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Zhu H, Hao H, Yu L. Identification of microbe-disease signed associations via multi-scale variational graph autoencoder based on signed message propagation. BMC Biol 2024; 22:172. [PMID: 39148051 PMCID: PMC11328394 DOI: 10.1186/s12915-024-01968-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 08/01/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND Plenty of clinical and biomedical research has unequivocally highlighted the tremendous significance of the human microbiome in relation to human health. Identifying microbes associated with diseases is crucial for early disease diagnosis and advancing precision medicine. RESULTS Considering that the information about changes in microbial quantities under fine-grained disease states helps to enhance a comprehensive understanding of the overall data distribution, this study introduces MSignVGAE, a framework for predicting microbe-disease sign associations using signed message propagation. MSignVGAE employs a graph variational autoencoder to model noisy signed association data and extends the multi-scale concept to enhance representation capabilities. A novel strategy for propagating signed message in signed networks addresses heterogeneity and consistency among nodes connected by signed edges. Additionally, we utilize the idea of denoising autoencoder to handle the noise in similarity feature information, which helps overcome biases in the fused similarity data. MSignVGAE represents microbe-disease associations as a heterogeneous graph using similarity information as node features. The multi-class classifier XGBoost is utilized to predict sign associations between diseases and microbes. CONCLUSIONS MSignVGAE achieves AUROC and AUPR values of 0.9742 and 0.9601, respectively. Case studies on three diseases demonstrate that MSignVGAE can effectively capture a comprehensive distribution of associations by leveraging signed information.
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Affiliation(s)
- Huan Zhu
- School of Computer Science and Technology, Xidian University, Xi'an, China
| | - Hongxia Hao
- School of Computer Science and Technology, Xidian University, Xi'an, China.
| | - Liang Yu
- School of Computer Science and Technology, Xidian University, Xi'an, China.
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Nasreen S, Ali S, Andleeb S, Summer M, Hussain T, Imdad K, Ara C, Tahir HM. Mechanisms of medicinal, pharmaceutical, and immunomodulatory action of probiotics bacteria and their secondary metabolites against disease management: an overview. Folia Microbiol (Praha) 2024; 69:549-565. [PMID: 38532057 DOI: 10.1007/s12223-024-01155-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 03/05/2024] [Indexed: 03/28/2024]
Abstract
Probiotics or bacteriotherapy is today's hot issue for public entities (Food and Agriculture Organization, and World Health Organization) as well as health and food industries since Metchnikoff and his colleagues hypothesized the correlation between probiotic consumption and human's health. They contribute to the newest and highly efficient arena of promising biotherapeutics. These are usually attractive in biomedical applications such as gut-related diseases like irritable bowel disease, diarrhea, gastrointestinal disorders, fungal infections, various allergies, parasitic and bacterial infections, viral diseases, and intestinal inflammation, and are also worth immunomodulation. The useful impact of probiotics is not limited to gut-related diseases alone. Still, these have proven benefits in various acute and chronic infectious diseases, like cancer, human immunodeficiency virus (HIV) diseases, and high serum cholesterol. Recently, different researchers have paid special attention to investigating biomedical applications of probiotics, but consolidated data regarding bacteriotherapy with a detailed mechanistically applied approach is scarce and controversial. The present article reviews the bio-interface of probiotic strains, mainly (i) why the demand for probiotics?, (ii) the current status of probiotics, (iii) an alternative to antibiotics, (iv) the potential applications towards disease management, (v) probiotics and industrialization, and (vi) futuristic approach.
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Affiliation(s)
- Sundas Nasreen
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Shaukat Ali
- Department of Zoology, Government College University, Lahore, 54000, Pakistan.
| | - Saiqa Andleeb
- Department of Zoology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Muhammad Summer
- Department of Zoology, Government College University, Lahore, 54000, Pakistan
| | - Tauqeer Hussain
- Department of Zoology, Government College University, Lahore, 54000, Pakistan
| | - Kaleem Imdad
- Department of Bioscience, COMSATS Institute of Information Technology (CIIT), Islamabad, 45550, Pakistan
| | - Chaman Ara
- Institute of Zoology, University of the Punjab, Lahore, Pakistan
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Lopez VA, Lim JL, Seguin RP, Dempsey JL, Kunzman G, Cui JY, Xu L. Oral Exposure to Benzalkonium Chlorides in Male and Female Mice Reveals Sex-Dependent Alteration of the Gut Microbiome and Bile Acid Profile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593991. [PMID: 38798482 PMCID: PMC11118417 DOI: 10.1101/2024.05.13.593991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Benzalkonium chlorides (BACs) are commonly used disinfectants in a variety of consumer and food-processing settings, and the COVID-19 pandemic has led to increased usage of BACs. The prevalence of BACs raises the concern that BAC exposure could disrupt the gastrointestinal microbiota, thus interfering with the beneficial functions of the microbes. We hypothesize that BAC exposure can alter the gut microbiome diversity and composition, which will disrupt bile acid homeostasis along the gut-liver axis. In this study, male and female mice were exposed orally to d 7 -C12- and d 7 -C16-BACs at 120 µg/g/day for one week. UPLC-MS/MS analysis of liver, blood, and fecal samples of BAC-treated mice demonstrated the absorption and metabolism of BACs. Both parent BACs and their metabolites were detected in all exposed samples. Additionally, 16S rRNA sequencing was carried out on the bacterial DNA isolated from the cecum intestinal content. For female mice, and to a lesser extent in males, we found that treatment with either d 7 -C12- or d 7 -C16-BAC led to decreased alpha diversity and differential composition of gut bacteria with notably decreased actinobacteria phylum. Lastly, through a targeted bile acid quantitation analysis, we observed decreases in secondary bile acids in BAC-treated mice, which was more pronounced in the female mice. This finding is supported by decreases in bacteria known to metabolize primary bile acids into secondary bile acids, such as the families of Ruminococcaceae and Lachnospiraceae. Together, these data signify the potential impact of BACs on human health through disturbance of the gut microbiome and gut-liver interactions.
