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Ferreira CR, Lima Gomes PCFD, Robison KM, Cooper BR, Shannahan JH. Implementation of multiomic mass spectrometry approaches for the evaluation of human health following environmental exposure. Mol Omics 2024. [PMID: 38623720 DOI: 10.1039/d3mo00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Omics analyses collectively refer to the possibility of profiling genetic variants, RNA, epigenetic markers, proteins, lipids, and metabolites. The most common analytical approaches used for detecting molecules present within biofluids related to metabolism are vibrational spectroscopy techniques, represented by infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies and mass spectrometry (MS). Omics-based assessments utilizing MS are rapidly expanding and being applied to various scientific disciplines and clinical settings. Most of the omics instruments are operated by specialists in dedicated laboratories; however, the development of miniature portable omics has made the technology more available to users for field applications. Variations in molecular information gained from omics approaches are useful for evaluating human health following environmental exposure and the development and progression of numerous diseases. As MS technology develops so do statistical and machine learning methods for the detection of molecular deviations from personalized metabolism, which are correlated to altered health conditions, and they are intended to provide a multi-disciplinary overview for researchers interested in adding multiomic analysis to their current efforts. This includes an introduction to mass spectrometry-based omics technologies, current state-of-the-art capabilities and their respective strengths and limitations for surveying molecular information. Furthermore, we describe how knowledge gained from these assessments can be applied to personalized medicine and diagnostic strategies.
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Affiliation(s)
- Christina R Ferreira
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | | | - Kiley Marie Robison
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Bruce R Cooper
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | - Jonathan H Shannahan
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
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Jia W, Yu S, Liu X, Le Q, He X, Yu L, He J, Yang L, Gao H. Ethanol Extract of Limonium bicolor Improves Dextran Sulfate Sodium-Induced Ulcerative Colitis by Alleviating Inflammation and Restoring Gut Microbiota Dysbiosis in Mice. Mar Drugs 2024; 22:175. [PMID: 38667792 PMCID: PMC11050939 DOI: 10.3390/md22040175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 04/05/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Ulcerative colitis (UC) is a kind of inflammatory bowel condition characterized by inflammation within the mucous membrane, rectal bleeding, diarrhea, and pain experienced in the abdominal region. Existing medications for UC have limited treatment efficacy and primarily focus on symptom relief. Limonium bicolor (LB), an aquatic traditional Chinese medicine (TCM), exerts multi-targeted therapeutic effects with few side effects and is used to treat anemia and hemostasis. Nevertheless, the impact of LB on UC and its mechanism of action remain unclear. Therefore, the objective of this study was to investigate the anti-inflammatory effects and mechanism of action of ethanol extract of LB (LBE) in lipopolysaccharide-induced RAW 264.7 macrophages and dextran sulfate sodium (DSS)-induced UC. The results showed that LBE suppressed the secretion of cytokines in LPS-stimulated RAW 264.7 cells in a dose-dependent manner. LBE had protective effects against DSS-induced colitis in mice, decreased the disease activity index (DAI) score, alleviated symptoms, increased colon length, and improved histological characteristics, thus having protective effects against DSS-induced colitis in mice. In addition, it reversed disturbances in the abundance of proteobacteria and probiotics such as Lactobacillus and Blautia in mice with DSS-induced UC. Based on the results of network pharmacology analysis, we identified four main compounds in LBE that are associated with five inflammatory genes (Ptgs2, Plg, Ppar-γ, F2, and Gpr35). These results improve comprehension of the biological activity and functionality of LB and may facilitate the development of LB-based compounds for the treatment of UC.
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Affiliation(s)
- Wei Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (W.J.); (S.Y.); (L.Y.)
- Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Q.L.); (X.H.); (J.H.)
| | - Siyu Yu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (W.J.); (S.Y.); (L.Y.)
- Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Q.L.); (X.H.); (J.H.)
| | - Xi Liu
- Key Laboratory of Chemical Biology of Fujian Province, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361000, China;
| | - Qingqing Le
- Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Q.L.); (X.H.); (J.H.)
| | - Xiwen He
- Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Q.L.); (X.H.); (J.H.)
| | - Lutao Yu
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (W.J.); (S.Y.); (L.Y.)
- Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Q.L.); (X.H.); (J.H.)
| | - Jianlin He
- Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Q.L.); (X.H.); (J.H.)
- Fujian Key Laboratory of Island Monitoring and Ecological Development (Island Research Center, Ministry of Natural Resources), Fuzhou 350400, China
| | - Longhe Yang
- Technical Innovation Center for Utilization of Marine Biological Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361000, China; (Q.L.); (X.H.); (J.H.)
- Fujian Key Laboratory of Island Monitoring and Ecological Development (Island Research Center, Ministry of Natural Resources), Fuzhou 350400, China
| | - Huiyuan Gao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang 110016, China; (W.J.); (S.Y.); (L.Y.)
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Saviano A, Schettino A, Iaccarino N, Mansour AA, Begum J, Marigliano N, Raucci F, Romano F, Riccardi G, Mitidieri E, d'Emmanuele di Villa Bianca R, Bello I, Panza E, Smimmo M, Vellecco V, Rimmer P, Cheesbrough J, Zhi Z, Iqbal TH, Pieretti S, D'Amore VM, Marinelli L, La Pietra V, Sorrentino R, Costa L, Caso F, Scarpa R, Cirino G, Randazzo A, Bucci M, McGettrick HM, Iqbal AJ, Maione F. A reverse translational approach reveals the protective roles of Mangifera indica in inflammatory bowel disease. J Autoimmun 2024; 144:103181. [PMID: 38522129 DOI: 10.1016/j.jaut.2024.103181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/05/2024] [Accepted: 02/10/2024] [Indexed: 03/26/2024]
Abstract
Inflammatory bowel diseases (IBDs) are chronic intestinal disorders often characterized by a dysregulation of T cells, specifically T helper (Th) 1, 17 and T regulatory (Treg) repertoire. Increasing evidence demonstrates that dietary polyphenols from Mangifera indica L. extract (MIE, commonly known as mango) mitigate intestinal inflammation and splenic Th17/Treg ratio. In this study, we aimed to dissect the immunomodulatory and anti-inflammatory properties of MIE using a reverse translational approach, by initially using blood from an adult IBD inception cohort and then investigating the mechanism of action in a preclinical model of T cell-driven colitis. Of clinical relevance, MIE modulates TNF-α and IL-17 levels in LPS spiked sera from IBD patients as an ex vivo model of intestinal barrier breakdown. Preclinically, therapeutic administration of MIE significantly reduced colitis severity, pathogenic T-cell intestinal infiltrate and intestinal pro-inflammatory mediators (IL-6, IL-17A, TNF-α, IL-2, IL-22). Moreover, MIE reversed colitis-induced gut permeability and restored tight junction functionality and intestinal metabolites. Mechanistic insights revealed MIE had direct effects on blood vascular endothelial cells, blocking TNF-α/IFN-γ-induced up-regulation of COX-2 and the DP2 receptors. Collectively, we demonstrate the therapeutic potential of MIE to reverse the immunological perturbance during the onset of colitis and dampen the systemic inflammatory response, paving the way for its clinical use as nutraceutical and/or functional food.
