct microbiome in DIO mice. Sci Rep 2022; 12:484. [PMID: 35013352 PMCID: PMC8748953 DOI: 10.1038/s41598-021-03670-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/01/2021] [Indexed: 11/29/2022] Open
Abstract
Treatment with a nicotinamide N-methyltransferase inhibitor (NNMTi; 5-amino-1-methylquinolinium) combined with low-fat diet (LD) promoted dramatic whole-body adiposity and weight loss in diet-induced obese (DIO) mice, rapidly normalizing these measures to age-matched lean animals, while LD switch alone was unable to restore these measures to age-matched controls in the same time frame. Since mouse microbiome profiles often highly correlate with body weight and fat composition, this study was designed to test whether the cecal microbiomes of DIO mice treated with NNMTi and LD were comparable to the microbiomes of age-matched lean counterparts and distinct from microbiomes of DIO mice maintained on a high-fat Western diet (WD) or subjected to LD switch alone. There were minimal microbiome differences between lean and obese controls, suggesting that diet composition and adiposity had limited effects. However, DIO mice switched from an obesity-promoting WD to an LD (regardless of treatment status) displayed several genera and phyla differences compared to obese and lean controls. While alpha diversity measures did not significantly differ between groups, beta diversity principal coordinates analyses suggested that mice from the same treatment group were the most similar. K-means clustering analysis of amplicon sequence variants by animal demonstrated that NNMTi-treated DIO mice switched to LD had a distinct microbiome pattern that was highlighted by decreased Erysipelatoclostridium and increased Lactobacillus relative abundances compared to vehicle counterparts; these genera are tied to body weight and metabolic regulation. Additionally, Parasutterella relative abundance, which was increased in both the vehicle- and NNMTi-treated LD-switched groups relative to the controls, significantly correlated with several adipose tissue metabolites' abundances. Collectively, these results provide a novel foundation for future investigations.
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Affiliation(s)
- Andrea Dimet-Wiley
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, USA
| | - Qinglong Wu
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Jerrin T Wiley
- Depatment of Computer Science, University of Houston, Houston, TX, USA
| | - Aditya Eswar
- New York University Stern School of Business, New York City, NY, USA
| | | | - Tor Savidge
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Stan Watowich
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX, USA.
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Hernandez J, Rouillé E, Chocteau F, Allard M, Haurogné K, Lezin F, Hervé JM, Bach JM, Abadie J, Lieubeau B. Nonhypoalbuminemic Inflammatory Bowel Disease in Dogs as Disease Model. Inflamm Bowel Dis 2021; 27:1975-1985. [PMID: 33783501 DOI: 10.1093/ibd/izab064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND The incidence of inflammatory bowel disease (IBD) is increasing worldwide, emphasizing the need of relevant models, as dogs spontaneously affected by IBD may be, for better knowledge of the disease's physiopathology. METHODS We studied 22 client-owned dogs suffering from IBD without protein loss and 14 control dogs. Biopsies were obtained from the duodenum, ileum, and colon. Inflammatory grade was assessed by histopathology, immunohistochemistry, and chemokine analysis. The expression of Toll-like receptors (TLR) in mucosa was immunohistochemically evaluated. Antibody levels against bacterial ligands (lipopolysaccharide [LPS] and flagellin) were measured in sera using enzyme-linked immunoassay. RESULTS Dogs with IBD showed low to severe clinical disease. Histopathologically, the gut of dogs with IBD did not exhibit significant alterations compared with controls except in the colon. The number of CD3+ T lymphocytes was decreased in the ileum and colon of dogs with IBD compared with controls, whereas the numbers of Foxp3+, CD20+, and CD204+ cells were similar in the 2 groups. Three chemokines, but no cytokines, were detected at the protein level in the mucosa, and the disease poorly affected their tissue concentrations. Dogs with IBD exhibited higher serum reactivity against LPS and flagellin than controls but similar immunoreactivity against the receptors TLR4 and TLR5. In addition, TLR2 and TLR9 showed similar expression patterns in both groups of dogs. CONCLUSIONS Our data described dysregulated immune responses in dogs affected by IBD without protein loss. Despite fairly homogeneous dog cohorts, we were still faced with interindividual variability, and new studies with larger cohorts are needed to validate the dog as a model.