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Wang X, Cao S, Huang Y, Li L, Xu D, Liu L. Salidroside alleviates cholestasis-induced liver fibrosis by inhibiting hepatic stellate cells via activation of the PI3K/AKT/GSK-3β signaling pathway and regulating intestinal flora distribution. Front Pharmacol 2024; 15:1396023. [PMID: 38808258 PMCID: PMC11130389 DOI: 10.3389/fphar.2024.1396023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/15/2024] [Indexed: 05/30/2024] Open
Abstract
Salidroside (SAL), a phenylpropanoid bioactive compound, has various pharmacological properties, including antioxidant, anti-inflammatory, and hepatoprotective effects. However, the pharmacological effects and mechanisms of action of SAL on cholestatic liver injury are unclear. This study investigated the mechanism and effects of salidroside (SAL) on intestinal flora distribution and hepatic stellate cell (HSC) activation in cholestatic hepatic fibrosis. Bile duct ligation was used to cause cholestasis BALB/c mice. The therapeutic efficacy of SAL in liver fibrosis was assessed via serum/tissue biochemical analyses and liver tissue hematoxylin and eosin and Masson staining. Inflammation and oxidative stress were analyzed using enzyme-linked immunosorbent assay and western blotting. HSC were activated in vitro using lipopolysaccharide, and the effects of SAL on HSC migration and inflammatory factor expression were detected via scratch, transwell, and western blotting assays. The effects of SAL on the PI3K/AKT/GSK-3β pathway in vivo and in vitro were detected using western blotting. 16sRNA sequencing was used to detect the effect of SAL on the diversity of the intestinal flora. Ileal histopathology and western blotting were used to detect the protective effect of SAL on the intestinal mucosal barrier. SAL reduces liver inflammation and oxidative stress and protects against liver fibrosis with cholestasis. It inhibits HSC activation and activates the PI3K/AKT/GSK-3β pathway in vitro and in vivo. Additionally, SAL restores the abundance of intestinal flora, which contributes to the repair of the intestinal mucosal barrier, inhibits endotoxin translocation, and indirectly inhibits HSC activation, reversing the course of cholestatic liver fibrosis. SAL inhibits HSC activation through the PI3K/AKT/GSK-3β pathway and improves intestinal flora distribution, thereby protecting and reversing the progression of hepatic fibrosis.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Cellular Function and Pharmacology of Jilin Province, Yanbian University, Yanji, China
| | - Shuxia Cao
- Key Laboratory of Cellular Function and Pharmacology of Jilin Province, Yanbian University, Yanji, China
| | - Yuan Huang
- Key Laboratory of Cellular Function and Pharmacology of Jilin Province, Yanbian University, Yanji, China
| | - Liangchang Li
- Key Laboratory of Cellular Function and Pharmacology of Jilin Province, Yanbian University, Yanji, China
| | - Dongyuan Xu
- Key Laboratory of Cellular Function and Pharmacology of Jilin Province, Yanbian University, Yanji, China
| | - Lan Liu
- Key Laboratory of Cellular Function and Pharmacology of Jilin Province, Yanbian University, Yanji, China
- Department of Pathology, Yanbian University Hospital, Yanji, China
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Silva-Caso W, Carrillo-Ng H, Aguilar-Luis MA, Tarazona-Castro Y, Valle LJD, Tinco-Valdez C, Palomares-Reyes C, Urteaga N, Bazán-Mayra J, del Valle-Mendoza J. Parasitosis by Fasciola hepatica and Variations in Gut Microbiota in School-Aged Children from Peru. Microorganisms 2024; 12:371. [PMID: 38399775 PMCID: PMC10891680 DOI: 10.3390/microorganisms12020371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
(1) Background: Human fascioliasis is considered an endemic and hyper-endemic disease in the Peruvian Andean valleys. Our objective was to determine variations in the composition of the gut microbiota among children with Fasciola hepatica and children who do not have this parasitosis. (2) Method: A secondary analysis was performed using fecal samples stored in our biobank. The samples were collected as part of an epidemiological Fasciola hepatica cross-sectional study in children from 4 through 14 years old from a community in Cajamarca, Peru. (3) Results: In a comparison of the bacterial genera that make up the intestinal microbiota between the F. hepatica positive and negative groups, it was found that there are significant differences in the determination of Lactobacillus (p = 0.010, CI: 8.5-61.4), Bacteroides (p = 0.020, CI: 18.5-61.4), Clostridium (p < 0.001, CI: 3.5-36.0), and Bifidobacterium (p = 0.018, CI: 1.1-28.3), with each of these genera being less frequent in children parasitized with F. hepatica. (4) Conclusions: These results show that F. hepatica may be associated with direct or indirect changes in the bacterial population of the intestinal microbiota, particularly affecting three bacterial genera.
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Affiliation(s)
- Wilmer Silva-Caso
- Research and Innovation Centre, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima 15023, Peru; (H.C.-N.); (M.A.A.-L.); (Y.T.-C.); (C.T.-V.); (C.P.-R.)
- Instituto de Investigación Nutricional, Lima 15024, Peru
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad Peruana de Ciencias Aplicadas, Lima 15023, Peru
| | - Hugo Carrillo-Ng
- Research and Innovation Centre, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima 15023, Peru; (H.C.-N.); (M.A.A.-L.); (Y.T.-C.); (C.T.-V.); (C.P.-R.)
- Instituto de Investigación Nutricional, Lima 15024, Peru
| | - Miguel Angel Aguilar-Luis
- Research and Innovation Centre, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima 15023, Peru; (H.C.-N.); (M.A.A.-L.); (Y.T.-C.); (C.T.-V.); (C.P.-R.)
- Instituto de Investigación Nutricional, Lima 15024, Peru
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad Peruana de Ciencias Aplicadas, Lima 15023, Peru
| | - Yordi Tarazona-Castro
- Research and Innovation Centre, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima 15023, Peru; (H.C.-N.); (M.A.A.-L.); (Y.T.-C.); (C.T.-V.); (C.P.-R.)
- Instituto de Investigación Nutricional, Lima 15024, Peru
| | - Luis J. Del Valle
- Barcelona Research Center for Multiscale Science and Engineering, Departament d’Enginyeria Química, EEBE, Universitat Politècnica de Catalunya (UPC), 08019 Barcelona, Spain;
| | - Carmen Tinco-Valdez
- Research and Innovation Centre, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima 15023, Peru; (H.C.-N.); (M.A.A.-L.); (Y.T.-C.); (C.T.-V.); (C.P.-R.)
| | - Carlos Palomares-Reyes
- Research and Innovation Centre, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima 15023, Peru; (H.C.-N.); (M.A.A.-L.); (Y.T.-C.); (C.T.-V.); (C.P.-R.)
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad Peruana de Ciencias Aplicadas, Lima 15023, Peru
| | - Numan Urteaga
- Puesto de Salud Callancas, Dirección Regional de Salud Cajamarca (DIRESA), Cajamarca 60101, Peru;
| | - Jorge Bazán-Mayra
- Laboratorio Regional de Cajamarca, Dirección Regional de Salud de Cajamarca (DIRESA), Cajamarca 60101, Peru;
| | - Juana del Valle-Mendoza
- Research and Innovation Centre, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas, Lima 15023, Peru; (H.C.-N.); (M.A.A.-L.); (Y.T.-C.); (C.T.-V.); (C.P.-R.)
- Instituto de Investigación Nutricional, Lima 15024, Peru
- Escuela de Medicina, Facultad de Ciencias de la Salud, Universidad Peruana de Ciencias Aplicadas, Lima 15023, Peru
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Sun C, Zhu D, Zhu Q, He Z, Lou Y, Chen D. The significance of gut microbiota in the etiology of autoimmune hepatitis: a narrative review. Front Cell Infect Microbiol 2024; 14:1337223. [PMID: 38404291 PMCID: PMC10884129 DOI: 10.3389/fcimb.2024.1337223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 01/04/2024] [Indexed: 02/27/2024] Open
Abstract
Autoimmune hepatitis (AIH) is a chronic inflammatory disease of the liver that is mediated by autoimmunity and has complex pathogenesis. Its prevalence has increased globally. Since the liver is the first organ to be exposed to harmful substances, such as gut-derived intestinal microbiota and its metabolites, gut health is closely related to liver health, and the "liver-gut axis" allows abnormalities in the gut microbiota to influence the development of liver-related diseases such as AIH. Changes in the composition of the intestinal microbiota and its resultant disruption of the intestinal barrier and microbial transport are involved in multiple ways in the disruption of immune homeostasis and inflammation, thereby influencing the development of AIH. In terms of the mechanisms involved in immune, the gut microbiota or its metabolites, which is decreased in secondary bile acids, short-chain fatty acids (SCFAs), and polyamines, and increased in lipopolysaccharide (LPS), branched-chain amino acids (BCAA), tryptophan metabolite, amino acid, and bile acid, can disrupt immune homeostasis by activating various immune cells and immune-related signaling pathways, resulting in aberrant activation of the immune system. Clarifying this mechanism has significant clinical implications for the treatment of AIH with drugs that target intestinal microbiota and related signaling pathways. Therefore, this narrative review summarizes the progress in exploring the involvement of gut microbiota in the pathogenesis of AIH, with the aim of helping to improve the precise targeting of therapeutic treatments against AIH for the benefit of clinical AIH treatment.