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Affiliation(s)
- Anella Saviano
- ImmunoPharmaLab, Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Anna Schettino
- ImmunoPharmaLab, Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Adel Abo Mansour
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Jenefa Begum
- Institute of Cardiovascular Sciences (ICVS), College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Noemi Marigliano
- ImmunoPharmaLab, Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Federica Raucci
- ImmunoPharmaLab, Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Francesca Romano
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Gelsomina Riccardi
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Emma Mitidieri
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | | | - Ivana Bello
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Elisabetta Panza
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Martina Smimmo
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Valentina Vellecco
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Peter Rimmer
- Institute of Cardiovascular Sciences (ICVS), College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Department of Gastroenterology, Queen Elizabeth Hospital Birmingham NHS Foundation Trust, Birmingham, UK
| | - Jonathan Cheesbrough
- Institute of Cardiovascular Sciences (ICVS), College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Department of Gastroenterology, Birmingham Heartlands Hospital, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Zhaogong Zhi
- Institute of Cardiovascular Sciences (ICVS), College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Tariq H Iqbal
- Department of Gastroenterology, Queen Elizabeth Hospital Birmingham NHS Foundation Trust, Birmingham, UK; Institute of Microbiology and Infection (IMI), College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2WB, UK
| | - Stefano Pieretti
- National Center for Drug Research and Evaluation, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161, Rome, Italy
| | - Vincenzo Maria D'Amore
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Luciana Marinelli
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Valeria La Pietra
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Raffaella Sorrentino
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Luisa Costa
- Rheumatology Research Unit, Department of Clinical Medicine and Surgery, University of Naples Federico II, via S. Pansini 5, 80131, Naples, Italy
| | - Francesco Caso
- Rheumatology Research Unit, Department of Clinical Medicine and Surgery, University of Naples Federico II, via S. Pansini 5, 80131, Naples, Italy
| | - Raffaele Scarpa
- Rheumatology Research Unit, Department of Clinical Medicine and Surgery, University of Naples Federico II, via S. Pansini 5, 80131, Naples, Italy
| | - Giuseppe Cirino
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Mariarosaria Bucci
- Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy
| | - Helen Michelle McGettrick
- Institute of Inflammation and Ageing (IIA), College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2WB, UK
| | - Asif Jilani Iqbal
- ImmunoPharmaLab, Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy; Institute of Cardiovascular Sciences (ICVS), College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Francesco Maione
- ImmunoPharmaLab, Department of Pharmacy, School of Medicine and Surgery, University of Naples Federico II, Via Domenico Montesano 49, 80131, Naples, Italy.
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Kapur N, Alam MA, Hassan SA, Patel PH, Wempe LA, Bhogoju S, Goretsky T, Kim JH, Herzog J, Ge Y, Awuah SG, Byndloss M, Baumler AJ, Zadeh MM, Sartor RB, Barrett T. Enhanced mucosal mitochondrial function corrects dysbiosis and OXPHOS metabolism in IBD. bioRxiv 2024:2024.03.14.584471. [PMID: 38559035 PMCID: PMC10979996 DOI: 10.1101/2024.03.14.584471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Background Mitochondrial (Mito) dysfunction in IBD reduces mucosal O2 consumption and increases O2 delivery to the microbiome. Increased enteric O2 promotes blooms of facultative anaerobes (eg. Proteobacteria ) and restricts obligate anaerobes (eg. Firmicutes ). Dysbiotic metabolites negatively affect host metabolism and immunity. Our novel compound (AuPhos) upregulates intestinal epithelial cell (IEC) mito function, attenuates colitis and corrects dysbiosis in humanized Il10-/- mice. We posit that AuPhos corrects IBD-associated dysbiotic metabolism. Methods Primary effect of AuPhos on mucosal Mito respiration and healing process was studied in ex vivo treated human colonic biopsies and piroxicam-accelerated (Px) Il10-/- mice. Secondary effect on microbiome was tested in DSS-colitis WT B6 and germ-free 129.SvEv WT or Il10-/- mice reconstituted with human IBD stool (Hu- Il10-/- ). Mice were treated orally with AuPhos (10- or 25- mg/kg; q3d) or vehicle, stool samples collected for fecal lipocalin-2 (f-LCN2) assay and microbiome analyses using 16S rRNA sequencing. AuPhos effect on microbial metabolites was determined using untargeted global metabolomics. AuPhos-induced hypoxia in IECs was assessed by Hypoxyprobe-1 staining in sections from pimonidazole HCl-infused DSS-mice. Effect of AuPhos on enteric oxygenation was assessed by E. coli Nissle 1917 WT (aerobic respiration-proficient) and cytochrome oxidase (cydA) mutant (aerobic respiration-deficient). Results Metagenomic (16S) analysis revealed AuPhos reduced relative abundances of Proteobacteria and increased blooms of Firmicutes in uninflamed B6 WT, DSS-colitis, Hu-WT and Hu- Il10-/- mice. AuPhos also increased hypoxyprobe-1 staining in surface IECs suggesting enhanced O2 utilization. AuPhos-induced anaerobiosis was confirmed by a significant increase in cydA mutant compared to WT (O2-utlizing) E.coli . Ex vivo treatment of human biopsies with AuPhos showed significant increase in Mito mass, and complexes I and IV. Further, gene expression analysis of AuPhos-treated biopsies showed increase in stem cell markers (Lgr4, Lgr5, Lrig1), with concomitant decreases in pro-inflammatory markers (IL1β,MCP1, RankL). Histological investigation of AuPhos-fed Px- Il10-/- mice showed significantly decreased colitis score in AuPhos-treated Px- Il10-/- mice, with decrease in mRNA of pro-inflammatory cytokines and increase in Mito complexes ( ND5 , ATP6 ). AuPhos significantly altered microbial metabolites associated with SCFA synthesis, FAO, TCA cycle, tryptophan and polyamine biosynthesis pathways. AuPhos increased pyruvate, 4-hydroxybutyrate, 2-hydroxyglutarate and succinate, suggesting an upregulation of pyruvate and glutarate pathways of butyrate production. AuPhos reduced IBD-associated primary bile acids (BA) with concomitant increase in secondary BA (SBA). AuPhos treatment significantly decreased acylcarnitines and increased L-carnitine reflective of enhanced FAO. AuPhos increases TCA cycle intermediates and creatine, energy reservoir substrates indicating enhanced OxPHOS. Besides, AuPhos also upregulates tryptophan metabolism, decreases Kynurenine and its derivatives, and increases polyamine biosynthesis pathway (Putresceine and Spermine). Conclusion These findings indicate that AuPhos-enhanced IEC mitochondrial function reduces enteric O2 delivery, which corrects disease-associated metabolomics by restoring short-chain fatty acids, SBA, AA and IEC energy metabolism. Graphical abstract
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Liang D, Shen X, Han L, Ren H, Zang T, Tan L, Lu Z, Liao X, Vetha BSS, Liu Y, Zhang C, Sun J. Dual-ROS Sensitive Moieties Conjugate Inhibits Curcumin Oxidative Degradation for Colitis Precise Therapy. Adv Healthc Mater 2024:e2303016. [PMID: 38431929 DOI: 10.1002/adhm.202303016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 01/01/2024] [Indexed: 03/05/2024]
Abstract
Curcumin, a natural bioactive polyphenol with diverse molecular targets, is well known for its anti-oxidation and anti-inflammatory potential. However, curcumin exhibits low solubility (<1 µg mL-1 ), poor tissue-targeting ability, and rapid oxidative degradation, resulting in poor bioavailability and stability for inflammatory therapy. Here, poly(diselenide-oxalate-curcumin) nanoparticle (SeOC-NP) with dual-reactive oxygen species (ROS) sensitive chemical moieties (diselenide and peroxalate ester bonds) is fabricated by a one-step synthetic strategy. The results confirmed that dual-ROS sensitive chemical moieties endowed SeOC-NP with the ability of targeted delivery of curcumin and significantly suppress oxidative degradation of curcumin for high-efficiency inflammatory therapy. In detail, the degradation amount of curcumin for SeOC is about 4-fold lower than that of free curcumin in an oxidative microenvironment. As a result, SeOC-NP significantly enhanced the antioxidant activity and anti-inflammatory efficacy of curcumin in vitro analysis by scavenging intracellular ROS and suppressing the secretion of nitric oxide and pro-inflammatory cytokines. In mouse colitis models, orally administered SeOC-NP can remarkably alleviate the symptoms of IBD and maintain the homeostasis of gut microbiota. This work provided a simple and effective strategy to fabricate ROS-responsive micellar and enhance the oxidation stability of medicine for precise therapeutic inflammation.
