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Lee J, Wellenstein K, Rahnavard A, Nelson AT, Holter MM, Cummings BP, Yeliseyev V, Castoldi A, Clish CB, Bry L, Siegel D, Kahn BB. Beneficial metabolic effects of PAHSAs depend on the gut microbiota in diet-induced obese mice but not in chow-fed mice. Proc Natl Acad Sci U S A 2024; 121:e2318691121. [PMID: 38968121 DOI: 10.1073/pnas.2318691121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/31/2024] [Indexed: 07/07/2024] Open
Abstract
Dietary lipids play an essential role in regulating the function of the gut microbiota and gastrointestinal tract, and these luminal interactions contribute to mediating host metabolism. Palmitic Acid Hydroxy Stearic Acids (PAHSAs) are a family of lipids with antidiabetic and anti-inflammatory properties, but whether the gut microbiota contributes to their beneficial effects on host metabolism is unknown. Here, we report that treating chow-fed female and male germ-free (GF) mice with PAHSAs improves glucose tolerance, but these effects are lost upon high fat diet (HFD) feeding. However, transfer of feces from PAHSA-treated, but not vehicle-treated, chow-fed conventional mice increases insulin sensitivity in HFD-fed GF mice. Thus, the gut microbiota is necessary for, and can transmit, the insulin-sensitizing effects of PAHSAs in HFD-fed GF male mice. Analyses of the cecal metagenome and lipidome of PAHSA-treated mice identified multiple lipid species that associate with the gut commensal Bacteroides thetaiotaomicron (Bt) and with insulin sensitivity resulting from PAHSA treatment. Supplementing live, and to some degree, heat-killed Bt to HFD-fed female mice prevented weight gain, reduced adiposity, improved glucose tolerance, fortified the colonic mucus barrier and reduced systemic inflammation compared to HFD-fed controls. These effects were not observed in HFD-fed male mice. Furthermore, ovariectomy partially reversed the beneficial Bt effects on host metabolism, indicating a role for sex hormones in mediating the Bt probiotic effects. Altogether, these studies highlight the fact that PAHSAs can modulate the gut microbiota and that the microbiota is necessary for the beneficial metabolic effects of PAHSAs in HFD-fed mice.
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Affiliation(s)
- Jennifer Lee
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215
| | - Kerry Wellenstein
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215
| | - Ali Rahnavard
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC 20052
| | - Andrew T Nelson
- Division of Pharmaceutical Chemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Marlena M Holter
- Department of Biomedical Sciences, Cornell University College of Veterinary Medicine, Cornell University, Ithaca, NY 14850
| | - Bethany P Cummings
- Department of Surgery, School of Medicine, University of California, Davis, Sacramento, CA 95817
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California Davis School of Veterinary Medicine, Davis, CA 95616
| | - Vladimir Yeliseyev
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Angela Castoldi
- Laboratory of Immunopathology Keizo Asami, Federal University of Pernambuco, Recife 50670-901, Brazil
| | - Clary B Clish
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Dionicio Siegel
- Division of Pharmaceutical Chemistry, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| | - Barbara B Kahn
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215
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Hankenson FC. The Elephant in the Room: Recognition and Documentation of Personnel Practices That Confound Reproducibility. JOURNAL OF THE AMERICAN ASSOCIATION FOR LABORATORY ANIMAL SCIENCE : JAALAS 2024; 63:232-237. [PMID: 38503489 PMCID: PMC11193430 DOI: 10.30802/aalas-jaalas-24-000002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 01/30/2024] [Accepted: 02/16/2024] [Indexed: 03/21/2024]
Abstract
The ability to apply findings from animal studies efficiently and effectively is predicated on an understanding of biology and pathobiology, how that biology relates to the human systems being modeled, and how the studies are conducted and reported. This overview discusses various factors in research within the animal environment (referred to as extrinsic factors) that the NIH now expects to be documented to foster replicability in science and expand interpretations of study outcomes. Specifically, an important extrinsic factor in research with animals is that of individual personnel who perform handling practices, participate in research interactions, and share an overall presence in the housing facility with animals, all of which can confound reproducibility efforts in biomedical science. An improved understanding of the influences and behaviors of animal research personnel on animal responses is critical with regard to research results and the interpretation of data collected from animal models of biomedical disease.