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Affiliation(s)
- Chen Sun
- Clinical Research Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Dongzi Zhu
- Department of General Surgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Zhu
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zeping He
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yichao Lou
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Desheng Chen
- Department of General Surgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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Chen Z, Zhang L, Li J, Fu M. MLFLHMDA: predicting human microbe-disease association based on multi-view latent feature learning. Front Microbiol 2024; 15:1353278. [PMID: 38371933 PMCID: PMC10869561 DOI: 10.3389/fmicb.2024.1353278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024] Open
Abstract
Introduction A growing body of research indicates that microorganisms play a crucial role in human health. Imbalances in microbial communities are closely linked to human diseases, and identifying potential relationships between microbes and diseases can help elucidate the pathogenesis of diseases. However, traditional methods based on biological or clinical experiments are costly, so the use of computational models to predict potential microbe-disease associations is of great importance. Methods In this paper, we present a novel computational model called MLFLHMDA, which is based on a Multi-View Latent Feature Learning approach to predict Human potential Microbe-Disease Associations. Specifically, we compute Gaussian interaction profile kernel similarity between diseases and microbes based on the known microbe-disease associations from the Human Microbe-Disease Association Database and perform a preprocessing step on the resulting microbe-disease association matrix, namely, weighting K nearest known neighbors (WKNKN) to reduce the sparsity of the microbe-disease association matrix. To obtain unobserved associations in the microbe and disease views, we extract different latent features based on the geometrical structure of microbes and diseases, and project multi-modal latent features into a common subspace. Next, we introduce graph regularization to preserve the local manifold structure of Gaussian interaction profile kernel similarity and add L p , q -norms to the projection matrix to ensure the interpretability and sparsity of the model. Results The AUC values for global leave-one-out cross-validation and 5-fold cross validation implemented by MLFLHMDA are 0.9165 and 0.8942+/-0.0041, respectively, which perform better than other existing methods. In addition, case studies of different diseases have demonstrated the superiority of the predictive power of MLFLHMDA. The source code of our model and the data are available on https://github.com/LiangzheZhang/MLFLHMDA_master.
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Liu Y, Li G, Lu F, Guo Z, Cai S, Huo T. Excess iron intake induced liver injury: The role of gut-liver axis and therapeutic potential. Biomed Pharmacother 2023; 168:115728. [PMID: 37864900 DOI: 10.1016/j.biopha.2023.115728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/23/2023] Open
Abstract
Excessive iron intake is detrimental to human health, especially to the liver, which is the main organ for iron storage. Excessive iron intake can lead to liver injury. The gut-liver axis (GLA) refers to the bidirectional relationship between the gut and its microbiota and the liver, which is a combination of signals generated by dietary, genetic and environmental factors. Excessive iron intake disrupts the GLA at multiple interconnected levels, including the gut microbiota, gut barrier function, and the liver's innate immune system. Excessive iron intake induces gut microbiota dysbiosis, destroys gut barriers, promotes liver exposure to gut microbiota and its derived metabolites, and increases the pro-inflammatory environment of the liver. There is increasing evidence that excess iron intake alters the levels of gut microbiota-derived metabolites such as secondary bile acids (BAs), short-chain fatty acids, indoles, and trimethylamine N-oxide, which play an important role in maintaining homeostasis of the GLA. In addition to iron chelators, antioxidants, and anti-inflammatory agents currently used in iron overload therapy, gut barrier intervention may be a potential target for iron overload therapy. In this paper, we review the relationship between excess iron intake and chronic liver diseases, the regulation of iron homeostasis by the GLA, and focus on the effects of excess iron intake on the GLA. It has been suggested that probiotics, fecal microbiota transfer, farnesoid X receptor agonists, and microRNA may be potential therapeutic targets for iron overload-induced liver injury by protecting gut barrier function.
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Affiliation(s)
- Yu Liu
- Department of Health Laboratory Technology, School of Public Health, China Medical University, Shenyang, Liaoning 110122, China
| | - Guangyan Li
- Department of Health Laboratory Technology, School of Public Health, China Medical University, Shenyang, Liaoning 110122, China
| | - Fayu Lu
- School of Public Health, China Medical University, Shenyang, Liaoning 110122, China
| | - Ziwei Guo
- Department of Health Laboratory Technology, School of Public Health, China Medical University, Shenyang, Liaoning 110122, China
| | - Shuang Cai
- The First Affiliated Hospital of China Medical University, Shenyang 110001, China.
| | - Taoguang Huo
- Key Laboratory of Environmental Stress and Chronic Disease Control and Prevention, Ministry of Education, China Medical University, Shenyang, Liaoning 110122, China; Department of Health Laboratory Technology, School of Public Health, China Medical University, Shenyang, Liaoning 110122, China.
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Habermaass V, Olivero D, Gori E, Mariti C, Longhi E, Marchetti V. Intestinal Microbiome in Dogs with Chronic Hepatobiliary Disease: Can We Talk about the Gut-Liver Axis? Animals (Basel) 2023; 13:3174. [PMID: 37893898 PMCID: PMC10603696 DOI: 10.3390/ani13203174] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
The gut-liver axis represents a current topic in human medicine. Extensive research investigates the gut microbiome (GM) modifications in relation to various kinds of chronic hepatobiliary diseases (CHD), with many mechanisms and therapeutical implications recognized. Those aspects in veterinary medicine are still quite unexplored. The aim of the present study was to evaluate GM in dogs diagnosed with CD. Comparison among CHD dogs were made considering some clinical and biochemical variables (lipemia and alanine-aminotransferase activities), presence of cholestasis or endocrine disorders, diet). Sixty-five dogs were prospectively enrolled with clinical and hematobiochemical evaluation and 16S-RNA GM sequencing assessed. Dogs that received antibiotics and/or pre/pro/symbiotics administration were excluded. Deeper GM alteration was observed between dogs with or without ultrasonographic and biochemical cholestatic CHD. Cholestasis was associated with a decrease in several bacterial taxa, including Clostridium hiranonis, Fusobacterium, Megamonas, Ruminococcus faecis, Turicibacter, and higher levels of Escherichia/Shigella and Serratia. Thus, the alteration in bile flow and composition, typical of cholestasis, may directly affect the local intestinal microbial environment. For the management of dogs with CHD and especially cholestatic CHD, clinicians should be aware that gut-liver interaction may lead to dysbiosis.
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Affiliation(s)
- Verena Habermaass
- Department of Veterinary Sciences, University of Pisa, Via Livornese Lato Monte, 56122 Pisa, Italy; (V.H.); (E.G.); (V.M.)
| | - Daniela Olivero
- Analysis Lab BSA Scilvet, Via A. D’Aosta 7, 20129 Milan, Italy
| | - Eleonora Gori
- Department of Veterinary Sciences, University of Pisa, Via Livornese Lato Monte, 56122 Pisa, Italy; (V.H.); (E.G.); (V.M.)
| | - Chiara Mariti
- Department of Veterinary Sciences, University of Pisa, Via Livornese Lato Monte, 56122 Pisa, Italy; (V.H.); (E.G.); (V.M.)
| | - Erika Longhi
- Analysis Lab Labospace, Via Apelle 41, 20128 Milan, Italy;
| | - Veronica Marchetti
- Department of Veterinary Sciences, University of Pisa, Via Livornese Lato Monte, 56122 Pisa, Italy; (V.H.); (E.G.); (V.M.)