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Affiliation(s)
- Dunsheng Liang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, P. R. China
| | - Xiaofan Shen
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, P. R. China
| | - Lu Han
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, P. R. China
| | - Hao Ren
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, P. R. China
| | - Tao Zang
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, P. R. China
| | - Lulu Tan
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, P. R. China
| | - Zhaoxiang Lu
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, P. R. China
| | - Xiaoping Liao
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, P. R. China
| | - Berwin Singh Swami Vetha
- Department of Foundational Sciences and Research, School of Dental Medicine, East Carolina University, Greenville, NC, 27834, USA
| | - Yahong Liu
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, P. R. China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Chaoqun Zhang
- Key Laboratory for Biobased Materials and Energy of Ministry of Education, College of Materials and Energy, South China Agricultural University, Guangzhou, 510642, P. R. China
| | - Jian Sun
- State Key Laboratory for Animal Disease Control and Prevention, Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, South China Agricultural University, Guangzhou, 510642, P. R. China
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Yang S, Li W, Bai X, Di Nunzio G, Fan L, Zhao Y, Ren L, Zhao R, Bian S, Liu M, Wei Y, Zhao D, Wang J. Ginseng-derived nanoparticles alleviate inflammatory bowel disease via the TLR4/MAPK and p62/Nrf2/Keap1 pathways. J Nanobiotechnology 2024; 22:48. [PMID: 38302938 PMCID: PMC10832157 DOI: 10.1186/s12951-024-02313-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/26/2024] [Indexed: 02/03/2024] Open
Abstract
Inflammatory bowel disease (IBD) is closely linked to the homeostasis of the intestinal environment, and exosomes can be used to treat IBD due to their high biocompatibility and ability to be effectively absorbed by the intestinal tract. However, Ginseng-derived nanoparticles (GDNPs) have not been studied in this context and their mechanism of action remains unclear. Here, we investigated GDNPs ability to mediate intercellular communication in a complex inflammatory microenvironment in order to treat IBD. We found that GDNPs scavenge reactive oxygen species from immune cells and intestinal epithelial cells, inhibit the expression of pro-inflammatory factors, promote the proliferation and differentiation of intestinal stem cells, as well as enhancing the diversity of the intestinal flora. GDNPs significantly stabilise the intestinal barrier thereby promoting tissue repair. Overall, we proved that GDNPs can ameliorate inflammation and oxidative stress in vivo and in vitro, acting on the TLR4/MAPK and p62/Keap1/Nrf2 pathways, and exerting an anti-inflammatory and antioxidant effect. GDNPs mitigated IBD in mice by reducing inflammatory factors and improving the intestinal environment. This study offers new evidence of the potential therapeutic effects of GDNPs in the context of IBD, providing the conceptual ground for an alternative therapeutic strategy.
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Affiliation(s)
- Song Yang
- Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun, 130117, Jilin, China
| | - Wenjing Li
- Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun, 130117, Jilin, China
| | - Xueyuan Bai
- Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun, 130117, Jilin, China
| | - Giada Di Nunzio
- Division of Cardiovascular Medicine, Department of Medicine, Solna, Karolinska Institutet, 17176, Stockholm, Sweden
| | - Liangliang Fan
- Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun, 130117, Jilin, China
| | - Yueming Zhao
- Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun, 130117, Jilin, China
| | - Limei Ren
- Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun, 130117, Jilin, China
| | - Ronghua Zhao
- Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun, 130117, Jilin, China
| | - Shuai Bian
- Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun, 130117, Jilin, China
| | - Meichen Liu
- Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun, 130117, Jilin, China
| | - Yuchi Wei
- Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun, 130117, Jilin, China
| | - Daqing Zhao
- Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun, 130117, Jilin, China
| | - Jiawen Wang
- Changchun University of Chinese Medicine, 1035 Boshuo Road, Changchun, 130117, Jilin, China.
- Division of Cardiovascular Medicine, Department of Medicine, Solna, Karolinska Institutet, 17176, Stockholm, Sweden.
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Oliver A, Kay M, Lemay DG. TaxaHFE: a machine learning approach to collapse microbiome datasets using taxonomic structure. Bioinform Adv 2023; 3:vbad165. [PMID: 38046097 PMCID: PMC10689668 DOI: 10.1093/bioadv/vbad165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 09/28/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
Motivation Biologists increasingly turn to machine learning models not just to predict, but to explain. Feature reduction is a common approach to improve both the performance and interpretability of models. However, some biological datasets, such as microbiome data, are inherently organized in a taxonomy, but these hierarchical relationships are not leveraged during feature reduction. We sought to design a feature engineering algorithm to exploit relationships in hierarchically organized biological data. Results We designed an algorithm, called TaxaHFE, to collapse information-poor features into their higher taxonomic levels. We applied TaxaHFE to six previously published datasets and found, on average, a 90% reduction in the number of features (SD = 5.1%) compared to using the most complete taxonomy. Using machine learning to compare the most resolved taxonomic level (i.e. species) against TaxaHFE-preprocessed features, models based on TaxaHFE features achieved an average increase of 3.47% in receiver operator curve area under the curve. Compared to other hierarchical feature engineering implementations, TaxaHFE introduces the novel ability to consider both categorical and continuous response variables to inform the feature set collapse. Importantly, we find TaxaHFE's ability to reduce hierarchically organized features to a more information-rich subset increases the interpretability of models. Availability and implementation TaxaHFE is available as a Docker image and as R code at https://github.com/aoliver44/taxaHFE.
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Affiliation(s)
- Andrew Oliver
- USDA-ARS Western Human Nutrition Research Center, Davis, CA 95616, United States
| | - Matthew Kay
- Independent Researcher, Washington, DC 20002, United States
| | - Danielle G Lemay
- USDA-ARS Western Human Nutrition Research Center, Davis, CA 95616, United States
- Department of Nutrition, University of California, Davis, Davis, CA 95616, United States
- Genome Center, University of California, Davis, Davis, CA 95616, United States
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Di Ciaula A, Bonfrate L, Khalil M, Portincasa P. The interaction of bile acids and gut inflammation influences the pathogenesis of inflammatory bowel disease. Intern Emerg Med 2023; 18:2181-2197. [PMID: 37515676 PMCID: PMC10635993 DOI: 10.1007/s11739-023-03343-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 06/08/2023] [Indexed: 07/31/2023]
Abstract
Bile acids (BA) are amphipathic molecules originating from cholesterol in the liver and from microbiota-driven biotransformation in the colon. In the gut, BA play a key role in fat digestion and absorption and act as potent signaling molecules on the nuclear farnesoid X receptor (FXR) and membrane-associated G protein-coupled BA receptor-1 (GPBAR-1). BA are, therefore, involved in the maintenance of gut barrier integrity, gene expression, metabolic homeostasis, and microbiota profile and function. Disturbed BA homeostasis can activate pro-inflammatory pathways in the gut, while inflammatory bowel diseases (IBD) can induce gut dysbiosis and qualitative and/or quantitative changes of the BA pool. These factors contribute to impaired repair capacity of the mucosal barrier, due to chronic inflammation. A better understanding of BA-dependent mechanisms paves the way to innovative therapeutic tools by administering hydrophilic BA and FXR agonists and manipulating gut microbiota with probiotics and prebiotics. We discuss the translational value of pathophysiological and therapeutic evidence linking BA homeostasis to gut inflammation in IBD.