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Affiliation(s)
- Juan Hernandez
- IECM, Oniris (Nantes-Atlantic National College of Veterinary Medicine, Food Science and Engineering), INRAE, Nantes, France
| | | | | | - Marie Allard
- IECM, Oniris (Nantes-Atlantic National College of Veterinary Medicine, Food Science and Engineering), INRAE, Nantes, France
| | - Karine Haurogné
- IECM, Oniris (Nantes-Atlantic National College of Veterinary Medicine, Food Science and Engineering), INRAE, Nantes, France
| | | | - Julie M Hervé
- IECM, Oniris (Nantes-Atlantic National College of Veterinary Medicine, Food Science and Engineering), INRAE, Nantes, France
| | - Jean-Marie Bach
- IECM, Oniris (Nantes-Atlantic National College of Veterinary Medicine, Food Science and Engineering), INRAE, Nantes, France
| | | | - Blandine Lieubeau
- IECM, Oniris (Nantes-Atlantic National College of Veterinary Medicine, Food Science and Engineering), INRAE, Nantes, France
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Basson AR, Rodriguez-Palacios A, Cominelli F. Artificial Sweeteners: History and New Concepts on Inflammation. Front Nutr 2021; 8:746247. [PMID: 34631773 PMCID: PMC8497813 DOI: 10.3389/fnut.2021.746247] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/23/2021] [Indexed: 12/12/2022] Open
Abstract
Since the introduction of artificial sweeteners (AS) to the North American market in the 1950s, a growing number of epidemiological and animal studies have suggested that AS may induce changes in gut bacteria and gut wall immune reactivity, which could negatively affect individuals with or susceptible to chronic inflammatory conditions such as inflammatory bowel disease (IBD), a disorder that has been growing exponentially in westernized countries. This review summarizes the history of current FDA-approved AS and their chemical composition, metabolism, and bacterial utilization, and provides a scoping overview of the disease mechanisms associated with the induction or prevention of inflammation in IBD. We provide a general outlook on areas that have been both largely and scarcely studied, emerging concepts using silica, and describe the effects of AS on acute and chronic forms of intestinal inflammation.
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Affiliation(s)
- Abigail Raffner Basson
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Alexander Rodriguez-Palacios
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
- Mouse Models, Silvio O'Conte Cleveland Digestive Diseases Research Core Center, Cleveland, OH, United States
- Germ-Free and Gut Microbiome Core, Digestive Health Research Institute, Case Western Reserve University, Cleveland, OH, United States
| | - Fabio Cominelli
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
- Mouse Models, Silvio O'Conte Cleveland Digestive Diseases Research Core Center, Cleveland, OH, United States
- Germ-Free and Gut Microbiome Core, Digestive Health Research Institute, Case Western Reserve University, Cleveland, OH, United States
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11
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Rodriguez-Palacios A, Basson AR, Cominelli F. Artificial Sweeteners and Whole-Food Science: Could Mice Help Clinicians Make Diet Recommendations for IBD Patients? Gastroenterology 2021; 161:8-14. [PMID: 33798527 PMCID: PMC8592564 DOI: 10.1053/j.gastro.2021.03.041] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 02/08/2023]
Affiliation(s)
- Alexander Rodriguez-Palacios
- Department of Medicine and Division of Gastroenterology and Liver Diseases Case Western Reserve University School of Medicine, and, Digestive Health Research Institute, University Hospitals Cleveland Medical Center, and, Germ-Free and Gut Microbiome Core, Cleveland Digestive Diseases Research Core Center, Case Western Reserve University, and, University Hospitals Research and Education Institute, University Hospital Cleveland Medical Center, Cleveland, Ohio
| | - Abigail Raffner Basson
- Department of Medicine and Division of Gastroenterology and Liver Diseases Case Western Reserve University School of Medicine, and, Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Fabio Cominelli
- Department of Medicine and Division of Gastroenterology and Liver Diseases Case Western Reserve University School of Medicine, and, Digestive Health Research Institute, University Hospitals Cleveland Medical Center, and, Department of Pathology, Case Western Reserve University, Cleveland, Ohio
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12
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Yang J, Chun J. Taxonomic composition and variation in the gut microbiota of laboratory mice. Mamm Genome 2021; 32:297-310. [PMID: 33893864 DOI: 10.1007/s00335-021-09871-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 04/10/2021] [Indexed: 12/14/2022]