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10
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Peng L, Huang L, Tian G, Wu Y, Li G, Cao J, Wang P, Li Z, Duan L. Predicting potential microbe-disease associations with graph attention autoencoder, positive-unlabeled learning, and deep neural network. Front Microbiol 2023; 14:1244527. [PMID: 37789848 PMCID: PMC10543759 DOI: 10.3389/fmicb.2023.1244527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/16/2023] [Indexed: 10/05/2023] Open
Abstract
Background Microbes have dense linkages with human diseases. Balanced microorganisms protect human body against physiological disorders while unbalanced ones may cause diseases. Thus, identification of potential associations between microbes and diseases can contribute to the diagnosis and therapy of various complex diseases. Biological experiments for microbe-disease association (MDA) prediction are expensive, time-consuming, and labor-intensive. Methods We developed a computational MDA prediction method called GPUDMDA by combining graph attention autoencoder, positive-unlabeled learning, and deep neural network. First, GPUDMDA computes disease similarity and microbe similarity matrices by integrating their functional similarity and Gaussian association profile kernel similarity, respectively. Next, it learns the feature representation of each microbe-disease pair using graph attention autoencoder based on the obtained disease similarity and microbe similarity matrices. Third, it selects a few reliable negative MDAs based on positive-unlabeled learning. Finally, it takes the learned MDA features and the selected negative MDAs as inputs and designed a deep neural network to predict potential MDAs. Results GPUDMDA was compared with four state-of-the-art MDA identification models (i.e., MNNMDA, GATMDA, LRLSHMDA, and NTSHMDA) on the HMDAD and Disbiome databases under five-fold cross validations on microbes, diseases, and microbe-disease pairs. Under the three five-fold cross validations, GPUDMDA computed the best AUCs of 0.7121, 0.9454, and 0.9501 on the HMDAD database and 0.8372, 0.8908, and 0.8948 on the Disbiome database, respectively, outperforming the other four MDA prediction methods. Asthma is the most common chronic respiratory condition and affects ~339 million people worldwide. Inflammatory bowel disease is a class of globally chronic intestinal disease widely existed in the gut and gastrointestinal tract and extraintestinal organs of patients. Particularly, inflammatory bowel disease severely affects the growth and development of children. We used the proposed GPUDMDA method and found that Enterobacter hormaechei had potential associations with both asthma and inflammatory bowel disease and need further biological experimental validation. Conclusion The proposed GPUDMDA demonstrated the powerful MDA prediction ability. We anticipate that GPUDMDA helps screen the therapeutic clues for microbe-related diseases.
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Affiliation(s)
- Lihong Peng
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
- College of Life Sciences and Chemistry, Hunan University of Technology, Zhuzhou, China
| | - Liangliang Huang
- School of Computer Science, Hunan University of Technology, Zhuzhou, China
| | - Geng Tian
- Geneis (Beijing) Co. Ltd., Beijing, China
| | - Yan Wu
- Geneis (Beijing) Co. Ltd., Beijing, China
| | - Guang Li
- Faculty of Pediatrics, The Chinese PLA General Hospital, Beijing, China
- Department of Pediatric Surgery, The Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Jianying Cao
- Faculty of Pediatrics, The Chinese PLA General Hospital, Beijing, China
- Department of Pediatric Surgery, The Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
| | - Peng Wang
- School of Computer Science, Hunan Institute of Technology, Hengyang, China
| | - Zejun Li
- School of Computer Science, Hunan Institute of Technology, Hengyang, China
| | - Lian Duan
- Faculty of Pediatrics, The Chinese PLA General Hospital, Beijing, China
- Department of Pediatric Surgery, The Seventh Medical Center of PLA General Hospital, Beijing, China
- National Engineering Laboratory for Birth Defects Prevention and Control of Key Technology, Beijing, China
- Beijing Key Laboratory of Pediatric Organ Failure, Beijing, China
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11
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Di Fazio P, Mielke S, Böhm IT, Buchholz M, Matrood S, Schuppan D, Wissniowski T. Toll-like receptor 5 tunes hepatic and pancreatic stellate cells activation. BMJ Open Gastroenterol 2023; 10:e001148. [PMID: 37433685 DOI: 10.1136/bmjgast-2023-001148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/21/2023] [Indexed: 07/13/2023] Open
Abstract
OBJECTIVE Stellate cells are responsible for liver and pancreas fibrosis and strictly correlate with tumourigenesis. Although their activation is reversible, an exacerbated signalling triggers chronic fibrosis. Toll-like receptors (TLRs) modulate stellate cells transition. TLR5 transduces the signal deriving by the binding to bacterial flagellin from invading mobile bacteria. DESIGN Human hepatic and pancreatic stellate cells were activated by the administration of transforming growth factor-beta (TGF-β). TLR5 was transiently knocked down by short-interference RNA transfection. Reverse Transcription-quantitativePCR and western blot were performed to analyse the transcript and protein level of TLR5 and the transition players. Fluorescence microscopy was performed to identify these targets in spheroids and in the sections of murine fibrotic liver. RESULTS TGF-β-activated human hepatic and pancreatic stellate cells showed an increase of TLR5 expression. TLR5 knockdown blocked the activation of those stellate cells. Furthermore, TLR5 busted during murine liver fibrosis and co-localised with the inducible Collagen I. Flagellin suppressed TLR5, COL1A1 and ACTA2 expression after the administration of TGF-β. Instead, the antagonist of TLR5 did not block the effect of TGF-β. Wortmannin, a specific AKT inhibitor, induced TLR5 but not COL1A1 and ACTA2 transcript and protein level. CONCLUSION TGF-β-mediated activation of hepatic and pancreatic stellate cells requires the over-expression of TLR5. Instead, its autonomous signalling inhibits the activation of the stellate cells, thus prompting a signalling through different regulatory pathways.