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Affiliation(s)
- Agostino Di Ciaula
- Clinica Medica "A. Murri" and Division Internal Medicine, Department of Precision and Regenerative Medicine and Ionian Area (DiMePre-J), University "Aldo Moro" Medical School, Policlinico Hospital, Piazza G. Cesare 11, 70124, Bari, Italy
| | - Leonilde Bonfrate
- Clinica Medica "A. Murri" and Division Internal Medicine, Department of Precision and Regenerative Medicine and Ionian Area (DiMePre-J), University "Aldo Moro" Medical School, Policlinico Hospital, Piazza G. Cesare 11, 70124, Bari, Italy.
| | - Mohamad Khalil
- Clinica Medica "A. Murri" and Division Internal Medicine, Department of Precision and Regenerative Medicine and Ionian Area (DiMePre-J), University "Aldo Moro" Medical School, Policlinico Hospital, Piazza G. Cesare 11, 70124, Bari, Italy
| | - Piero Portincasa
- Clinica Medica "A. Murri" and Division Internal Medicine, Department of Precision and Regenerative Medicine and Ionian Area (DiMePre-J), University "Aldo Moro" Medical School, Policlinico Hospital, Piazza G. Cesare 11, 70124, Bari, Italy
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9
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Duan Y, Zhang E, Fang RH, Gao W, Zhang L. Capsulated Cellular Nanosponges for the Treatment of Experimental Inflammatory Bowel Disease. ACS Nano 2023; 17:15893-15904. [PMID: 37565604 DOI: 10.1021/acsnano.3c03959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Inflammatory bowel disease (IBD) is a chronic gastrointestinal tract disorder characterized by uncontrolled inflammatory responses to the disrupted intestinal epithelial barrier and gut microbiome dysbiosis. Currently available small-molecule immunosuppressive agents and anticytokine biologics show limited potency, mainly due to the complexity of the inflammatory network involved in IBD. Here, we develop an oral formulation of macrophage membrane-coated nanoparticles capsulated in enteric polymer-coated gelatin capsules (denoted "cp-MΦ-NPs") for IBD treatment. The capsules protect the nanoparticles from gastric degradation and allow for targeted delivery to the colon. At the inflamed colon, cp-MΦ-NPs act as macrophage decoys that bind and neutralize pro-inflammatory cytokines. The in vivo treatment efficacy of cp-MΦ-NPs is tested in a mouse model of dextran sulfate sodium-induced colitis. In both prophylactic and delayed treatment regimens, the oral delivery of cp-MΦ-NPs significantly alleviates IBD severity, reflected by reduced intestinal inflammation and intestinal barrier restoration. Overall, cp-MΦ-NPs provide a biomimetic nanomedicine strategy for the treatment of IBD.
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Affiliation(s)
- Yaou Duan
- Department of Nanoengineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Edward Zhang
- Department of Nanoengineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Ronnie H Fang
- Department of Nanoengineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Weiwei Gao
- Department of Nanoengineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, California 92093, United States
| | - Liangfang Zhang
- Department of Nanoengineering, Chemical Engineering Program, and Moores Cancer Center, University of California San Diego, La Jolla, California 92093, United States
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10
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Vich Vila A, Hu S, Andreu-Sánchez S, Collij V, Jansen BH, Augustijn HE, Bolte LA, Ruigrok RAAA, Abu-Ali G, Giallourakis C, Schneider J, Parkinson J, Al-Garawi A, Zhernakova A, Gacesa R, Fu J, Weersma RK. Faecal metabolome and its determinants in inflammatory bowel disease. Gut 2023; 72:1472-1485. [PMID: 36958817 PMCID: PMC10359577 DOI: 10.1136/gutjnl-2022-328048] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 03/05/2023] [Indexed: 03/25/2023]
Abstract
OBJECTIVE Inflammatory bowel disease (IBD) is a multifactorial immune-mediated inflammatory disease of the intestine, comprising Crohn's disease and ulcerative colitis. By characterising metabolites in faeces, combined with faecal metagenomics, host genetics and clinical characteristics, we aimed to unravel metabolic alterations in IBD. DESIGN We measured 1684 different faecal metabolites and 8 short-chain and branched-chain fatty acids in stool samples of 424 patients with IBD and 255 non-IBD controls. Regression analyses were used to compare concentrations of metabolites between cases and controls and determine the relationship between metabolites and each participant's lifestyle, clinical characteristics and gut microbiota composition. Moreover, genome-wide association analysis was conducted on faecal metabolite levels. RESULTS We identified over 300 molecules that were differentially abundant in the faeces of patients with IBD. The ratio between a sphingolipid and L-urobilin could discriminate between IBD and non-IBD samples (AUC=0.85). We found changes in the bile acid pool in patients with dysbiotic microbial communities and a strong association between faecal metabolome and gut microbiota. For example, the abundance of Ruminococcus gnavus was positively associated with tryptamine levels. In addition, we found 158 associations between metabolites and dietary patterns, and polymorphisms near NAT2 strongly associated with coffee metabolism. CONCLUSION In this large-scale analysis, we identified alterations in the metabolome of patients with IBD that are independent of commonly overlooked confounders such as diet and surgical history. Considering the influence of the microbiome on faecal metabolites, our results pave the way for future interventions targeting intestinal inflammation.
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Affiliation(s)
- Arnau Vich Vila
- Department of Genetics, University Medical Centre, Groningen, The Netherlands
- Department of Pediatrics, University Medical Centre, Groningen, The Netherlands
| | - Shixian Hu
- Department of Genetics, University Medical Centre, Groningen, The Netherlands
- Department of Pediatrics, University Medical Centre, Groningen, The Netherlands
| | - Sergio Andreu-Sánchez
- Department of Pediatrics, University Medical Centre, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, Groningen, The Netherlands
| | - Valerie Collij
- Department of Genetics, University Medical Centre, Groningen, The Netherlands
- Department of Pediatrics, University Medical Centre, Groningen, The Netherlands
| | - Bernadien H Jansen
- Department of Genetics, University Medical Centre, Groningen, The Netherlands
| | - Hannah E Augustijn
- Department of Pediatrics, University Medical Centre, Groningen, The Netherlands
| | - Laura A Bolte
- Department of Genetics, University Medical Centre, Groningen, The Netherlands
| | - Renate A A A Ruigrok
- Department of Genetics, University Medical Centre, Groningen, The Netherlands
- Department of Pediatrics, University Medical Centre, Groningen, The Netherlands
| | - Galeb Abu-Ali
- Gastroenterology Drug Discovery Unit, Takeda Pharmaceutical, Cambridge, Massachusetts, USA
| | - Cosmas Giallourakis
- Gastroenterology Drug Discovery Unit, Takeda Pharmaceutical, Cambridge, Massachusetts, USA
| | - Jessica Schneider
- Gastroenterology Drug Discovery Unit, Takeda Pharmaceutical, Cambridge, Massachusetts, USA
| | - John Parkinson
- Gastroenterology Drug Discovery Unit, Takeda Pharmaceutical, Cambridge, Massachusetts, USA
| | - Amal Al-Garawi
- Gastroenterology Drug Discovery Unit, Takeda Pharmaceutical, Cambridge, Massachusetts, USA
| | | | - Ranko Gacesa
- Department of Genetics, University Medical Centre, Groningen, The Netherlands
- Department of Pediatrics, University Medical Centre, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Pediatrics, University Medical Centre, Groningen, The Netherlands
- Department of Gastroenterology and Hepatology, University Medical Centre, Groningen, The Netherlands
| | - Rinse K Weersma
- Department of Genetics, University Medical Centre, Groningen, The Netherlands
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11
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Shi L, Jin L, Huang W. Bile Acids, Intestinal Barrier Dysfunction, and Related Diseases. Cells 2023; 12:1888. [PMID: 37508557 PMCID: PMC10377837 DOI: 10.3390/cells12141888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 07/11/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
The intestinal barrier is a precisely regulated semi-permeable physiological structure that absorbs nutrients and protects the internal environment from infiltration of pathological molecules and microorganisms. Bile acids are small molecules synthesized from cholesterol in the liver, secreted into the duodenum, and transformed to secondary or tertiary bile acids by the gut microbiota. Bile acids interact with bile acid receptors (BARs) or gut microbiota, which plays a key role in maintaining the homeostasis of the intestinal barrier. In this review, we summarize and discuss the recent studies on bile acid disorder associated with intestinal barrier dysfunction and related diseases. We focus on the roles of bile acids, BARs, and gut microbiota in triggering intestinal barrier dysfunction. Insights for the future prevention and treatment of intestinal barrier dysfunction and related diseases are provided.
