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Knudsen LA, Zachariassen LS, Strube ML, Havelund JF, Pilecki B, Nexoe AB, Møller FT, Sørensen SB, Marcussen N, Faergeman NJ, Franke A, Bang C, Holmskov U, Hansen AK, Andersen V. Assessment of the Inflammatory Effects of Gut Microbiota from Human Twins Discordant for Ulcerative Colitis on Germ-free Mice. Comp Med 2024; 74:55-69. [PMID: 38508697 PMCID: PMC11078274 DOI: 10.30802/aalas-cm-23-000065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/12/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
Disturbances in gut microbiota are prevalent in inflammatory bowel disease (IBD), which includes ulcerative colitis (UC). However, whether these disturbances contribute to development of the disease or are a result of the disease is unclear. In pairs of human twins discordant for IBD, the healthy twin has a higher risk of developing IBD and a gut microbiota that is more similar to that of IBD patients as compared with healthy individuals. Furthermore, appropriate medical treatment may mitigate these disturbances. To study the correlation between microbiota and IBD, we transferred stool samples from a discordant human twin pair: one twin being healthy and the other receiving treatment for UC. The stool samples were transferred from the disease-discordant twins to germ-free pregnant dams. Colitis was induced in the offspring using dextran sodium sulfate. As compared with offspring born to mice dams inoculated with stool from the healthy cotwin, offspring born to dams inoculated with stool from the UC-afflicted twin had a lower disease activity index, less gut inflammation, and a microbiota characterized by higher α diversity and a more antiinflammatory profile that included the presence and higher abundance of antiinflammatory species such as Akkermansia spp., Bacteroides spp., and Parabacteroides spp. These findings suggest that the microbiota from the healthy twin may have had greater inflammatory properties than did that of the twin undergoing UC treatment.
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Affiliation(s)
- Lina A Knudsen
- Medical Department, Molecular Diagnostic and Clinical Research, University Hospital of Southern Denmark, Aabenraa, Denmark; IRS-Center Sonderjylland, University of South- ern Denmark, Odense, Denmark
| | - Line Sf Zachariassen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Mikael L Strube
- DTU Bioengineering, Technical University of Denmark, Lyngby, Denmark
| | - Jesper F Havelund
- VILLUM Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Bartosz Pilecki
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Anders B Nexoe
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Frederik T Møller
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Signe B Sørensen
- Medical Department, Molecular Diagnostic and Clinical Research, University Hospital of Southern Denmark, Aabenraa, Denmark; Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Niels Marcussen
- Department of Clinical Pathology, Odense University Hospital, Odense, Denmark
| | - Nils J Faergeman
- VILLUM Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Uffe Holmskov
- Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Axel K Hansen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark;,
| | - Vibeke Andersen
- Medical Department, Molecular Diagnostic and Clinical Research, University Hospital of Southern Denmark, Aabenraa, Denmark; IRS-Center Sonderjylland, University of Southern Denmark, Odense, Denmark; Department of Molecular Medicine, University of Southern Denmark, Odense, Denmark
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Ammar A, Singh V, Ilic S, Samiksha F, Marsh A, Rodriguez-Palacios A. Rodent Gut Bacteria Coexisting with an Insect Gut Virus in Parasitic Cysts: Metagenomic Evidence of Microbial Translocation and Co-adaptation in Spatially-Confined Niches. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.585885. [PMID: 38562820 PMCID: PMC10983908 DOI: 10.1101/2024.03.22.585885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In medicine, parasitic cysts or cysticerci (fluid-filled cysts, larval stage of tapeworms) are believed to be sterile (no bacteria), and therein, the treatment of cysticerci infestations of deep extra-intestinal tissues (e.g., brain) relies almost exclusively on the use of antiparasitic medications, and rarely antibiotics. To date, however, it is unclear why common post-treatment complications include abscessation. This study quantified the microbial composition of parasitic cyst contents in a higher-order rodent host, using multi-kingdom shotgun metagenomics, to improve our understanding of gut microbial translocation and adaptation strategies in wild environments. Analysis was conducted on DNA from two hepatic parasitic cysts (Hydatigera (Taeenia) taeniaeformis) in an adult vole mouse (Microtus arvalis), and from feces, liver, and peritoneal fluid of three other vole family members living in a vegetable garden in Ohio, USA. Bacterial metagenomics revealed the presence of gut commensal/opportunistic species, including Parabacteroides distasonis, Klebsiella variicola, Enterococcus faecium, and Lactobacillus acidophilus, inhabiting the cysts. Parabacteroides distasonis and other species were also present outside the cyst in the peritoneal fluid. Remarkably, viral metagenomics revealed various murine viral species, but unexpectedly, it detected an insect-origin virus from the army moth (Pseudaletia/Mythimna unipuncta) known as Mythimna unipuncta granulovirus A (MyunGV-A) in both cysts, and in one fecal and one peritoneal sample from two different voles, indicating survival of the insect virus and adaption in voles. Metagenomics also revealed a significantly lower probability of fungal detection in the cysts compared to other samples (peritoneal fluid, p<0.05; and feces p<0.05), with single taxon detection in each cyst for Malassezia and Pseudophaeomoniella oleicola. The samples with a higher probability of fungi were the peritoneal fluid. In conclusion, commensal/pathobiont bacterial species can inhabit parasitic tapeworm cysts, which needs to be considered during therapeutic decisions of cysticerci or other chronic disease scenarios where immune privileged and spatially restricted ecosystems with limited nutrients and minimal presence of immune cells could facilitate microbial adaptation, such as within gut wall cavitating micropathologies in Crohn's disease.