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Affiliation(s)
- Pietro Di Fazio
- Department of Visceral Thoracic and Vascular Surgery, Philipps-Universität Marburg, Marburg, Germany
| | - Sophia Mielke
- Department of Visceral Thoracic and Vascular Surgery, Philipps-Universität Marburg, Marburg, Germany
| | - Isabell T Böhm
- Department of Visceral Thoracic and Vascular Surgery, Philipps-Universität Marburg, Marburg, Germany
| | - Malte Buchholz
- Department of Gastroenterology, Philipps-Universität Marburg, Marburg, Germany
| | - Sami Matrood
- Department of Visceral Thoracic and Vascular Surgery, Philipps-Universität Marburg, Marburg, Germany
| | - Detlef Schuppan
- Institute of Translational Immunology, Johannes Gutenberg Universitat Mainz, Mainz, Germany
- Division of Gastroenterology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
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12
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Deng Q, Wang W, Zhang L, Chen L, Zhang Q, Zhang Y, He S, Li J. Gougunao tea polysaccharides ameliorate high-fat diet-induced hyperlipidemia and modulate gut microbiota. Food Funct 2023; 14:703-719. [PMID: 36511170 DOI: 10.1039/d2fo01828d] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Many natural polysaccharides have been proven to have ameliorative effects on high-fat diet-induced hyperlipidemia with fewer side effects. However, similar data on Gougunao tea polysaccharides remain obscure. In this study, we aimed to investigate the role of Gougunao tea polysaccharides (GTP40) in the alleviation of hyperlipidemia and regulation of gut microbiota in C57BL/6J mice induced by a high-fat diet. The results indicated that GTP40 intervention inhibited the abnormal growth of body weight and the excessive accumulation of lipid droplets in the livers and ameliorated the biochemical parameters of serum/liver related to lipid metabolism in hyperlipidemia mice. The elevated levels of antioxidant enzyme and anti-inflammation cytokine in serum, as well as the up-regulating anti-inflammation gene in the liver, reflected that GTP40 might mitigate the oxidative and inflammatory stress induced by a high-fat diet. In addition, GTP40 could modulate the composition, abundance, and diversity of gut microbiota in hyperlipidemia mice. Besides, Spearman's correlation analysis implied that GTP40 intervention could enrich beneficial bacteria (e.g., Akkermansia, Bacteroides, Roseburia, and Alistipes), and decrease harmful bacteria (e.g., Blautia, Faecalibaculum, Streptococcus, and norank_f_Desulfovibrionaceae), which were correlated with the lipid metabolic parameters associated with hyperlipidemia. Moreover, it also indicated that there was a significant correlation between gut microbiota and SCFAs. Thus, GTP40 may be a novel strategy against fat accumulation, oxidative stress, and inflammation, as well as restoring the normal microbial balance of the gut in hyperlipidemia mice.
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Affiliation(s)
- Qihuan Deng
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Wenjun Wang
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Lieyuan Zhang
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China. .,Technical Center of Nanchang Customs, Nanchang 330038, China
| | - Lingli Chen
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Qingfeng Zhang
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Ying Zhang
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Sichen He
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China.
| | - Jingen Li
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang 330045, China.
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13
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Protective Effects of Clinacanthus nutans (Burm.f.) Lindau Aqueous Extract on HBV Mouse Model by Modulating Gut Microbiota and Liver Metabolomics. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2023; 2023:5625222. [PMID: 36636608 PMCID: PMC9831714 DOI: 10.1155/2023/5625222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/04/2022] [Accepted: 12/13/2022] [Indexed: 01/14/2023]
Abstract
Background Clinacanthus nutans (Burm.f.) Lindau (C. nutans) has been used in the therapy of hepatitis B (HB) and is effective; however, the mechanism of action has not been elucidated. Objective To investigate the protective effects of C. nutans aqueous extract on the hepatitis B virus (HBV) mouse model based on correlation analysis between gut microbiota and liver metabolomics. Materials and Methods We firstly constructed the animal model by high-pressure injection of pcDNA3.1(+)/HBV plasmid into the tail vein and treated it with C. nutans. The biomarkers and inflammatory cytokines of HB were detected by enzyme-linked immunosorbent assay and quantitative PCR; the Illumina-MiSeq platform was used for investigating gut microbiota; the LC-MS/MS method was utilized on screening liver tissue metabolites; multiomics joint analysis was performed using the R program. Results Compared with the modeling group, C. nutans significantly decreased the expression levels of HBsAg, IL-1β, TNF-α(P < 0.05) in the serum, and cccDNA (P < 0.05) in the liver tissues of mice. C. nutans dramatically reduced the ratio of Firmicutes and Bacteroidetes (P < 0.05) and significantly declined the proportion of Lactobacillaceae and Lactobacillus(P < 0.05), dramatically increasing the relative abundance of Bacteroidales_S24-7_group, Rikenellaceae, and Alistipes(P < 0.05); LC-MS/MS analysis results showed that C. nutans dramatically upregulate hippuric acid, L-histidine, trehalose, D-threitol, and stachyose and downregulate uridine 5'-diphosphate, cholic acid, trimethylamine N-oxide, CDP-ethanolamine, and phosphorylcholine (P < 0.05). The correlation analysis revealed that C. nutans affects the related metabolite levels of hippuric acid and cholic acid through the modulation of crucial bacteria (Alistipes) (P < 0.01), exerting specific anti-inflammatory effects. Conclusion These results suggest that C. nutans exerts protective effects in HBV model mice, showing the therapeutic potential for anti-HBV infection.
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14
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Apoptotic biliary epithelial cells and gut dysbiosis in the induction of murine primary biliary cholangitis. J Transl Autoimmun 2022; 6:100182. [PMID: 36619656 PMCID: PMC9811212 DOI: 10.1016/j.jtauto.2022.100182] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Primary biliary cholangitis (PBC) is a female-predominant liver autoimmune disease characterized by the specific immune-mediated destruction of the intrahepatic small bile duct. Although apoptosis of biliary epithelial cells (BECs) and alterations in gut microbiota are observed in patients with PBC, it is still unclear whether these events happen in the early stage and cause the breakdown of tolerance in PBC. In this study, we examined the early events in the loss of tolerance in our well-defined 2-OA-OVA-induced murine autoimmune cholangitis (AIC) model. We report herein that apoptosis of BECs was notable in the early stage of murine AIC. An altered gut microbiota, in particular, an increased percentage of gram-positive Firmicutes in AIC mice was also observed. BECs in AIC mice expressed adhesion molecule ICAM-1, cytokines/chemokines TNF-α, CCL2, CXCL9, CXCL10, and toll-like receptor (TLR) 2. Moreover, BECs treated with TLR2 ligand had elevated apoptosis and CXCL10 production. These data collectively suggest a new mechanism of tolerance breakdown in AIC. Altered gut microbiota induces apoptosis of BECs through TLR2 signaling. BECs secrete chemokines to recruit CD8 T cells to damage BECs further.
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15
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Ozlu T, Yilmaz Y, Gunes FE. The effects of dietary intervention on fibrosis and biochemical parameters in metabolic-associated fatty liver disease. Minerva Gastroenterol (Torino) 2022; 68:426-433. [PMID: 33829726 DOI: 10.23736/s2724-5985.21.02809-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND Metabolic-associated fatty liver disease (MAFLD) affects nearly one quarter of the world's adult population creating large health loads and economic loads in society with no approved pharmacotherapy found yet. The number of studies showing the effect of nutrition on fibrosis accompanying MAFLD are insufficient. This study was planned with the aim of investigating the effect of nutritional treatment on liver injury. METHODS This research is a prospective, non-medication interventional study completed with 39 participants chosen from MAFLD patients with fibrosis. Post-treatment lasted three months, patients had liver stiffness measurements (LSM), anthropometric measurements and biochemical tests repeated. RESULTS In pre- and post-treatment, there were statistically significant correlations found between LSM with serum gamma glutamyl transferase (GGT) values, and between controlled attenuation parameter (CAP) with Body Mass Index (BMI) and fat mass (P<0.05). Post-treatment, statistically significant improvements were determined in the anthropometric measurements and biochemical findings. Moreover, post-treatment LSM and CAP values showed significant positive correlation compared to pretreatment (P<0.05). CONCLUSIONS This study found dietary interventions have an important place within the scope of fibrosis treatment. Preparation and application of medical nutrition treatment suitable for the clinical features of patients and completing correct lifestyle changes has an ameliorating effect on disease prognosis. There is a need for advanced studies with larger sample groups to further enlighten this topic.