Abstract
The gut microbiota can affect host health, including humans. Mouse models have been used extensively to study the relationships between the host and the gut microbiota. With the development of cost-effective high-throughput DNA sequencing, several methods have been used to identify members of the gut microbiota of laboratory mice. In recent years, the amount of research and knowledge about the mouse gut microbiota has exploded, leading to significant breakthroughs in understanding of the taxonomic composition of and variation in this community. In addition, the rapidly increasing volume of data has allowed the development of public resources for exploring the mouse gut microbiota. In this review, we describe the concepts and pros and cons of basic methodologies that can be used to determine the gut bacterial profile in laboratory mice. We also present the key bacterial components of the mouse gut microbiota from the phylum to the species level and then compare them with those identified in other references. Additionally, we discuss variations in the mouse gut microbiota and their association with experiments using mice. Finally, we summarize the properties and functions of currently available public resources for exploring the mouse gut microbiota.
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Affiliation(s)
- Junwon Yang
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea.,Institute of Molecular Biology & Genetics, Seoul National University, Seoul, 08826, Korea.,Department of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jongsik Chun
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Korea. .,Institute of Molecular Biology & Genetics, Seoul National University, Seoul, 08826, Korea. .,Department of Biological Sciences, Seoul National University, Seoul, 08826, Korea.
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13
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Jarett JK, Kingsbury DD, Dahlhausen KE, Ganz HH. Best Practices for Microbiome Study Design in Companion Animal Research. Front Vet Sci 2021; 8:644836. [PMID: 33898544 PMCID: PMC8062777 DOI: 10.3389/fvets.2021.644836] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/09/2021] [Indexed: 12/31/2022] Open
Abstract
The gut microbiome is a community of microorganisms that inhabits an animal host's gastrointestinal tract, with important effects on animal health that are shaped by multiple environmental, dietary, and host-associated factors. Clinical and dietary trials in companion animals are increasingly including assessment of the microbiome, but interpretation of these results is often hampered by suboptimal choices in study design. Here, we review best practices for conducting feeding trials or clinical trials that intend to study the effects of an intervention on the microbiota. Choices for experimental design, including a review of basic designs, controls, and comparison groups, are discussed in the context of special considerations necessary for microbiome studies. Diet is one of the strongest influences on the composition of gut microbiota, so applications specific to nutritional interventions are discussed in detail. Lastly, we provide specific advice for successful recruitment of colony animals and household pets into an intervention study. This review is intended to serve as a resource to academic and industry researchers, clinicians, and veterinarians alike, for studies that test many different types of interventions.
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Basson AR, Ahmed S, Almutairi R, Seo B, Cominelli F. Regulation of Intestinal Inflammation by Soybean and Soy-Derived Compounds. Foods 2021; 10:foods10040774. [PMID: 33916612 PMCID: PMC8066255 DOI: 10.3390/foods10040774] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/30/2021] [Accepted: 04/02/2021] [Indexed: 02/06/2023] Open
Abstract
Environmental factors, particularly diet, are considered central to the pathogenesis of the inflammatory bowel diseases (IBD), Crohn’s disease and ulcerative colitis. In particular, the Westernization of diet, characterized by high intake of animal protein, saturated fat, and refined carbohydrates, has been shown to contribute to the development and progression of IBD. During the last decade, soybean, as well as soy-derived bioactive compounds (e.g., isoflavones, phytosterols, Bowman-Birk inhibitors) have been increasingly investigated because of their anti-inflammatory properties in animal models of IBD. Herein we provide a scoping review of the most studied disease mechanisms associated with disease induction and progression in IBD rodent models after feeding of either the whole food or a bioactive present in soybean.