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Affiliation(s)
- Linsen Shi
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Lihua Jin
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, 1500 E. Duarte Road, Duarte, CA 91010, USA
| | - Wendong Huang
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, 1500 E. Duarte Road, Duarte, CA 91010, USA
- Irell & Manella Graduate School of Biomedical Science, City of Hope National Medical Center, 1500 E. Duarte Road, Duarte, CA 91010, USA
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12
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Zhao Q, Jiang Y, Zhao Q, Patrick Manzi H, Su L, Liu D, Huang X, Long D, Tang Z, Zhang Y. The benefits of edible mushroom polysaccharides for health and their influence on gut microbiota: a review. Front Nutr 2023; 10:1213010. [PMID: 37485384 PMCID: PMC10358859 DOI: 10.3389/fnut.2023.1213010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
The gut microbiome is a complex biological community that deeply affects various aspects of human health, including dietary intake, disease progression, drug metabolism, and immune system regulation. Edible mushroom polysaccharides (EMPs) are bioactive fibers derived from mushrooms that possess a range of beneficial properties, including anti-tumor, antioxidant, antiviral, hypoglycemic, and immunomodulatory effects. Studies have demonstrated that EMPs are resistant to human digestive enzymes and serve as a crucial source of energy for the gut microbiome, promoting the growth of beneficial bacteria. EMPs also positively impact human health by modulating the composition of the gut microbiome. This review discusses the extraction and purification processes of EMPs, their potential to improve health conditions by regulating the composition of the gut microbiome, and their application prospects. Furthermore, this paper provides valuable guidance and recommendations for future studies on EMPs consumption in disease management.
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Affiliation(s)
- Qilong Zhao
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Yu Jiang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Qian Zhao
- School of Public Health, Lanzhou University, Lanzhou, China
| | | | - Li Su
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Diru Liu
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Xiaodan Huang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Danfeng Long
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Zhenchuang Tang
- Institute of Food and Nutrition Development, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Ying Zhang
- School of Public Health, Lanzhou University, Lanzhou, China
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13
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Ge L, Song L, Wang L, Li Y, Sun Y, Wang C, Chen J, Wu G, Pan A, Wu Y, Quan Z, Li P. Evaluating response mechanisms of soil microbiomes and metabolomes to Bt toxin additions. J Hazard Mater 2023; 448:130904. [PMID: 36860032 DOI: 10.1016/j.jhazmat.2023.130904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
The accumulation and persistence of Bt toxins in soils from Bt plants and Bt biopesticides may result in environmental hazards such as adverse impacts on soil microorganisms. However, the dynamic relationships among exogenous Bt toxins, soil characteristics, and soil microorganisms are not well understood. Cry1Ab is one of the most commonly used Bt toxins and was added to soils in this study to evaluate subsequent changes in soil physiochemical properties, microbial taxa, microbial functional genes, and metabolites profiles via 16S rRNA gene pyrosequencing, high-throughput qPCR, metagenomic shotgun sequencing, and untargeted metabolomics. Higher additions of Bt toxins led to higher concentrations of soil organic matter (SOM), ammonium (NH+4-N), and nitrite (NO2--N) compared against controls without addition after 100 days of soil incubation. High-throughput qPCR analysis and shotgun metagenomic sequencing analysis revealed that the 500 ng/g Bt toxin addition significantly affected profiles of soil microbial functional genes involved in soil carbon (C), nitrogen (N), and phosphorus (P) cycling after 100 days of incubation. Furthermore, combined metagenomic and metabolomic analyses indicated that the 500 ng/g Bt toxin addition significantly altered low molecular weight metabolite profiles of soils. Importantly, some of these altered metabolites are involved in soil nutrient cycling, and robust associations were identified among differentially abundant metabolites and microorganisms due to Bt toxin addition treatments. Taken together, these results suggest that higher levels of Bt toxin addition can alter soil nutrients, probably by affecting the activities of Bt toxin-degrading microorganisms. These dynamics would then activate other microorganisms involved in nutrient cycling, finally leading to broad changes in metabolite profiles. Notably, the addition of Bt toxins did not cause the accumulation of potential microbial pathogens in soils, nor did it adversely affect the diversity and stability of microbial communities. This study provides new insights into the putative mechanistic associations among Bt toxins, soil characteristics, and microorganisms, providing new understanding into the ecological impacts of Bt toxins on soil ecosystems.
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Affiliation(s)
- Lei Ge
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Lili Song
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Luyao Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yujie Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yu Sun
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Cui Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Jun Chen
- East China University of Technology, Nanchang 330013, China
| | - Guogan Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Aihu Pan
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
| | - Yunfei Wu
- The College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Zhexue Quan
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Peng Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
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14
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Li P, Ye S, Chen J, Wang L, Li Y, Ge L, Wu G, Song L, Wang C, Sun Y, Wang J, Pan A, Quan Z, Wu Y. Combined metagenomic and metabolomic analyses reveal that Bt rice planting alters soil C-N metabolism. ISME Commun 2023; 3:4. [PMID: 36690796 PMCID: PMC9870860 DOI: 10.1038/s43705-023-00217-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 01/25/2023]
Abstract
The environmental impacts of genetically modified (GM) plants remain a controversial global issue. To address these issues, comprehensive environmental risk assessments of GM plants is critical for the sustainable development and application of transgenic technology. In this paper, significant differences were not observed between microbial metagenomic and metabolomic profiles in surface waters of the Bt rice (T1C-1, the transgenic line) and non-Bt cultivars (Minghui 63 (the isogenic line) and Zhonghua 11 (the conventional japonica cultivar)). In contrast, differences in these profiles were apparent in the rhizospheres. T1C-1 planting increased soil microbiome diversity and network stability, but did not significantly alter the abundances of potential probiotic or phytopathogenic microorganisms compared with Minghui 63 and Zhonghua 11, which revealed no adverse effects of T1C-1 on soil microbial communities. T1C-1 planting could significantly alter soil C and N, probably via the regulation of the abundances of enzymes related to soil C and N cycling. In addition, integrated multi-omic analysis of root exudate metabolomes and soil microbiomes showed that the abundances of various metabolites released as root exudates were significantly correlated with subsets of microbial populations including the Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes that were differentially abundant in T1C-1 and Mnghui 63 soils. Finally, the potential for T1C-1-associated root metabolites to exert growth effects on T1C-1-associated species was experimentally validated by analysis of bacterial cultures, revealing that Bt rice planting could selectively modulate specific root microbiota. Overall, this study indicate that Bt rice can directly modulate rhizosphere microbiome assemblages by altering the metabolic compositions of root exudates that then alters soil metabolite profiles and physiochemical properties. This study unveils the mechanistic associations of Bt plant-microorganism-environment, which provides comprehensive insights into the potential ecological impacts of GM plants.
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Affiliation(s)
- Peng Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China.
- Shanghai Co-Elite Agricultural Sci-Tech (Group) Co., Ltd, 201106, Shanghai, China.
| | - Shuifeng Ye
- College of Life Sciences, Shangrao Normal University, 334001, Shangrao, China
| | - Jun Chen
- East China University of Technology, 330013, Nanchang, China
| | - Luyao Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Yujie Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Lei Ge
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Guogan Wu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Lili Song
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Cui Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Yu Sun
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Jinbin Wang
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Aihu Pan
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, 201106, Shanghai, China
| | - Zhexue Quan
- School of Life Sciences, Fudan University, 200433, Shanghai, China.
| | - Yunfei Wu
- The College of Bioscience and Biotechnology, Yangzhou University, 225009, Yangzhou, China.