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Key Words
- acd wg: nih advisory committee to the director working group
- faseb, federation of american societies for experimental biology
- ilar, institute for laboratory animal research (note ilar is now part of the board on animal health sciences, conservation, and research (bahscr))
- nasem, national academies of science, engineering, and medicine
- nc3rs, national center for the replacement, refinement, and reduction of animals in research
- nih, national institutes of health
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Affiliation(s)
- F Claire Hankenson
- University Laboratory Animal Resources and Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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3
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Lee J, Wellenstein K, Rahnavard A, Nelson AT, Holter MM, Cummings B, Yeliseyev V, Castoldi A, Clish CB, Bry L, Siegel D, Kahn BB. Beneficial metabolic effects of PAHSAs depend on the gut microbiota in diet-induced obese mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.558803. [PMID: 37808673 PMCID: PMC10557726 DOI: 10.1101/2023.09.28.558803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Dietary lipids play an essential role in regulating the function of the gut microbiota and gastrointestinal tract, and these luminal interactions contribute to mediating host metabolism. PAHSAs are a class of lipids with anti-diabetic and anti-inflammatory properties, but whether the gut microbiota contributes to their beneficial effects on host metabolism is unknown. Here, we report that treating high fat diet (HFD)-fed germ-free mice with PAHSAs does not improve insulin sensitivity. However, transfer of feces from PAHSA-treated, but not Vehicle-treated, chow-fed mice increases insulin-sensitivity in HFD-fed germ free mice. Thus, the gut microbiota is necessary for and can transmit the insulin-sensitizing effects of PAHSAs in HFD-fed germ-free mice. Functional analyses of the cecal metagenome and lipidome of PAHSA-treated mice identified multiple lipid species that associate with the gut commensal Bacteroides thetaiotaomicron ( Bt ) and with insulin sensitivity resulting from PAHSA treatment. Bt supplementation in HFD-fed female mice prevented weight gain, reduced adiposity, improved glucose tolerance, fortified the colonic mucus barrier and reduced systemic inflammation versus chow-fed controls, effects that were not observed in HFD-fed male mice. Furthermore, ovariectomy partially reversed the beneficial Bt effects on host metabolism, indicating a role for sex hormones in mediating probiotic effects. Altogether, these studies highlight the fact that lipids can modulate the gut microbiota resulting in improvement in host metabolism and that PAHSA-induced changes in the microbiota result in at least some of their insulin-sensitizing effects in female mice.
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Long LL, Svenson KL, Mourino AJ, Michaud M, Fahey JR, Waterman L, Vandegrift KL, Adams MD. Shared and distinctive features of the gut microbiome of C57BL/6 mice from different vendors and production sites, and in response to a new vivarium. Lab Anim (NY) 2021; 50:185-195. [PMID: 34127866 DOI: 10.1038/s41684-021-00777-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 05/07/2021] [Indexed: 02/08/2023]
Abstract
Animal models play a critical role in establishing causal relationships between gut microbiota and disease. The laboratory mouse is widely used to study the role of microbes in various disorders; however, differences between mouse vendors, genetic lineages and husbandry protocols have been shown to contribute to variation in phenotypes and to non-reproducibility of experimental results. We sought to understand how gut microbiome profiles of mice vary by vendor, vendor production facility and health status upon receipt into an academic facility and how they change over 12 weeks in the new environment. C57BL/6 mice were sourced from two different production sites for each of three different vendors. Mice were shipped to an academic research vivarium, and fresh-catch stool samples were collected from mice immediately from the shipping box upon receipt, and again after 2, 6 and 12 weeks in the new facility. Substantial variation in bacterial proportional abundance was observed among mice from each vendor at the time of receipt, but shared microbes accounted for most sequence reads. Vendor-specific microbes were generally of low abundance. Microbial profiles of mice from all vendors exhibited shifts over time, highlighting the importance of environmental conditions on microbial dynamics. Our results emphasize the need for continued efforts to account for sources of variation in animal models and understand how they contribute to experimental reproducibility.
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Affiliation(s)
- Lauren L Long
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Karen L Svenson
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | | | - Michael Michaud
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - James R Fahey
- The Jackson Laboratory for Mammalian Genetics, Bar Harbor, ME, USA
| | - Linda Waterman
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Mark D Adams
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
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5
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Zhang J, Lee H, Macpherson LJ. Mechanisms for the Sour Taste. Handb Exp Pharmacol 2021; 275:229-245. [PMID: 34117536 DOI: 10.1007/164_2021_476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Sour, the taste of acids, provides important sensory information to prevent the ingestion of unripe, spoiled, or fermented foods. In mammals, acids elicit disgust and pain by simultaneously activating taste and somatosensory neurons innervating the oral cavity. Early researchers detected electrical activity in taste nerves upon presenting acids to the tongue, establishing this as the bona fide sour taste. Recent studies have made significant contributions to our understanding of the mechanisms underlying acid sensing in the taste receptor cells at the periphery and the neural circuitry that convey this information to the brain. In this chapter, we discuss the characterization of sour taste receptor cells, the twists and turns eventually leading to the identification of Otopetrin1 (OTOP1) as the sour taste receptor, the pathway of sour taste signaling from the tongue to the brainstem, and other roles sour taste receptor cells play in the taste bud.