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Affiliation(s)
- Abigail Raffner Basson
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA; (S.A.); (B.S.)
- Correspondence:
| | - Saleh Ahmed
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA; (S.A.); (B.S.)
| | - Rawan Almutairi
- Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Brian Seo
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA; (S.A.); (B.S.)
| | - Fabio Cominelli
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA;
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA; (S.A.); (B.S.)
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15
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'Statistical Irreproducibility' Does Not Improve with Larger Sample Size: How to Quantify and Address Disease Data Multimodality in Human and Animal Research. J Pers Med 2021; 11:jpm11030234. [PMID: 33806843 PMCID: PMC8005169 DOI: 10.3390/jpm11030234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 12/18/2022] Open
Abstract
Poor study reproducibility is a concern in translational research. As a solution, it is recommended to increase sample size (N), i.e., add more subjects to experiments. The goal of this study was to examine/visualize data multimodality (data with >1 data peak/mode) as cause of study irreproducibility. To emulate the repetition of studies and random sampling of study subjects, we first used various simulation methods of random number generation based on preclinical published disease outcome data from human gut microbiota-transplantation rodent studies (e.g., intestinal inflammation and univariate/continuous). We first used unimodal distributions (one-mode, Gaussian, and binomial) to generate random numbers. We showed that increasing N does not reproducibly identify statistical differences when group comparisons are repeatedly simulated. We then used multimodal distributions (>1-modes and Markov chain Monte Carlo methods of random sampling) to simulate similar multimodal datasets A and B (t-test-p = 0.95; N = 100,000), and confirmed that increasing N does not improve the ‘reproducibility of statistical results or direction of the effects’. Data visualization with violin plots of categorical random data simulations with five-integer categories/five-groups illustrated how multimodality leads to irreproducibility. Re-analysis of data from a human clinical trial that used maltodextrin as dietary placebo illustrated multimodal responses between human groups, and after placebo consumption. In conclusion, increasing N does not necessarily ensure reproducible statistical findings across repeated simulations due to randomness and multimodality. Herein, we clarify how to quantify, visualize and address disease data multimodality in research. Data visualization could facilitate study designs focused on disease subtypes/modes to help understand person–person differences and personalized medicine.
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16
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Raffner Basson A, Gomez-Nguyen A, LaSalla A, Buttó L, Kulpins D, Warner A, Di Martino L, Ponzani G, Osme A, Rodriguez-Palacios A, Cominelli F. Replacing Animal Protein with Soy-Pea Protein in an "American Diet" Controls Murine Crohn Disease-Like Ileitis Regardless of Firmicutes: Bacteroidetes Ratio. J Nutr 2021; 151:579-590. [PMID: 33484150 PMCID: PMC7948210 DOI: 10.1093/jn/nxaa386] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 08/26/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The current nutritional composition of the "American diet" (AD; also known as Western diet) has been linked to the increasing incidence of chronic diseases, including inflammatory bowel disease (IBD), namely Crohn disease (CD). OBJECTIVES This study investigated which of the 3 major macronutrients (protein, fat, carbohydrates) in the AD has the greatest impact on preventing chronic inflammation in experimental IBD mouse models. METHODS We compared 5 rodent diets designed to mirror the 2011-2012 "What We Eat in America" NHANES. Each diet had 1 macronutrient dietary source replaced. The formulated diets were AD, AD-soy-pea (animal protein replaced by soy + pea protein), AD-CHO ("refined carbohydrate" by polysaccharides), AD-fat [redistribution of the ω-6:ω-3 (n-6:n-3) PUFA ratio; ∼10:1 to 1:1], and AD-mix (all 3 "healthier" macronutrients combined). In 3 separate experiments, 8-wk-old germ-free SAMP1/YitFC mice (SAMP) colonized with human gut microbiota ("hGF-SAMP") from CD or healthy