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15
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Wang Y, An M, Zhang Z, Zhang W, Kulyar MFEA, Iqbal M, He Y, Li F, An T, Li H, Luo X, Yang S, Li J. Effects of Milk Replacer-Based Lactobacillus on Growth and Gut Development of Yaks' Calves: a Gut Microbiome and Metabolic Study. Microbiol Spectr 2022; 10:e0115522. [PMID: 35771011 PMCID: PMC9431445 DOI: 10.1128/spectrum.01155-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/08/2022] [Indexed: 01/01/2023] Open
Abstract
The gut microbiota and its metabolic activities are crucial for maintaining host homoeostasis and health, of which the role of probiotics has indeed been emphasized. The current study delves into the performance of probiotics as a beneficial managemental strategy, which further highlights their impact on growth performance, serologic investigation, gut microbiota, and metabolic profiling in yaks' calves. A field experiment was employed consisting of 2 by 3 factorial controls, including two development stages, namely, 21 and 42 days (about one and a half month), with three different feeding treatments. Results showed a positive impact of probiotic supplements on growth performance by approximately 3.16 kg (P < 0.01) compared with the blank control. Moreover, they had the potential to improve serum antioxidants and biochemical properties. We found that microorganisms that threaten health were enriched in the gut of the blank control with the depletion of beneficial bacteria, although all yaks were healthy. Additionally, the gut was colonized by a microbial succession that assembled into a more mature microbiome, driven by the probiotics strategy. The gut metabolic profiling was also changed significantly after the probiotic strategy, i.e., the concentrations of metabolites and the metabolic pattern, including enrichments in protein digestion and absorption, vitamin digestion and absorption, and biosynthesis of secondary metabolites. In summary, probiotics promoted gut microbiota/metabolites, developing precise interventions and achieving physiological benefits based on intestinal microecology. Hence, it is important to understand probiotic dietary changes to the gut microbiome, metabolome, and the host phenotype. IMPORTANCE The host microbiome is a composite of the trillion microorganisms colonizing host bodies. It can be impacted by various factors, including diet, environmental conditions, and physical activities. The yaks' calves have a pre-existing imbalance in the intestinal microbiota with an inadequate feeding strategy, resulting in poor growth performance, diarrhea, and other intestinal diseases. Hence, targeting gut microbiota might provide a new effective feeding strategy for enhancing performance and maintaining a healthy intestinal environment. Based on the current findings, milk replacer-based Lactobacillus feeding may improve growth performance and health in yaks' calves.
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Affiliation(s)
- Yaping Wang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Miao An
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhao Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wenqian Zhang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | | | - Mudassar Iqbal
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Yuanyuan He
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Feiran Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Tianwu An
- Sichuan Academy of Grassland Science, Chengdu, People’s Republic of China
| | - Huade Li
- Sichuan Academy of Grassland Science, Chengdu, People’s Republic of China
| | - Xiaolin Luo
- Sichuan Academy of Grassland Science, Chengdu, People’s Republic of China
| | - Shan Yang
- Sichuan Academy of Grassland Science, Chengdu, People’s Republic of China
| | - Jiakui Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- College of Animals Husbandry and Veterinary Medicine, Tibet Agriculture and Animal Husbandry University, Linzhi, Tibet, People’s Republic of China
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16
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Li Y, Xie HQ, Liu Y, Xu L, Zheng L, Yu S, Chen G, Ji J, Jiang S, Guo TL, Zhao B. Subacute effects of the chlorinated flame retardant dechlorane 602 on intestinal microenvironment in mice. Environ Int 2022; 166:107394. [PMID: 35820366 DOI: 10.1016/j.envint.2022.107394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Chlorinated flame retardant Dechlorane 602 (Dec 602) has been detected in daily food, indicating that it may pose a risk to intestinal health. The intestinal microenvironment plays an important role in intestinal health. Intestinal microbiota and metabolites are two important factors for maintaining the microenvironment. However, little is known about the effects of Dec 602 on intestinal microbiota and metabolites. OBJECTIVES We aimed to probe the effects of Dec 602 on the intestine by revealing the changes that Dec 602 caused to the intestinal microbiota and metabolites. METHODS Adult female C57BL/6 mice were exposed to Dec 602 (low/high doses: 1.0/10.0 μg/kg body weight per day) orally for 7 consecutive days, and sacrificed after 7 days of recovery. The composition of colonic microbiota was measured by 16S rRNA gene sequencing, and the colonic metabolites were determined by LC-ESI-MS/MS. Finally, the effects of Dec 602 on the colon were validated by histopathological analysis. RESULTS The intestinal microbiota composition was altered toward a pro-inflammatory status after exposure to Dec 602. Dec 602 exposure also up-regulated oxidative metabolites (glutathione disulfide, taurine and retinoic acid) and pro-inflammatory metabolites (prostaglandin E2). On the other hand, antioxidative metabolites (s-adenosylmethionine and 11-cis-retinol) and anti-inflammatory metabolites (alpha-linolenic acid, eicosapentaenoic acid and docosahexaenoic acid) were down-regulated after exposure to Dec 602. Infiltration of lymphocytes in the colonic lamina propria was observed in the mice treated with Dec 602 for 7 days, and it was not recovered after another 7 days without further treatment. CONCLUSION Dec 602 interfered with the colonic microbiota and metabolome, and exhibited inflammatory features. Histopathological studies confirmed that Dec 602 exposure did induce colonic inflammation.
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Affiliation(s)
- Yunping Li
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Heidi Qunhui Xie
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yin Liu
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Li Xu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liping Zheng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyuan Yu
- Environment and Health Department, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Guomin Chen
- Environment and Health Department, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Jiajia Ji
- Environment and Health Department, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Shuai Jiang
- Environment and Health Department, Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong 518055, China
| | - Tai L Guo
- Department of Veterinary Biomedical Sciences, University of Georgia, Athens, GA 30602, USA.
| | - Bin Zhao
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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17
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Wen Y, Li S, Wang Z, Feng H, Yao X, Liu M, Chang J, Ding X, Zhao H, Ma W. Intestinal Microbial Diversity of Free-Range and Captive Yak in Qinghai Province. Microorganisms 2022; 10:754. [PMID: 35456805 PMCID: PMC9028582 DOI: 10.3390/microorganisms10040754] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/16/2022] [Accepted: 03/23/2022] [Indexed: 02/06/2023] Open
Abstract
Background: The gut microbiome is a large and complex organic assemblage with subtle and close relationships with the host. This symbiotic mechanism is important for the health and adaptability of the host to the environment. Compared with other ruminants, there are few studies on yak intestinal microbes. The study of the gut microbiota of the yak will help us better understand the correlation between the microbiota and the environmental adaptability of the host. In this study, we adapted 16S rDNA sequencing technology to investigate the diversity and composition of the intestinal microbial community in free-range yaks and captive yaks living on the Qinghai–Tibet Plateau (QTP). Results: Sequencing results showed that the intestinal microbial community diversity was significantly different between free-range yaks and captive yaks. Firmicutes and Bacteroidetes were the dominant bacteria in both free-range and captive yaks. However, there were differences between the microbes of the two analyzed feeding styles in different classification levels. Compared with the captive type, free-range yaks had a higher abundance of Ruminococcaceae, Eubacteriaceae, Desulfovibrionaceae, Elusimicrobium, and Oscillibacter, while the abundance of Succinivibrionaceae, Clostridiales, Lachnospiraceae, Prevotellaceae, Roseburia, and Barnesiella was relatively low. The feeding method may be the key factor for the formation of intestinal flora differences in yaks, while altitude did not significantly affect Qinghai yak. Conclusions: In this study, we used 16S rDNA sequencing technology to investigate the composition of intestinal flora in free-range and captive yaks living on the QTP. The exploration of dietary factors can provide a theoretical basis for scientifically and rationally breeding yaks and provides a new direction for the development of prebiotics and microecological agents.
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Abstract
Besides its contribution to the development of rheumatic diseases, the gut microbiota interact with anti-rheumatic drugs. The intestinal microbiota can directly metabolize many drugs and indirectly change drug metabolism through a complex multi-dimensional interaction with the host, thus affecting individual response to drug therapy and adverse effects. The focus of the current review is to address recent advances and important progress in our understanding of how the gut microbiota interact with anti-rheumatic drugs and provide perspectives on promoting precision treatment, drug discovery, and better therapy for rheumatic diseases.