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Affiliation(s)
- Jin Zhang
- Mortimer B. Zukerman Mind Brain and Behavior Institute, Columbia University, New York, NY, USA.
| | - Hojoon Lee
- Department of Neurobiology, Northwestern University, Evanston, IL, USA.
| | - Lindsey J Macpherson
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA.
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6
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Klurfeld DM, Gregory JF, Fiorotto ML. Should the AIN-93 Rodent Diet Formulas be Revised? J Nutr 2021; 151:1380-1382. [PMID: 33693751 DOI: 10.1093/jn/nxab041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/25/2021] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Affiliation(s)
- David M Klurfeld
- USDA Agricultural Research Service, Office of National Programs, Beltsville, MD, USA
| | - Jesse F Gregory
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL, USA
| | - Marta L Fiorotto
- USDA/Agricultural Research Service Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
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7
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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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McDonough LK, Meredith KT, Nikagolla C, Middleton RJ, Tan JK, Ranasinghe AV, Sierro F, Banati RB. The water chemistry and microbiome of household wells in Medawachchiya, Sri Lanka, an area with high prevalence of chronic kidney disease of unknown origin (CKDu). Sci Rep 2020; 10:18295. [PMID: 33106529 PMCID: PMC7589467 DOI: 10.1038/s41598-020-75336-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/12/2020] [Indexed: 01/08/2023] Open
Abstract
Chronic kidney disease (CKD) of unknown etiology (CKDu) mostly affects agricultural communities in Central America, South Asia, Africa, but likely also in North America and Australia. One such area with increased CKDu prevalence is the Medawachchiya District Secretariat Division of the Anuradhapura District in the North Central Province of Sri Lanka. Recent research has focused on the presence of various microbial pathogens in drinking water as potential causal or contributing factors to CKDu, yet no study to date has performed a more comprehensive microbial and water chemistry assessment of household wells used for domestic water supply in areas of high CKDu prevalence. In this study, we describe the chemical composition and total microbial content in 30 domestic household wells in the Medawachchiya District Secretariat Division. While the chemical composition in the tested wells mostly lies within standard drinking water limits, except for high levels of fluoride (F), magnesium (Mg), sodium (Na), chloride (Cl) and calcium (Ca) in some samples, we find a frequent presence of cyanotoxin-producing Microcystis, confirming earlier studies in Sri Lanka. Since the total microbial content of drinking water also directly influences the composition of the human gut microbiome, it can be considered an important determinant of health. Several bacterial phyla were previously reported in the gut microbiome of patients with CKD. Using these bacteria phyla to define operational taxonomic units, we found that these bacteria also occur in the microbiome of the sampled well water. Based on available environmental data, our study demonstrates associations between the abundances of these bacteria with geographical distribution, well water temperature and likely fertilizer use in the local surface water catchment area of the individual household wells. Our results reinforce the recommendation that household wells with stagnant or infrequently used water should be purged prior to use for drinking water, bathing and irrigation. The latter is suggested because of the reported potential accumulation of bacterial toxins by agricultural crops. The observation that bacteria previously found in chronic kidney disease patients are also present in household wells requires a more detailed systematic study of both the human gut and drinking water microbiomes in CKDu patients, in relation to disease prevalence and progression.
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Affiliation(s)
- Liza K McDonough
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, 2234, Australia. .,School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, NSW, 2052, Australia.