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Affiliation(s)
- Amro Ammar
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Vaidhvi Singh
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Sanja Ilic
- Department of Human Sciences, Human Nutrition and Food Microbiology, Ohio State University, Columbus, OH, USA
| | - Fnu Samiksha
- Department of Cancer Biology, Learner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Antoinette Marsh
- The Veterinary Medical Center Diagnostic Parasitology, The Ohio State University College of Veterinary Medicine Department of Veterinary Preventive Medicine, Columbus, OH, USA
| | - Alex Rodriguez-Palacios
- Division of Gastroenterology and Liver Disease, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Digestive Health Research Institute, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- University Hospitals Research and Education Institute, University Hospitals Cleveland Medical Center Cleveland, OH 44106, USA
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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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Pai YC, Li YH, Turner JR, Yu LCH. Transepithelial Barrier Dysfunction Drives Microbiota Dysbiosis to Initiate Epithelial Clock-driven Inflammation. J Crohns Colitis 2023; 17:1471-1488. [PMID: 37004200 PMCID: PMC10588795 DOI: 10.1093/ecco-jcc/jjad064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Indexed: 04/03/2023]
Abstract
BACKGROUND Factors that contribute to inflammatory bowel disease [IBD] pathogenesis include genetic polymorphisms, barrier loss, and microbial dysbiosis. A major knowledge gap exists in the origins of the colitogenic microbiome and its relationship with barrier impairment. Epithelial myosin light chain kinase [MLCK] is a critical regulator of the paracellular barrier, but the effects of MLCK activation on the intraepithelial bacteria [IEB] and dysbiosis are incompletely understood. We hypothesise that MLCK-dependent bacterial endocytosis promotes pathobiont conversion and shapes a colitogenic microbiome. METHODS To explore this, transgenic [Tg] mice with barrier loss induced by intestinal epithelium-specific expression of a constitutively active MLCK were compared with wild-type [WT] mice. RESULTS When progeny of homozygous MLCK-Tg mice were separated after weaning by genotype [Tg/Tg, Tg/WT, WT/WT], increased IEB numbers associated with dysbiosis and more severe colitis were present in Tg/Tg and Tg/WT mice, relative to WT/WT mice. Cohousing with MLCK-Tg mice induced dysbiosis, increased IEB abundance, and exacerbated colitis in WT mice. Conversely, MLCK-Tg mice colonised with WT microbiota at birth displayed increased Escherichia abundance and greater colitis severity by 6 weeks of age. Microarray analysis revealed circadian rhythm disruption in WT mice co-housed with MLCK-Tg mice relative to WT mice housed only with WT mice. This circadian disruption required Rac1/STAT3-dependent microbial invasion but not MLCK activity, and resulted in increased proinflammatory cytokines and glucocorticoid downregulation. CONCLUSIONS The data demonstrate that barrier dysfunction induces dysbiosis and expansion of invasive microbes that lead to circadian disruption and mucosal inflammation. These results suggest that barrier-protective or bacterium-targeted precision medicine approaches may be of benefit to IBD patients.