donors were fed an AD, an AD-"modified," or laboratory rodent diet for 24 wk. Two subsequent dextran sodium sulfate-colitis experiments in hGF-SAMP (12-wk-old) and specific-pathogen-free (SPF) C57BL/6 (20-wk-old) mice, and a 6-wk feeding trial in 24-wk-old SPF SAMP were performed. Intestinal inflammation, gut metagenomics, and MS profiles were assessed. RESULTS The AD-soy-pea diet resulted in lower histology scores [mean ± SD (56.1% ± 20.7% reduction)] in all feeding trials and IBD mouse models than did other diets (P < 0.05). Compared with the AD, the AD-soy-pea correlated with increased abundance in Lactobacillaceae and Leuconostraceae (1.5-4.7 log2 and 3.0-5.1 log2 difference, respectively), glutamine (6.5 ± 0.8 compared with 3.9 ± 0.3 ng/μg stool, P = 0.0005) and butyric acid (4:0; 3.3 ± 0.5 compared with 2.54 ± 0.4 ng/μg stool, P = 0.006) concentrations, and decreased linoleic acid (18:2n-6; 5.4 ± 0.4 compared with 8.6 ± 0.3 ng/μL plasma, P = 0.01). CONCLUSIONS Replacement of animal protein in an AD by plant-based sources reduced the severity of experimental IBD in all mouse models studied, suggesting that similar, feasible adjustments to the daily human diet could help control/prevent IBD in humans.
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Affiliation(s)
- Abigail Raffner Basson
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Adrian Gomez-Nguyen
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Alexandria LaSalla
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Ludovica Buttó
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Danielle Kulpins
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Alexandra Warner
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Luca Di Martino
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Gina Ponzani
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Abdullah Osme
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Pathology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Alexander Rodriguez-Palacios
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Fabio Cominelli
- Division of Gastroenterology & Liver Diseases, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
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17
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Basson AR, Chen C, Sagl F, Trotter A, Bederman I, Gomez-Nguyen A, Sundrud MS, Ilic S, Cominelli F, Rodriguez-Palacios A. Regulation of Intestinal Inflammation by Dietary Fats. Front Immunol 2021; 11:604989. [PMID: 33603741 PMCID: PMC7884479 DOI: 10.3389/fimmu.2020.604989] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
With the epidemic of human obesity, dietary fats have increasingly become a focal point of biomedical research. Epidemiological studies indicate that high-fat diets (HFDs), especially those rich in long-chain saturated fatty acids (e.g., Western Diet, National Health Examination survey; NHANES 'What We Eat in America' report) have multi-organ pro-inflammatory effects. Experimental studies have confirmed some of these disease associations, and have begun to elaborate mechanisms of disease induction. However, many of the observed effects from epidemiological studies appear to be an over-simplification of the mechanistic complexity that depends on dynamic interactions between the host, the particular fatty acid, and the rather personalized genetics and variability of the gut microbiota. Of interest, experimental studies have shown that certain saturated fats (e.g., lauric and myristic fatty acid-rich coconut oil) could exert the opposite effect; that is, desirable anti-inflammatory and protective mechanisms promoting gut health by unanticipated pathways. Owing to the experimental advantages of laboratory animals for the study of mechanisms under well-controlled dietary settings, we focus this review on the current understanding of how dietary fatty acids impact intestinal biology. We center this discussion on studies from mice and rats, with validation in cell culture systems or human studies. We provide a scoping overview of the most studied diseases mechanisms associated with the induction or prevention of Inflammatory Bowel Disease in rodent models relevant to Crohn's Disease and Ulcerative Colitis after feeding either high-fat diet (HFD) or feed containing specific fatty acid or other target dietary molecule. Finally, we provide a general outlook on areas that have been largely or scarcely studied, and assess the effects of HFDs on acute and chronic forms of intestinal inflammation.