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Affiliation(s)
- Lingshu Zhang
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu, China.,Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Portland, OR, United States
| | - Cong-Qiu Chu
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University, Portland, OR, United States.,Section of Rheumatology, Veterans Affairs (VA) Portland Healthcare System, Portland, OR, United States
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19
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Ryvchin R, Dubinsky V, Rabinowitz K, Wasserberg N, Dotan I, Gophna U. Alteration in Urease-producing Bacteria in the Gut Microbiomes of Patients with Inflammatory Bowel Diseases. J Crohns Colitis 2021; 15:2066-2077. [PMID: 34111242 DOI: 10.1093/ecco-jcc/jjab101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Bacterial urease is a major virulence factor of human pathogens, and murine models have shown that it can contribute to the pathogenesis of inflammatory bowel diseases [IBD]. METHODS The distribution of urease-producing bacteria in IBD was assessed using public faecal metagenomic data from various cohorts, including non-IBD controls [n = 55], patients with Crohn's disease [n = 291] or ulcerative colitis [n = 214], and patients with a pouch [n = 53]. The ureA gene and the taxonomic markers gyrA, rpoB, and recA were used to estimate the percentage of urease producers in each sample. RESULTS Levels of urease producers in patients with IBD and non-IBD controls were comparable. In non-IBD controls and most IBD patients, urease producers were primarily acetate-producing genera such as Blautia and Ruminococcus. A shift in the type of the dominant urease producers towards Proteobacteria and Bacilli was observed in a subset of all IBD subtypes, which correlated with faecal calprotectin levels in one cohort. Some patients with IBD had no detectable urease producers. In patients with a pouch, the probiotic-associated species Streptococcus thermophilus was more common as a main urease producer than in other IBD phenotypes, and it generally did not co-occur with other Bacilli or with Proteobacteria. CONCLUSIONS Unlike all non-IBD controls, patients with IBD often showed a shift towards Bacilli or Proteobacteria or a complete loss of urease production. Probiotics containing the species S. thermophilus may have a protective effect against colonisation by undesirable urease-producing bacteria in a subset of patients with a pouch.
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Affiliation(s)
- Ron Ryvchin
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Vadim Dubinsky
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Keren Rabinowitz
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nir Wasserberg
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Division of Surgery, Rabin Medical Center, Petah-Tikva, Israel
| | - Iris Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Uri Gophna
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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20
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Ventin-Holmberg R, Eberl A, Saqib S, Korpela K, Virtanen S, Sipponen T, Salonen A, Saavalainen P, Nissilä E. Bacterial and Fungal Profiles as Markers of Infliximab Drug Response in Inflammatory Bowel Disease. J Crohns Colitis 2021; 15:1019-1031. [PMID: 33300552 DOI: 10.1093/ecco-jcc/jjaa252] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Inflammatory bowel diseases [IBDs], Crohn's disease [CD] and ulcerative colitis [UC], are globally increasing chronic gastro-intestinal inflammatory disorders associated with altered gut microbiota. Infliximab [IFX], a tumour necrosis factor [TNF]-alpha blocker, is used to treat IBD patients successfully, though one-third of the patients do not respond to therapy. No reliable biomarkers are available for prediction of IFX response. Our aims were to investigate the faecal bacterial and fungal communities during IFX therapy and find predictors for IFX treatment response in IBD patients. METHODS A total of 72 IBD patients [25 CD and 47 UC] started IFX therapy and were followed for 1 year or until IFX treatment was discontinued. An amplicon sequencing approach, targeting the bacterial 16S rRNA gene and fungal ITS 1 region separately, was used to determine the microbiota profiles in faecal samples collected before IFX therapy and 2, 6, and 12 weeks and 1 year after initiation of therapy. The response to IFX was evaluated by colonoscopy and clinically at 12 weeks after initiation. RESULTS Both faecal bacterial and fungal profiles differed significantly between response groups before start of IFX treatment. Non-responders had lower abundances of short chain fatty acid producers, particularly of the class Clostridia, and higher abundances of pro-inflammatory bacteria and fungi, such as the genus Candida, compared with responders. This was further indicated by bacterial taxa predicting the response in both CD and UC patients [area under the curve >0.8]. CONCLUSIONS Faecal bacterial and fungal microbiota composition could provide a predictive tool to estimate IFX response in IBD patients.
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Affiliation(s)
| | - Anja Eberl
- Department of Gastroenterology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Schahzad Saqib
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Katri Korpela
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Seppo Virtanen
- Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Taina Sipponen
- Department of Gastroenterology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Anne Salonen
- Human Microbiome Research Program, University of Helsinki, Helsinki, Finland
| | - Päivi Saavalainen
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Eija Nissilä
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
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21
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Hernández-Rocha C, Borowski K, Turpin W, Filice M, Nayeri S, Raygoza Garay JA, Stempak JM, Silverberg MS. Integrative Analysis of Colonic Biopsies from Inflammatory Bowel Disease Patients Identifies an Interaction Between Microbial Bile Acid-inducible Gene Abundance and Human Angiopoietin-like 4 Gene Expression. J Crohns Colitis 2021; 15:2078-2087. [PMID: 34077506 PMCID: PMC8684456 DOI: 10.1093/ecco-jcc/jjab096] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND AND AIMS Microbial-derived bile acids can modulate host gene expression, and their faecal abundance is decreased in active inflammatory bowel disease [IBD]. We analysed the impact of endoscopic inflammation on microbial genes involved in bile acid biotransformation, and their interaction with host transcriptome in the intestinal mucosa of IBD patients. METHODS Endoscopic mucosal biopsies were collected from non-inflamed and inflamed terminal ileum, ascending and sigmoid colon of IBD patients. Prediction of imputed metagenome functional content from 16S rRNA profile and real-time quantitative polymerase chain reaction [qPCR] were utsed to assess microbial bile acid biotransformation gene abundance, and RNA-seq was used for host transcriptome analysis. Linear regression and partial Spearman correlation accounting for age, sex, and IBD type were used to assess the association between microbial genes, inflammation, and host transcriptomics in each biopsy location. A Bayesian network [BN] analysis was fitted to infer the direction of interactions between IBD traits and microbial and host genes. RESULTS The inferred microbial gene pathway involved in secondary bile acid biosynthesis [ko00121 pathway] was depleted in inflamed terminal ileum of IBD patients compared with non-inflamed tissue. In non-inflamed sigmoid colon, the relative abundance of bile acid-inducible [baiCD] microbial genes was positively correlated with the host Angiopoietin-like 4 [Angptl4] gene expression. The BN analysis suggests that the microbial baiCD gene abundance could affect Angptl4 expression, and this interaction appears to be lost in the presence of inflammation. CONCLUSIONS Endoscopic inflammation affects the abundance of crucial microbial bile acid-metabolising genes and their interaction with Angptl4 in intestinal mucosa of IBD patients.
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Affiliation(s)
- Cristian Hernández-Rocha
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada,Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Krzysztof Borowski
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Williams Turpin
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Melissa Filice
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Shadi Nayeri
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Juan Antonio Raygoza Garay
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Joanne M Stempak
- Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Mark S Silverberg
- Division of Gastroenterology, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada,Zane Cohen Centre for Digestive Diseases, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada,Corresponding author: Mark S. Silverberg, MD, PhD, FRCPC, University of Toronto, Division of Gastroenterology, Mount Sinai Hospital Inflammatory Bowel Disease Centre, 441–600 University Avenue, Toronto, ON, M5G1X5, Canada. Tel.: 1-416-586-4800 ext 8236; fax: 1-416-619-5524;
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22
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Abstract
BACKGROUND AND AIMS The inflammatory bowel diseases [IBD], Crohn's disease and ulcerative colitis, are chronic, idiopathic gastrointestinal diseases. Although their precise aetiology is unknown, it is thought to involve a complex interaction between genetic predisposition and an abnormal host immune response to environmental exposures, probably microbial. Microbial dysbiosis has frequently been documented in IBD. Metabolomics [the study of small molecular intermediates and end products of metabolism in biological samples] provides a unique opportunity to characterize disease-associated metabolic changes and may be of particular use in quantifying gut microbial metabolism. Numerous metabolomic studies have been undertaken in IBD populations, identifying consistent alterations in a range of molecules across several biological matrices. This systematic review aims to summarize these findings. METHODS A comprehensive, systematic search was carried out using Medline and Embase. All studies were reviewed by two authors independently using predefined exclusion criteria. Sixty-four relevant papers were assessed for quality and included in the review. RESULTS Consistent metabolic perturbations were identified, including increases in levels of branched chain amino acids and lipid classes across stool, serum, plasma and tissue biopsy samples, and reduced levels of microbially modified metabolites in both urine [such as hippurate] and stool [such as secondary bile acids] samples. CONCLUSIONS This review provides a summary of metabolomic research in IBD to date, highlighting underlying themes of perturbed gut microbial metabolism and mammalian-microbial co-metabolism associated with disease status.