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Affiliation(s)
- Tugce Ozlu
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Bahcesehir University, Istanbul, Turkey -
| | - Yusuf Yilmaz
- Department of Gastroenterology, School of Medicine, Marmara University, Istanbul, Turkey.,Liver Research Unit, Institute of Gastroenterology, Marmara University, Istanbul, Turkey
| | - Fatma E Gunes
- Department of Nutrition and Dietetics, Faculty of Health Sciences, Marmara University, Istanbul, Turkey
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16
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Polyphenol-Rich Liupao Tea Extract Prevents High-Fat Diet-Induced MAFLD by Modulating the Gut Microbiota. Nutrients 2022; 14:nu14224930. [PMID: 36432617 PMCID: PMC9697786 DOI: 10.3390/nu14224930] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
The modulation of gut microbiota dysbiosis might regulate the progression of metabolic-associated fatty liver disease (MAFLD). Here, we found that polyphenol-rich Liupao tea extract (PLE) prevents high-fat diet (HFD)-induced MAFLD in ApoE-/- male mice accompanied by protection of the intestinal barrier and downregulation of lipopolysaccharide (LPS)-related Toll-like receptor 4 (TLR4)-myeloid differentiation primary response 88 (MyD88) signaling in the liver. Fecal microbiome transplantation (FMT) from PLE-and-HFD-treated mice delayed MAFLD development significantly compared with FMT from HFD-treated mice. In this case, 16S rRNA gene sequencing revealed that Rikenellaceae and Odoribacter were significantly enriched and that Helicobacter was significantly decreased in not only the HFD+PLE group but also the HFD+PLE-FMT group. Furthermore, the level of 3-sulfodeoxycholic acid was significantly decreased in the HFD+PLE-FMT group compared with the HFD-FMT group. In conclusion, our data demonstrate that PLE could modulate the MAFLD phenotype in mice and that this effect is partly mediated through modulation of the gut microbiota.
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17
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Liu D, Liu J, Luo Y, He Q, Deng L. MGATMDA: Predicting Microbe-Disease Associations via Multi-Component Graph Attention Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3578-3585. [PMID: 34587092 DOI: 10.1109/tcbb.2021.3116318] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Microbes are parasitic in various human body organs and play significant roles in a wide range of diseases. Identifying microbe-disease associations is conducive to the identification of potential drug targets. Considering the high cost and risk of biological experiments, developing computational approaches to explore the relationship between microbes and diseases is an alternative choice. However, most existing methods are based on unreliable or noisy similarity, and the prediction accuracy could be affected. Besides, it is still a great challenge for most previous methods to make predictions for the large-scale dataset. In this work, we develop a multi-component Graph Attention Network (GAT) based framework, termed MGATMDA, for predicting microbe-disease associations. MGATMDA is built on a bipartite graph of microbes and diseases. It contains three essential parts: decomposer, combiner, and predictor. The decomposer first decomposes the edges in the bipartite graph to identify the latent components by node-level attention mechanism. The combiner then recombines these latent components automatically to obtain unified embedding for prediction by component-level attention mechanism. Finally, a fully connected network is used to predict unknown microbes-disease associations. Experimental results showed that our proposed method outperformed eight state-of-the-art methods. Case studies for two common diseases further demonstrated the effectiveness of MGATMDA in predicting potential microbe-disease associations. The codes are available at Github https://github.com/dayunliu/MGATMDA.
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18
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Li X, Wang Y, Zhang J, Lu G, You Y, Wang Y, Sun H, Nan B, Wang Y. The effect of Lactobacillus rhamnosus B10 on alcoholic liver injury and intestinal microbiota in alcohol-induced mice model. J Food Biochem 2022; 46:e14372. [PMID: 35929524 DOI: 10.1111/jfbc.14372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 06/22/2022] [Accepted: 07/22/2022] [Indexed: 11/28/2022]
Abstract
Lactobacillus rhamnosus B10 (L. rhamnosus B10) isolated from the baby feces was given to an alcohol mice model, aiming to investigate the effects of L. rhamnosus B10 on alcoholic liver injury by regulating intestinal microbiota. C57BL/6N mice were fed with liquid diet Lieber-DeCarli with or without 5% (v/v) ethanol for 8 weeks, and treated with L. rhamnosus B10 at the last 2 weeks. The results showed that L. rhamnosus B10 decreased the serum total cholesterol (1.48 mmol/L), triglycerides (0.97 mmol/L), alanine aminotransferase (26.4 U/L), aspartate aminotransferase (14.2 U/L), lipopolysaccharide (0.23 EU/mL), and tumor necrosis factor-α (138 pg/mL). In addition, L. rhamnosus B10 also reduced the liver triglycerides (1.02 mmol/g prot), alanine aminotransferase (17.8 mmol/g prot) and aspartate aminotransferase (12.5 mmol/g prot) in alcohol mice, thereby ameliorating alcohol-induced liver injury. The changes of intestinal microbiota composition on class, family and genus level in cecum were analyzed. The intestinal symbiotic abundance of Firmicutes was elevated while gram-negative bacteria Proteobacteria and Deferribacteres was decreased in alcohol mice treated with L. rhamnosus B10 for 2 weeks. In summary, this study provided evidence for the therapeutic effects of probiotics on alcoholic liver injury by regulating intestinal flora.
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Affiliation(s)
- Xia Li
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China.,National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China.,National Processing Laboratory for Soybean Industry and Technology, Changchun, China
| | - Yushan Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China.,National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China
| | - Jun Zhang
- Changchun Shengjinnuo Biological Pharmaceutical Co., Ltd, Changchun, China
| | - Guijiao Lu
- Jilin Correction Health Co., Ltd, Changchun, China
| | - Ying You
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China.,National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China.,National Processing Laboratory for Soybean Industry and Technology, Changchun, China
| | - Yu Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China.,National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China.,National Processing Laboratory for Soybean Industry and Technology, Changchun, China
| | - Haiyue Sun
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China.,National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China.,National Processing Laboratory for Soybean Industry and Technology, Changchun, China
| | - Bo Nan
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China.,National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China.,National Processing Laboratory for Soybean Industry and Technology, Changchun, China
| | - Yuhua Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China.,National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China.,National Processing Laboratory for Soybean Industry and Technology, Changchun, China
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19
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Wang Y, Yu Y, Ding L, Xu P, Zhou J. Matcha green tea targets the gut-liver axis to alleviate obesity and metabolic disorders induced by a high-fat diet. Front Nutr 2022; 9:931060. [PMID: 35978960 PMCID: PMC9376390 DOI: 10.3389/fnut.2022.931060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Obesity induced by a high-fat diet (HFD) is an increasing global health problem, leading to many metabolic syndromes. As the emerging food additive rich in tea polyphenols, theanine, caffeine, and so on, matcha green tea has gained more and more popularity for its outstanding potential in ameliorating metabolic disorders. This study investigated the composition and antioxidant activity of matcha green tea and further explored its effects on gut-liver axis homeostasis in an HFD-induced obese mouse model. Male (7-8 weeks old) C57BL/6J mice were divided into four groups with the following dietary supplementation for 8 weeks: a normal chow diet (NCD), a normal chow diet+1.0% matcha (NCM), a high-fat diet (HFD), and a high-fat diet+1.0% matcha (HFM). The results demonstrated that matcha green tea ameliorated the development of obesity, lipid accumulation, and hepatic steatosis induced by HFD. Subsequently, dietary matcha supplementation restored the alterations in fecal bile acid profile and gut microbial composition. Meanwhile, the levels of mRNA expression in hepatocytes demonstrated that matcha intervention made significant regulatory on the multiple metabolic pathways of hosts involved in glucose, lipid, and bile acid metabolism. These findings present new evidence for matcha green tea as an effective nutritional strategy to mitigate obesity and relevant metabolic disorders through the gut-liver axis.