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Affiliation(s)
- Abigail R. Basson
- Division of Gastroenterology and Liver Diseases, School of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Cleveland Digestive Diseases Research Core, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Digestive Health Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Christy Chen
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Filip Sagl
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Ashley Trotter
- Division of Gastroenterology and Liver Diseases, School of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Hospital Medicine, Pritzker School of Medicine, NorthShore University Health System, Chicago, IL, United States
| | - Ilya Bederman
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Adrian Gomez-Nguyen
- Division of Gastroenterology and Liver Diseases, School of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Cleveland Digestive Diseases Research Core, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Mark S. Sundrud
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, United States
| | - Sanja Ilic
- Department of Human Sciences, Human Nutrition, College of Education and Human Ecology, The Ohio State University, Columbus, OH, United States
| | - Fabio Cominelli
- Division of Gastroenterology and Liver Diseases, School of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Cleveland Digestive Diseases Research Core, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Digestive Health Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
| | - Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Diseases, School of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Digestive Health Research Institute, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Cleveland Digestive Diseases Research Core, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Digestive Health Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
- University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
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18
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Breznik JA, Schulz C, Ma J, Sloboda DM, Bowdish DME. Biological sex, not reproductive cycle, influences peripheral blood immune cell prevalence in mice. J Physiol 2021; 599:2169-2195. [PMID: 33458827 DOI: 10.1113/jp280637] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 12/03/2020] [Indexed: 12/16/2022] Open
Abstract
KEY POINTS Traditionally the female sex, compared with the male sex, has been perceived as having greater variability in many physiological traits, including within the immune system. We investigated effects of biological sex and the female reproductive cycle on numbers of circulating leukocytes in C57BL/6J mice. We show that biological sex, but not female reproductive cyclicity, has a significant effect on peripheral blood immune cell prevalence and variability, and that sex differences were not consistent amongst common inbred laboratory mouse strains. We found that male C57BL/6J mice, compared with female mice, have greater variability in peripheral blood immunophenotype, and that this was influenced by body weight. We created summary tables for researchers to facilitate experiment planning and sample size calculations for peripheral immune cells that consider the effects of biological sex. ABSTRACT Immunophenotyping (i.e. quantifying the number and types of circulating leukocytes) is used to characterize immune changes during health and disease, and in response to pharmacological and other interventions. Despite the importance of biological sex in immune function, there is considerable uncertainty amongst researchers as to the extent to which biological sex or the female reproductive cycle influence blood immunophenotype. We quantified circulating leukocytes by multicolour flow cytometry in young C57BL/6J mice and assessed the effects of the reproductive cycle, biological sex, and other experimental and biological factors on data variability. We found that there are no significant effects of the female reproductive cycle on the prevalence of peripheral blood B cells, NK cells, CD4+ T cells, CD8+ T cells, monocytes, or neutrophils. Immunophenotype composition and variability do not significantly change between stages of the female reproductive cycle. There are, however, sex-specific differences in immune cell prevalence, with fewer monocytes, neutrophils, and NK cells in female mice. Surprisingly, immunophenotype is more variable in male mice, and weight is a significant contributing factor. We provide tools for researchers to perform a priori sample size calculations for two-group and factorial analyses. We show that immunophenotype varies between inbred mouse strains, and that using equal sample sizes of male and female mice is not always appropriate for within-sex evaluations of immune cell populations in peripheral blood.
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Affiliation(s)
- Jessica A Breznik
- McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Christian Schulz
- McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
| | - Jinhui Ma
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Deborah M Sloboda
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.,Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada.,Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Dawn M E Bowdish
- McMaster Immunology Research Centre, McMaster University, Hamilton, Ontario, Canada.,Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada
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19
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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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20
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Qin X. Inhibition of Experimental Colitis by Saccharin in Animals: Should We Dismiss or Raise Concerns Regarding Possible Adverse Effects of Saccharin on Human Gut Microbiota and Health? Inflamm Bowel Dis 2020; 26:e159-e160. [PMID: 32651958 DOI: 10.1093/ibd/izaa180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Affiliation(s)
- Xiaofa Qin
- GI Biopharma Inc., Westfield, New Jersey, USA
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21
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Affiliation(s)
- Florian Frommlet
- Center for Medical Statistics, Informatics and Intelligent Systems, Section for Medical Statistics, Medical University Vienna, Vienna, Austria.