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Affiliation(s)
- Kate Gallagher
- Department of Metabolism Digestion and Reproduction, Imperial College London, UK
| | - Alexandra Catesson
- Department of Metabolism Digestion and Reproduction, Imperial College London, UK
| | - Julian L Griffin
- Department of Metabolism Digestion and Reproduction, Imperial College London, UK
| | - Elaine Holmes
- Department of Metabolism Digestion and Reproduction, Imperial College London, UK.,Institute of Health Futures, Murdoch University, Perth, WA, Australia
| | - Horace R T Williams
- Department of Metabolism Digestion and Reproduction, Imperial College London, UK.,Department of Gastroenterology, St Mary's Hospital, Imperial College Healthcare NHS Trust, London, UK
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23
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Brown T, Sykes D, Allen AR. Implications of Breast Cancer Chemotherapy-Induced Inflammation on the Gut, Liver, and Central Nervous System. Biomedicines 2021; 9:biomedicines9020189. [PMID: 33668580 PMCID: PMC7917715 DOI: 10.3390/biomedicines9020189] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/10/2021] [Accepted: 02/10/2021] [Indexed: 12/18/2022] Open
Abstract
Breast Cancer is still one of the most common cancers today; however, with advancements in diagnostic and treatment methods, the mortality and survivorship of patients continues to decrease and increase, respectively. Commonly used treatments today consist of drug combinations, such as doxorubicin and cyclophosphamide; docetaxel, doxorubicin, and cyclophosphamide; or doxorubicin, cyclophosphamide, and paclitaxel. Although these combinations are effective at destroying cancer cells, there is still much to be understood about the effects that chemotherapy can have on normal organ systems such as the nervous system, gastrointestinal tract, and the liver. Patients can experience symptoms of cognitive impairments or “chemobrain”, such as difficulty in concentrating, memory recollection, and processing speed. They may also experience gastrointestinal (GI) distress symptoms such as diarrhea and vomiting, as well as hepatotoxicity and long term liver damage. Chemotherapy treatment has also been shown to induce peripheral neuropathy resulting in numbing, pain, and tingling sensations in the extremities of patients. Interestingly, researchers have discovered that this array of symptoms that cancer patients experience are interconnected and mediated by the inflammatory response.
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Affiliation(s)
- Taurean Brown
- Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Neurobiology & Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - DeLawrence Sykes
- Department of Biology, Pomona College, Claremont, CA 91711, USA;
| | - Antiño R. Allen
- Division of Radiation Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
- Department of Pharmaceutical Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Department of Neurobiology & Developmental Sciences, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Correspondence: ; Tel.: +1-501-686-7335
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24
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Zhang Y, Jia Q, Hu C, Han M, Guo Q, Li S, Bo C, Zhang Y, Qi X, Sai L, Peng C. Effects of chlorpyrifos exposure on liver inflammation and intestinal flora structure in mice. Toxicol Res (Camb) 2021; 10:141-149. [PMID: 33613981 DOI: 10.1093/toxres/tfaa108] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/02/2020] [Accepted: 12/07/2020] [Indexed: 12/19/2022] Open
Abstract
Chlorpyrifos (CPF) is an organophosphate insecticide commonly used to treat fruit and vegetable crops. CPF can cause severe adverse effects on body organs including the liver and central nervous system. This study investigated the CPF-induced inflammation in mice and explored the role of intestinal flora changes in liver inflammation. Adult C57BL/6 male mice were exposed to a CPF of 0.01-, 0.1-, 1- and 10-mg/kg bodyweight for 12 weeks. The mice in experimental group given CPF solution dissolved in corn oil vehicle by gavage, was administered by intraoral gavage for 5 days per week for 12 weeks. Histopathological examination and inflammatory factor detection were performed on mice liver tissue. Faeces were used for 16S ribosomal RNA high-throughput sequencing to explore the impact of CPF on intestinal flora structure and diversity. The results showed that 1- and 10-mg/kg CPF caused different degrees of liver focal inflammation. The structure of intestinal flora changed significantly in mice including the decreased beneficial bacteria (Akkermansia, Prevotella and Butyricimonas) and increased pathogenic bacteria (Helicobacter and Desulfovibrio). Meanwhile, the results of Q-RT-PCR showed that there was more total bacterial DNA in the liver tissue of the mice treated with 10-mg/kg groups. In conclusion, the imbalance of intestinal flora, the decreased abundance of beneficial bacteria and the increased abundance of pathogenic bacteria, as well as the increase of total bacterial DNA in the liver tissues, maybe associated with the liver focal inflammation induced by CPF.
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Affiliation(s)
- Yecui Zhang
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China
| | - Qiang Jia
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China
| | - Chenyang Hu
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China
| | - Mingming Han
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China
| | - Qiming Guo
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China
| | - Shumin Li
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China
| | - Cunxiang Bo
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China
| | - Yu Zhang
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China
| | - Xuejie Qi
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China
| | - Linlin Sai
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China
| | - Cheng Peng
- Shandong Academy of Occupational Health and Occupational Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong 250062, China.,Queensland Alliance for Environmental Health Sciences (QAEHS), The University of Queensland, Brisbane, QLD 4102, Australia
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25
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Zhou L, Hao N, Li X, Chen J, Yang R, Song C, Sun Y, Zhang Q. Nattokinase mitigated dextran sulfate sodium-induced chronic colitis by regulating microbiota and suppressing tryptophan metabolism via inhibiting IDO-1. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.104251] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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26
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Wojciech L, Tan KSW, Gascoigne NRJ. Taming the Sentinels: Microbiome-Derived Metabolites and Polarization of T Cells. Int J Mol Sci 2020; 21:E7740. [PMID: 33086747 DOI: 10.3390/ijms21207740] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/27/2020] [Accepted: 10/11/2020] [Indexed: 02/07/2023] Open
Abstract
A global increase in the prevalence of metabolic syndromes and digestive tract disorders, like food allergy or inflammatory bowel disease (IBD), has become a severe problem in the modern world. Recent decades have brought a growing body of evidence that links the gut microbiome’s complexity with host physiology. Hence, understanding the mechanistic aspects underlying the synergy between the host and its associated gut microbiome are among the most crucial questions. The functionally diversified adaptive immune system plays a central role in maintaining gut and systemic immune homeostasis. The character of the reciprocal interactions between immune components and host-dwelling microbes or microbial consortia determines the outcome of the organisms’ coexistence within the holobiont structure. It has become apparent that metabolic by-products of the microbiome constitute crucial multimodal transmitters within the host–microbiome interactome and, as such, contribute to immune homeostasis by fine-tuning of the adaptive arm of immune system. In this review, we will present recent insights and discoveries regarding the broad landscape of microbiome-derived metabolites, highlighting the role of these small compounds in the context of the balance between pro- and anti-inflammatory mechanisms orchestrated by the host T cell compartment.
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27
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Abstract
The pathogenesis of inflammatory bowel disease (IBD) involves perturbation of intestinal immune homeostasis in genetically susceptible individuals. A mutual interplay between intestinal epithelial cells (IECs) and gut resident microbes maintains a homeostatic environment across the gut. An idiopathic gastrointestinal (GI) complication triggers aberrant physiological stress in the epithelium and peripheral myeloid cells, leading to a chronic inflammatory condition. Indeed, events in the endoplasmic reticulum (ER) and mitochondria contribute to orchestrating intracellular mechanisms such as the unfolded protein response (UPR) and oxidative stress, respectively, to resolve aberrant cellular stress. This review highlights the signaling cascades encrypted within ER and mitochondria in IECs and/or myeloid cells to dissipate chronic stress in maintaining intestinal homeostasis.
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