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Affiliation(s)
| | | | | | | | - Jihong Zhou
- Tea Research Institute, Zhejiang University, Hangzhou, China
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20
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Centa M, Weinstein EG, Clemente JC, Faith JJ, Fiel MI, Lyallpuri R, Herbin O, Alexandropoulos K. Impaired central tolerance induces changes in the gut microbiota that exacerbate autoimmune hepatitis. J Autoimmun 2022; 128:102808. [PMID: 35276587 PMCID: PMC8963681 DOI: 10.1016/j.jaut.2022.102808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/10/2022] [Accepted: 02/19/2022] [Indexed: 12/18/2022]
Abstract
Medullary thymic epithelial cells (mTECs) induce T cell tolerance in the thymus through the elimination of self-reactive thymocytes. Commensal bacteria are also critical for shaping T cell responses in the gut and distal organs. We previously showed that mice depleted of mTECs (Traf6ΔTEC) generated autoreactive T cells and developed autoimmune hepatitis (AIH). In this report, we found that Toll-like receptor (TLR)-mediated microbial sensing on liver hematopoietic cells and the gut microbiota contributed to AIH development in Traf6ΔTEC mice. While adoptive transfer of thymic Traf6ΔTEC T cells in immune-deficient mice was sufficient for AIH development, colonization of germ-free mice with Traf6ΔTEC microbiota failed to induce AIH, suggesting that the gut microbiota contributes to but is not sufficient for AIH development. Microbiota-mediated exacerbation of AIH associated with increased numbers of hepatic Foxp3+ T cells and their increase was proportional to the degree of inflammation. The contribution of the gut microbiota to AIH development associated with an altered microbial signature whose composition was influenced by the qualitative nature of the thymic T cell compartment. These results suggest that aberrant selection of T cells in the thymus can induce changes in the gut microbiota that lead to exacerbation of organ-specific autoimmunity and AIH. Our results add to our understanding of the mechanisms of AIH development and create a platform towards developing novel therapeutic approaches for treating this disease.
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Affiliation(s)
- Monica Centa
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Jose C Clemente
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremiah J Faith
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Isabel Fiel
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Robby Lyallpuri
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Konstantina Alexandropoulos
- Department of Medicine, Division of Clinical Immunology, Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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21
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Tsay CJ, Lim JK. NASH and the Gut Microbiome: Implications for New Therapies. Clin Liver Dis (Hoboken) 2022; 19:97-100. [PMID: 35355843 PMCID: PMC8958237 DOI: 10.1002/cld.1170] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/10/2021] [Accepted: 09/22/2021] [Indexed: 02/04/2023] Open
Abstract
Content available: Author Audio Recording.
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Affiliation(s)
| | - Joseph K. Lim
- Yale Liver Center and Section of Digestive DiseasesYale UniversityNew HavenCT
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22
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Mendiola PJ, Naik JS, Gonzalez Bosc LV, Gardiner AS, Birg A, Kanagy NL. Hydrogen Sulfide Actions in the Vasculature. Compr Physiol 2021; 11:2467-2488. [PMID: 34558672 DOI: 10.1002/cphy.c200036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Hydrogen sulfide (H2 S) is a small, gaseous molecule with poor solubility in water that is generated by multiple pathways in many species including humans. It acts as a signaling molecule in many tissues with both beneficial and pathological effects. This article discusses its many actions in the vascular system and the growing evidence of its role to regulate vascular tone, angiogenesis, endothelial barrier function, redox, and inflammation. Alterations in some disease states are also discussed including potential roles in promoting tumor growth and contributions to the development of metabolic disease. © 2021 American Physiological Society. Compr Physiol 11:1-22, 2021.
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Affiliation(s)
| | - Jay S Naik
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | | | - Amy S Gardiner
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Aleksandr Birg
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Nancy L Kanagy
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
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23
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Liu L, Wang Y, Zhang J, Wang C, Li Y, Dai W, Piao C, Liu J, Yu H, Li X, Wang Y, Liu J. Probiotics in treating with alcoholic liver disease and nonalcoholic fatty liver disease. FOOD REVIEWS INTERNATIONAL 2021. [DOI: 10.1080/87559129.2021.1967380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lingchong Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
- College of Life Science, Changchun Sci-Tech University, Changchun, China
| | - Yu Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Jing Zhang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Chao Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Youbao Li
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, National Processing Laboratory for Soybean Industry and Technology, Changchun, China
- Department of Food Science and Engineering, National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China
| | - Weichang Dai
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, National Processing Laboratory for Soybean Industry and Technology, Changchun, China
- Department of Food Science and Engineering, National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China
| | - Chunhong Piao
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, National Processing Laboratory for Soybean Industry and Technology, Changchun, China
- Department of Food Science and Engineering, National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China
| | - Junmei Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, National Processing Laboratory for Soybean Industry and Technology, Changchun, China
- Department of Food Science and Engineering, National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China
| | - Hansong Yu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, National Processing Laboratory for Soybean Industry and Technology, Changchun, China
- Department of Food Science and Engineering, National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China
| | - Xia Li
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, National Processing Laboratory for Soybean Industry and Technology, Changchun, China
- Department of Food Science and Engineering, National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China
| | - Yuhua Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, National Processing Laboratory for Soybean Industry and Technology, Changchun, China
- Department of Food Science and Engineering, National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China
| | - Jingsheng Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
- Department of Food Science and Engineering, National Processing Laboratory for Soybean Industry and Technology, Changchun, China
- Department of Food Science and Engineering, National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China
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Liu Y, Wang SL, Zhang JF, Zhang W, Zhou S, Li W. DMFMDA: Prediction of Microbe-Disease Associations Based on Deep Matrix Factorization Using Bayesian Personalized Ranking. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:1763-1772. [PMID: 32816678 DOI: 10.1109/tcbb.2020.3018138] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Identifying the microbe-disease associations is conducive to understanding the pathogenesis of disease from the perspective of microbe. In this paper, we propose a deep matrix factorization prediction model (DMFMDA) based on deep neural network. First, the disease one-hot encoding is fed into neural network, which is transformed into a low-dimensional dense vector in implicit semantic space via embedding layer, and so is microbe. Then, matrix factorization is realized by neural network with embedding layer. Furthermore, our model synthesizes the non-linear modeling advantages of multi-layer perceptron based on the linear modeling advantages of matrix factorization. Finally, different from other methods using square error loss function, Bayesian Personalized Ranking optimizes the model from a ranking perspective to obtain the optimal model parameters, which makes full use of the unobserved data. Experiments show that DMFMDA reaches average AUCs of 0.9091 and 0.9103 in the framework of 5-fold cross validation and Leave-one-out cross validation, which is superior to three the-state-of-art methods. In case studies, 10, 9 and 9 out of top-10 candidate microbes are verified by recently published literature for asthma, inflammatory bowel disease and colon cancer, respectively. In conclusion, DMFMDA is successful application of deep learning in the prediction of microbe-disease association.