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22
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Voikar V, Gaburro S. Three Pillars of Automated Home-Cage Phenotyping of Mice: Novel Findings, Refinement, and Reproducibility Based on Literature and Experience. Front Behav Neurosci 2020; 14:575434. [PMID: 33192366 PMCID: PMC7662686 DOI: 10.3389/fnbeh.2020.575434] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/05/2020] [Indexed: 12/12/2022] Open
Abstract
Animal models of neurodegenerative and neuropsychiatric disorders require extensive behavioral phenotyping. Currently, this presents several caveats and the most important are: (i) rodents are nocturnal animals, but mostly tested during the light period; (ii) the conventional behavioral experiments take into consideration only a snapshot of a rich behavioral repertoire; and (iii) environmental factors, as well as experimenter influence, are often underestimated. Consequently, serious concerns have been expressed regarding the reproducibility of research findings on the one hand, and appropriate welfare of the animals (based on the principle of 3Rs-reduce, refine and replace) on the other hand. To address these problems and improve behavioral phenotyping in general, several solutions have been proposed and developed. Undisturbed, 24/7 home-cage monitoring (HCM) is gaining increased attention and popularity as demonstrating the potential to substitute or complement the conventional phenotyping methods by providing valuable data for identifying the behavioral patterns that may have been missed otherwise. In this review, we will briefly describe the different technologies used for HCM systems. Thereafter, based on our experience, we will focus on two systems, IntelliCage (NewBehavior AG and TSE-systems) and Digital Ventilated Cage (DVC®, Tecniplast)-how they have been developed and applied during recent years. Additionally, we will touch upon the importance of the environmental/experimenter artifacts and propose alternative suggestions for performing phenotyping experiments based on the published evidence. We will discuss how the integration of telemetry systems for deriving certain physiological parameters can help to complement the description of the animal model to offer better translation to human studies. Ultimately, we will discuss how such HCM data can be statistically interpreted and analyzed.
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Affiliation(s)
- Vootele Voikar
- Neuroscience Center, University of Helsinki, Helsinki, Finland
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23
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Rodriguez-Palacios A, Conger M, Cominelli F. Germ-Free Mice Under Two-Layer Textiles Are Fully Protected From Bacteria in Sprayed Microdroplets: A Functional in vivo Test Method of Facemask/Filtration Materials. Front Med (Lausanne) 2020; 7:504. [PMID: 32984381 PMCID: PMC7479817 DOI: 10.3389/fmed.2020.00504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/22/2020] [Indexed: 01/30/2023] Open
Abstract
Several studies have measured the effectiveness of masks at retaining particles of various sizes in vitro. To identify a functional in vivo model, herein we used germ-free (GF) mice to test the effectiveness of textiles as filtration material and droplet barriers to complement available in vitro-based knowledge. Herein, we report a study conducted in vivo with bacteria-carrying microdroplets to determine to what extent household textiles prevent contamination of GF mice in their environment. Using a recently validated spray-simulation method (mimicking a sneeze), herein we first determined that combed-cotton textiles used as two-layer-barriers covering the mouse cages prevented the contamination of all GF animals when sprayed 10-20 bacterial-droplet units/cm2. In additional to exposure trials, the model showed that GF mice were again protected by the combed-cotton textile after the acute exposure to 10 times more droplets (20 "spray-sneezes", ~200 bacterial-droplet units/cm2). Overall, two-layer combed-cotton protected 100% of the GF mice from bacteria-carrying droplets (n = 20 exposure-events), which was significantly superior compared to 100% mouse contamination without textile coverage or when 95% partly covered (n = 18, Fisher-exact, p < 0.0001). Of relevance is that two different densities of cotton were equally effective (100%) in preventing contamination regardless of density (120-vs. 200 g/m2; T-test, p = 0.0028), suggesting that similar density materials could prevent droplet contamination. As a practical message, we conducted a speech trial (counting numbers, 1-100) with/without the protection of the same cotton textile used as face cover. The trial illustrated that contamination of surfaces occurs at a rate of >2-6 bacteria-carrying saliva-droplets per word (2.6 droplets/cm2, 30 cm) when speaking at 60-70 decibels and that cotton face covers fully prevent bacterial surface contamination.