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Affiliation(s)
- Yu-Chen Pai
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan ROC
| | - Yi-Hsuan Li
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan ROC
| | - Jerrold R Turner
- Brigham's Women Hospital, Harvard Medical School, Boston, MA, USA
| | - Linda Chia-Hui Yu
- Graduate Institute of Physiology, National Taiwan University College of Medicine, Taipei, Taiwan ROC
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Singh RP, Bhardwaj A. β-glucans: a potential source for maintaining gut microbiota and the immune system. Front Nutr 2023; 10:1143682. [PMID: 37215217 PMCID: PMC10198134 DOI: 10.3389/fnut.2023.1143682] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/03/2023] [Indexed: 05/24/2023] Open
Abstract
The human gastrointestinal (GI) tract holds a complex and dynamic population of microbial communities, which exerts a marked influence on the host physiology during homeostasis and disease conditions. Diet is considered one of the main factors in structuring the gut microbiota across a lifespan. Intestinal microbial communities play a vital role in sustaining immune and metabolic homeostasis as well as protecting against pathogens. The negatively altered gut bacterial composition has related to many inflammatory diseases and infections. β-glucans are a heterogeneous assemblage of glucose polymers with a typical structure comprising a leading chain of β-(1,4) and/or β-(1,3)-glucopyranosyl units with various branches and lengths as a side chain. β-glucans bind to specific receptors on immune cells and initiate immune responses. However, β-glucans from different sources differ in their structures, conformation, physical properties, and binding affinity to receptors. How these properties modulate biological functions in terms of molecular mechanisms is not known in many examples. This review provides a critical understanding of the structures of β-glucans and their functions for modulating the gut microbiota and immune system.
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Affiliation(s)
- Ravindra Pal Singh
- Department of Industrial Biotechnology, Gujarat Biotechnology University, Gandhinagar, Gujarat, India
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Lin Q, Liu M, Yue GGL, Cheung MK, Lai Z, Kwok FHF, Lee JKM, Wang Z, Lau CBS, Tan N. Anti-inflammatory activities of natural cyclopeptide RA-XII in colitis-associated colon cancer mouse model and its effect on gut microbiome. Phytother Res 2022; 36:2641-2659. [PMID: 35537703 DOI: 10.1002/ptr.7482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/07/2022] [Accepted: 04/09/2022] [Indexed: 12/19/2022]
Abstract
Colorectal cancer (CRC), the third most common cancer globally, is associated with intestinal inflammation that leads to poor prognosis. RA-XII, a natural cyclopeptide, has previously been reported to possess anti-tumor activities. Here, the anti-inflammatory activities of RA-XII were investigated in colitis-associated colon cancer mice and a co-culture in vitro model, in which colon cancer cells HCT116 and macrophages RAW264.7 were grown together to mimic the inflammatory microenvironment of CRC. Changes of inflammatory-related molecules and protein expressions in cells were evaluated after RA-XII incubation. Besides, azoxymethane and dextran sulfate sodium-induced colitis-associated colon cancer mice were treated with RA-XII for 24 days, inflammatory parameters and gut microbiome alterations were studied. Our results showed that RA-XII reversed the inflammatory responses of RAW264.7 cells induced by LPS and modulated the protein expressions of AKT, STAT3/p-STAT3, P70S6K, NF-κB and GSK3β and suppressed the expression of LC3A/B in HCT116 cells in co-culture system. RA-XII treatment restored the colitis damage in colon, reduced colon tumors numbers and decreased inflammatory factors (IL-6, IL-10 and TNF-α). The role of RA-XII on regulating gut microbiome was also demonstrated for the first time. In conclusion, our findings provided new scientific evidence for developing RA-XII as a potent anti-inflammatory agent for CRC.