| | - Karina T Meredith
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, 2234, Australia
| | - Chandima Nikagolla
- School of Civil and Environmental Engineering, Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Ryan J Middleton
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, 2234, Australia
| | - Jian K Tan
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, 2234, Australia.,Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia.,Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Asanga V Ranasinghe
- National Renal Disease Prevention and Research Unit, Ministry of Health, Colombo 10, Sri Lanka
| | - Frederic Sierro
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, 2234, Australia.,Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Richard B Banati
- Australian Nuclear Science and Technology Organisation (ANSTO), New Illawarra Rd, Lucas Heights, NSW, 2234, Australia.,Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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Nutritional profile of rodent diets impacts experimental reproducibility in microbiome preclinical research. Sci Rep 2020; 10:17784. [PMID: 33082369 PMCID: PMC7575541 DOI: 10.1038/s41598-020-74460-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 09/29/2020] [Indexed: 02/08/2023] Open
Abstract
The lack of reproducibility of animal experimental results between laboratories, particularly in studies investigating the microbiota, has raised concern among the scientific community. Factors such as environment, stress and sex have been identified as contributors, whereas dietary composition has received less attention. This study firstly evaluated the use of commercially available rodent diets across research institutions, with 28 different diets reported by 45 survey respondents. Secondly, highly variable ingredient, FODMAP (Fermentable Oligo-, Di-, Mono-saccharides And Polyols) and gluten content was found between different commercially available rodent diets. Finally, 40 mice were randomized to four groups, each receiving a different commercially available rodent diet, and the dietary impact on cecal microbiota, short- and branched-chain fatty acid profiles was evaluated. The gut microbiota composition differed significantly between diets and sexes, with significantly different clusters in β-diversity. Total BCFA were highest (p = 0.01) and SCFA were lowest (p = 0.03) in mice fed a diet lower in FODMAPs and gluten. These results suggest that nutritional composition of commercially available rodent diets impact gut microbiota profiles and fermentation patterns, with major implications for the reproducibility of results across laboratories. However, further studies are required to elucidate the specific dietary factors driving these changes.
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10
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Kurtz DM, Feeney WP. The Influence of Feed and Drinking Water on Terrestrial Animal Research and Study Replicability. ILAR J 2020; 60:175-196. [PMID: 32706372 DOI: 10.1093/ilar/ilaa012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/16/2020] [Accepted: 04/22/2020] [Indexed: 12/29/2022] Open
Abstract
For more than 50 years, the research community has made strides to better determine the nutrient requirements for many common laboratory animal species. This work has resulted in high-quality animal feeds that can optimize growth, maintenance, and reproduction in most species. We have a much better understanding of the role that individual nutrients play in physiological responses. Today, diet is often considered as an independent variable in experimental design, and specialized diet formulations for experimental purposes are widely used. In contrast, drinking water provided to laboratory animals has rarely been a consideration in experimental design except in studies of specific water-borne microbial or chemical contaminants. As we advance in the precision of scientific measurements, we are constantly discovering previously unrecognized sources of experimental variability. This is the nature of science. However, science is suffering from a lack of experimental reproducibility or replicability that undermines public trust. The issue of reproducibility/replicability is especially sensitive when laboratory animals are involved since we have the ethical responsibility to assure that laboratory animals are used wisely. One way to reduce problems with reproducibility/replicability is to have a strong understanding of potential sources of inherent variability in the system under study and to provide "…a clear, specific, and complete description of how the reported results were reached [1]." A primary intent of this review is to provide the reader with a high-level overview of some basic elements of laboratory animal nutrition, methods used in the manufacturing of feeds, sources of drinking water, and general methods of water purification. The goal is to provide background on contemporary issues regarding how diet and drinking water might serve as a source of extrinsic variability that can impact animal health, study design, and experimental outcomes and provide suggestions on how to mitigate these effects.
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Affiliation(s)
- David M Kurtz
- National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - William P Feeney
- Global Comparative and Translational Sciences, Integrated Biological Platform Sciences Department, GlaxoSmithKline, Collegeville, Pennsylvania
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Basson AR, LaSalla A, Lam G, Kulpins D, Moen EL, Sundrud MS, Miyoshi J, Ilic S, Theriault BR, Cominelli F, Rodriguez-Palacios A. Artificial microbiome heterogeneity spurs six practical action themes and examples to increase study power-driven reproducibility. Sci Rep 2020; 10:5039. [PMID: 32193395 PMCID: PMC7081340 DOI: 10.1038/s41598-020-60900-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 02/17/2020] [Indexed: 12/25/2022] Open
Abstract
With >70,000 yearly publications using mouse data, mouse models represent the best engrained research system to address numerous biological questions across all fields of science. Concerns of poor study and microbiome reproducibility also abound in the literature. Despite the well-known, negative-effects of data clustering on interpretation and study power, it is unclear why scientists often house >4 mice/cage during experiments, instead of ≤2. We hypothesized that this high animal-cage-density practice abounds in published literature because more mice/cage could be perceived as a strategy to reduce housing costs. Among other sources of 'artificial' confounding, including cyclical oscillations of the 'dirty-cage/excrement microbiome', we ranked by priority the heterogeneity of modern husbandry practices/perceptions across three professional organizations that we surveyed in the USA. Data integration (scoping-reviews, professional-surveys, expert-opinion, and 'implementability-score-statistics') identified Six-Actionable Recommendation Themes (SART) as a framework to re-launch emerging protocols and intuitive statistical strategies to use/increase study power. 'Cost-vs-science' discordance was a major aspect explaining heterogeneity, and scientists' reluctance to change. With a 'housing-density cost-calculator-simulator' and fully-annotated statistical examples/code, this themed-framework streamlines the rapid analysis of cage-clustered-data and promotes the use of 'study-power-statistics' to self-monitor the success/reproducibility of basic and translational research. Examples are provided to help scientists document analysis for study power-based sample size estimations using preclinical mouse data to support translational clinical trials, as requested in NIH/similar grants or publications.