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Affiliation(s)
- Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Germ-Free and Gut Microbiome Core, Cleveland Digestive Diseases Research Core Center, Case Western Reserve University, Cleveland, OH, United States
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
- University Hospitals Research and Education Institute, University Hospital Cleveland Medical Center, Cleveland, OH, United States
| | - Mathew Conger
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Germ-Free and Gut Microbiome Core, Cleveland Digestive Diseases Research Core Center, Case Western Reserve University, Cleveland, OH, United States
| | - Fabio Cominelli
- Division of Gastroenterology and Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, United States
- Germ-Free and Gut Microbiome Core, Cleveland Digestive Diseases Research Core Center, Case Western Reserve University, Cleveland, OH, United States
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, United States
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24
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McCoy KD, Ohland CL. Innate responses to gut microbiota; critical assessment of the necessary experimental controls. Curr Opin Microbiol 2020; 59:34-41. [PMID: 32846371 DOI: 10.1016/j.mib.2020.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 01/20/2023]
Abstract
The intestinal microbiota is comprises a diverse community of micro-organisms that interact with many host processes. Innate immune responses to the gut microbiota are of particular importance as they influence many other downstream responses. This fascinating host-microbe crosstalk is a rapidly expanding field of study; thus, it is critical to ensure reproducibility between studies and applicability to human clinical trials through standardization of experiments. We discuss here recent advances in the field including the spectrum of colonization statuses available, the critical importance of colonization timing, the dynamics of the microbial community, and the required housing of animals, as they pertain to appropriate experimental control and design.
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Affiliation(s)
- Kathy D McCoy
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada.
| | - Christina L Ohland
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
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25
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Li Y, Xiao H, Dong J, Luo D, Wang H, Zhang S, Zhu T, Zhu C, Cui M, Fan S. Gut Microbiota Metabolite Fights Against Dietary Polysorbate 80-Aggravated Radiation Enteritis. Front Microbiol 2020; 11:1450. [PMID: 32670255 PMCID: PMC7332576 DOI: 10.3389/fmicb.2020.01450] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 06/04/2020] [Indexed: 12/12/2022] Open
Abstract
Radiation therapy is a cornerstone of modern management methods for malignancies but is accompanied by diverse side effects. In the present study, we showed that food additives such as polysorbate 80 (P80) exacerbate irradiation-induced gastrointestinal (GI) tract toxicity. A 16S ribosomal RNA high-throughput sequencing analysis indicated that P80 consumption altered the abundance and composition of the gut microbiota, leading to severe radiation-induced GI tract injury. Mice harboring fecal microbes from P80-treated mice were highly susceptible to irradiation, and antibiotics-challenged mice also represented more sensitive to radiation following P80 treatment. Importantly, butyrate, a major metabolite of enteric microbial fermentation of dietary fibers, exhibited beneficial effects against P80 consumption-aggravated intestinal toxicity via the activation of G-protein-coupled receptors (GPCRs) and maintenance of the intestinal bacterial composition in irradiated animals. Moreover, butyrate had broad therapeutic effects on common radiation-induced injury. Collectively, our findings demonstrate that P80 are potential risk factors for cancer patients during radiotherapy and indicate that butyrate might be employed as a therapeutic option to mitigate the complications associated with radiotherapy.
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Affiliation(s)
- Yuan Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Huiwen Xiao
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Jiali Dong
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Dan Luo
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Haichao Wang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.,Department of Emergency Medicine, North Shore University Hospital, Manhasset, NY, United States.,Laboratory of Emergency Medicine, The Feinstein Institute for Medical Research, Manhasset, NY, United States
| | - Shuqin Zhang
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Tong Zhu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Changchun Zhu
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Ming Cui
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Saijun Fan
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
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