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Affiliation(s)
- Qianwen Lin
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Mingyu Liu
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Grace Gar-Lee Yue
- Institute of Chinese Medicine and State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Man Kit Cheung
- Department of Surgery, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhixing Lai
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Frankie Hin-Fai Kwok
- Institute of Chinese Medicine and State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Julia Kin-Ming Lee
- Institute of Chinese Medicine and State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zhe Wang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Clara Bik-San Lau
- Institute of Chinese Medicine and State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Ninghua Tan
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, China
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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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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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Gheorghe CE, Ritz NL, Martin JA, Wardill HR, Cryan JF, Clarke G. Investigating causality with fecal microbiota transplantation in rodents: applications, recommendations and pitfalls. Gut Microbes 2021; 13:1941711. [PMID: 34328058 PMCID: PMC8331043 DOI: 10.1080/19490976.2021.1941711] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 06/02/2021] [Accepted: 06/04/2021] [Indexed: 02/04/2023] Open
Abstract
In recent years, studies investigating the role of the gut microbiota in health and diseases have increased enormously - making it essential to deepen and question the research methodology employed. Fecal microbiota transplantation (FMT) in rodent studies (either from human or animal donors) allows us to better understand the causal role of the intestinal microbiota across multiple fields. However, this technique lacks standardization and requires careful experimental design in order to obtain optimal results. By comparing several studies in which rodents are the final recipients of FMT, we summarize the common practices employed. In this review, we document the limitations of this method and highlight different parameters to be considered while designing FMT Studies. Standardizing this method is challenging, as it differs according to the research topic, but avoiding common pitfalls is feasible. Several methodological questions remain unanswered to this day and we offer a discussion on issues to be explored in future studies.
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Affiliation(s)
- Cassandra E. Gheorghe
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Nathaniel L. Ritz
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Jason A. Martin
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Hannah R. Wardill
- Precision Medicine, South Australian Health and Medical Research Institute (SAHMRI), Adelaide, Australia
- Adelaide Medical School, the University of Adelaide, Adelaide, Australia
| | - John F. Cryan
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- Department of Anatomy and Neuroscience, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Gerard Clarke
- Department of Psychiatry and Neurobehavioral Science, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- INFANT Research Centre, University College Cork, Cork, Ireland
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10
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Basson AR, Zhou Y, Seo B, Rodriguez-Palacios A, Cominelli F. Autologous fecal microbiota transplantation for the treatment of inflammatory bowel disease. Transl Res 2020; 226:1-11. [PMID: 32585148 PMCID: PMC7308243 DOI: 10.1016/j.trsl.2020.05.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/20/2020] [Accepted: 05/23/2020] [Indexed: 12/12/2022]
Abstract
The term autologous fecal microbiota transplantation (a-FMT) refers herein to the use of one's feces during a healthy state for later use to restore gut microbial communities after perturbations. Generally, heterologous fecal microbiota transplantation (h-FMT), where feces from a ``healthy" donor is transplanted into a person with illness, has been used to treat infectious diseases such as recurrent Clostridioides difficile infection (CDI), with cure rates of up to 90%. In humans, due to limited response to medicines, h-FMT has become a hallmark intervention to treat CDI. Extrapolating the benefits from CDI, h-FMT has been attempted in various diseases, including inflammatory bowel disease (IBD), but clinical response has been variable and less effective (ranging between 24% and 50%). Differences in h-FMT clinical response could be because CDI is caused by a Clostridial infection, whereas IBD is a complex, microbiome-driven immunological inflammatory disorder that presents predominantly within the gut wall of genetically-susceptible hosts. FMT response variability could also be due to differences in microbiome composition between donors, recipients, and within individuals, which vary with diet, and environments, across regions. While donor selection has emerged as a key factor in FMT success, the use of heterologous donor stool still places the recipient at risk of exposure to infectious/pathogenic microorganisms. As an implementable solution, herein we review the available literature on a-FMT, and list some considerations on the benefits of a-FMT for IBD.
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Key Words
- a-fmt, autologous fecal microbiota transplantation
- cd, crohn's disease
- cdi, clostridium difficile infection
- ci, confidence interval
- fmt, fecal microbiota transplantation
- hgm, human gut microbiota
- h-fmt, heterologous fecal microbiota transplantation
- ibd, inflammatory bowel disease
- ibs, irritable bowel syndrome
- rct, randomized controlled trial
- uc, ulcerative colitis
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Affiliation(s)
- Abigail R Basson
- Division of Gastroenterology & Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, Ohio; Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Yibing Zhou
- Division of Gastroenterology & Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Brian Seo
- Division of Gastroenterology & Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, Ohio
| | - Alexander Rodriguez-Palacios
- Division of Gastroenterology & Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, Ohio; Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Fabio Cominelli
- Division of Gastroenterology & Liver Diseases, Case Western Reserve University School of Medicine, Cleveland, Ohio; Digestive Health Research Institute, University Hospitals Cleveland Medical Center, Cleveland, Ohio.
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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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