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Affiliation(s)
- Abigail R Basson
- Division of Gastroenterology & Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Alexandria LaSalla
- Division of Gastroenterology & Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Gretchen Lam
- Division of Gastroenterology & Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Danielle Kulpins
- Division of Gastroenterology & Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Erika L Moen
- Department of Biomedical Data Science, Geisel School of Medicine, The Dartmouth Institute for Health Policy and Clinical Practice, Lebanon, NH, USA
| | - Mark S Sundrud
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL, USA
| | - Jun Miyoshi
- Department of Gastroenterology and Hepatology, Kyorin University School of Medicine, Tokyo, Japan
| | - Sanja Ilic
- Department of Human Sciences and Nutrition, The Ohio State University, Columbus, OH, USA
| | | | - Fabio Cominelli
- Division of Gastroenterology & Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
- Mouse Models Core, Silvio O'Conte Cleveland Digestive Diseases Research Core Center, Cleveland, OH, USA
- Germ-free and Gut Microbiome Core, Digestive Health Research Institute, Case Western Reserve University, Cleveland, OH, USA
| | - Alexander Rodriguez-Palacios
- Division of Gastroenterology & Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
- Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
- Mouse Models Core, Silvio O'Conte Cleveland Digestive Diseases Research Core Center, Cleveland, OH, USA.
- Germ-free and Gut Microbiome Core, Digestive Health Research Institute, Case Western Reserve University, Cleveland, OH, USA.
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12
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Calcium Oxalate Nephrolithiasis and Gut Microbiota: Not just a Gut-Kidney Axis. A Nutritional Perspective. Nutrients 2020; 12:nu12020548. [PMID: 32093202 PMCID: PMC7071363 DOI: 10.3390/nu12020548] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 02/14/2020] [Accepted: 02/18/2020] [Indexed: 12/13/2022] Open
Abstract
Recent studies have shown that patients with kidney stone disease, and particularly calcium oxalate nephrolithiasis, exhibit dysbiosis in their fecal and urinary microbiota compared with controls. The alterations of microbiota go far beyond the simple presence and representation of Oxalobacter formigenes, a well-known symbiont exhibiting a marked capacity of degrading dietary oxalate and stimulating oxalate secretion by the gut mucosa. Thus, alterations of the intestinal microbiota may be involved in the pathophysiology of calcium kidney stones. However, the role of nutrition in this gut-kidney axis is still unknown, even if nutritional imbalances, such as poor hydration, high salt, and animal protein intake and reduced fruit and vegetable intake, are well-known risk factors for kidney stones. In this narrative review, we provide an overview of the gut-kidney axis in nephrolithiasis from a nutritional perspective, summarizing the evidence supporting the role of nutrition in the modulation of microbiota composition, and their relevance for the modulation of lithogenic risk.
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13
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Abstract
Low-cost, high-throughput nucleic acid sequencing ushered the field of microbial ecology into a new era in which the microbial composition of nearly every conceivable environment on the planet is under examination. However, static "screenshots" derived from sequence-only approaches belie the underlying complexity of the microbe-microbe and microbe-host interactions occurring within these systems. Reductionist experimental models are essential to identify the microbes involved in interactions and to characterize the molecular mechanisms that manifest as complex host and environmental phenomena. Herein, we focus on three models (Bacillus-Streptomyces, Aliivibrio fischeri-Hawaiian bobtail squid, and gnotobiotic mice) at various levels of taxonomic complexity and experimental control used to gain molecular insight into microbe-mediated interactions. We argue that when studying microbial communities, it is crucial to consider the scope of questions that experimental systems are suited to address, especially for researchers beginning new projects. Therefore, we highlight practical applications, limitations, and tradeoffs inherent to each model.
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Affiliation(s)
- Marc G Chevrette
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jennifer R Bratburd
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Reed M Stubbendieck
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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