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Birg A, Lin HC, Kanagy N. Portal Venous Flow Is Increased by Jejunal but Not Colonic Hydrogen Sulfide in a Nitric Oxide-Dependent Fashion in Rats. Dig Dis Sci 2021; 66:2661-2668. [PMID: 32918175 PMCID: PMC8022870 DOI: 10.1007/s10620-020-06597-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/29/2020] [Indexed: 12/09/2022]
Abstract
Hydrogen sulfide (H2S) is a recently discerned endogenous signaling molecule that modulates the vascular system. Endogenous hydrogen sulfide has been shown to dilate both the mesenteric and portal vasculature. Gut microbiome, via sulfur reducing bacteria, is another source of H2S production within the gut lumen; this source of H2S is primarily produced and detoxified in the colon under physiologic conditions. Nitric oxide (NO), a major endogenous vasodilator in the portal circulation, participates in H2S-induced vasodilation in some vascular beds. We hypothesize that jejunal but not colonic H2S increases portal vein flow in a NO-dependent fashion. To evaluate the effects of luminal H2S, venous blood flow, portal venous pressure, and systemic venous pressure were measured in rats after administration of either vehicle or an H2S donor (NaHS) into the jejunum or the colon. We found that portal venous pressure and systemic pressure did not change and were similar between the three study groups. However, portal venous blood flow significantly increased following jejunal administration of NaHS but not in response to colonic NaHS or vehicle administration. To test the contribution of NO production to this response, another group of animals was treated with either an NO synthase inhibitor (N-Ω-nitro-L-arginine, L-NNA) or saline prior to jejunal NaHS infusion. After L-NNA pretreatment, NaHS caused a significant fall rather than increase in portal venous flow compared to saline pretreatment. These data demonstrate that H2S within the small intestine significantly increases portal venous blood flow in a NO-dependent fashion.
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Affiliation(s)
- Aleksandr Birg
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, MSC10-5550, 1 University of New Mexico, Albuquerque, NM, 87131, USA.
| | - Henry C Lin
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, MSC10-5550, 1 University of New Mexico, Albuquerque, NM, 87131, USA
- New Mexico VA Health Care System, Albuquerque, NM, 87108, USA
| | - Nancy Kanagy
- Department of Cell Biology and Physiology, University of New Mexico, Albuquerque, NM, 87131, USA
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[Characteristics of gut microbiota and its association with the activity of β-glucuronidase in neonates with hyperbilirubinemia]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2021; 23. [PMID: 34266523 PMCID: PMC8292660 DOI: 10.7499/j.issn.1008-8830.2102039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To study the characteristics of gut microbiota and its association with the activity of β-glucuronidase (β-GD) in neonates with hyperbilirubinemia. METHODS A total of 50 neonates with hyperbilirubinemia who were admitted in January to December, 2018, were enrolled as the hyperbilirubinemia group, and 30 neonates without hyperbilirubinemia were enrolled as the control group. The 16S rRNA high-throughput sequencing method was used to compare gut microbiota between the two groups. The phenolphthalein-glucuronic acid substrate method was used to measure the activity of β-GD in the intestinal tract of neonates with hyperbilirubinemia before and after treatment. RESULTS The comparison of the distribution of gut microbiota at the genus level showed a significant difference in the abundance of 52 bacteria between the hyperbilirubinemia and control groups before treatment (P < 0.05), as well as a significant difference in the abundance of 42 bacteria between the hyperbilirubinemia group on day 3 after treatment and the control group on day 3 after enrollment (P < 0.05). After treatment, the hyperbilirubinemia group had significant reductions in the content of Escherichia and Staphylococcus in the intestinal tract (P < 0.05) and the activity of β-GD in feces (P < 0.05). The activity of β-GD in feces was positively correlated with the abundance of Staphylococcus and Escherichia before and after treatment in the neonates with hyperbilirubinemia (rs=0.5948-0.7245, P < 0.01). CONCLUSIONS There are differences in gut microbiota between the neonates with hyperbilirubinemia and those without hyperbilirubinemia. The activity of β-GD in feces is positively correlated with the abundance of Staphylococcus and Escherichia in neonates with hyperbilirubinemia. Gut microbiota may affect the development of neonatal hyperbilirubinemia by regulating the activity of β-GD. The determination and analysis of gut microbiota and β-GD activity may have certain clinical significance for the early assessment of the development of neonatal hyperbilirubinemia.
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Mu J, Tan F, Zhou X, Zhao X. Lactobacillus fermentum CQPC06 in naturally fermented pickles prevents non-alcoholic fatty liver disease by stabilizing the gut-liver axis in mice. Food Funct 2021; 11:8707-8723. [PMID: 32945305 DOI: 10.1039/d0fo01823f] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Herein, we used a HFD/F to induce NAFLD in mice and intervened with CQPC06 to determine the preventive effect of CQPC06 on NAFLD and its potential regulatory mechanism. C57BL/6J mice were fed with LFD, HFD/F, HFD/F supplemented with CQPC06, and HFD/F supplemented with LDBS for 8 weeks to test the properties of the probiotic. Biochemical and molecular biology methods were used to determine the levels of related indexes in mouse serum, liver tissue, epididymal fat, small intestine tissue, and feces. The results showed that CQPC06 exhibited satisfactory probiotic properties, significantly inhibited mouse weight gain, and decreased the liver index and serum lipid levels, including ALT, AKP, AST, TC, TG, LDL-C, LPS, and HDL-C levels. The HOMA-IR index calculated based on the blood glucose levels and serum insulin levels showed that the HOMA-IR index of NAFLD mice treated with CQPC06 significantly decreased. From the molecular biology level, CQPC06 significantly increased the mRNA and protein expression of PPAR-α, CYP7A1, CPT1, and LPL in NAFLD mouse livers, and decreased the expression of PPAR-γ and C/EBP-α. Furthermore, CQPC06 enhanced the expression of ZO-1, occludin, and claudin-1 in the small intestine of NAFLD mice, and decreased the expression of CD36. CQPC06 decreased the level of Firmicutes and increased the levels of Bacteroides and Akkermansia in the feces of NAFLD mice, and the ratio of Firmicutes/Bacteroides was significantly decreased. CQPC06 is highly resistant in vitro and survived in the gastrointestinal tract and exerted its probiotic effect, altered the intestinal microecology of NAFLD mice, and played an important role in NAFLD prevention through the unique anatomical advantages of the gut-liver axis. There was a clear preventive effect with high concentrations of CQPC06 and it was stronger than that of l-carnitine.
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Affiliation(s)
- Jianfei Mu
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing 400067, China. and Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing 400067, China and Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing 400067, China and College of Food Science, Southwest University, Chongqing 400715, China
| | - Fang Tan
- Department of Public Health, Our Lady of Fatima University, Valenzuela 838, Philippines
| | - Xianrong Zhou
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing 400067, China. and Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing 400067, China and Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing 400067, China
| | - Xin Zhao
- Chongqing Collaborative Innovation Center for Functional Food, Chongqing University of Education, Chongqing 400067, China. and Chongqing Engineering Research Center of Functional Food, Chongqing University of Education, Chongqing 400067, China and Chongqing Engineering Laboratory for Research and Development of Functional Food, Chongqing University of Education, Chongqing 400067, China
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Hintikka J, Lensu S, Mäkinen E, Karvinen S, Honkanen M, Lindén J, Garrels T, Pekkala S, Lahti L. Xylo-Oligosaccharides in Prevention of Hepatic Steatosis and Adipose Tissue Inflammation: Associating Taxonomic and Metabolomic Patterns in Fecal Microbiomes with Biclustering. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:4049. [PMID: 33921370 PMCID: PMC8068902 DOI: 10.3390/ijerph18084049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/26/2021] [Accepted: 04/08/2021] [Indexed: 12/15/2022]
Abstract
We have shown that prebiotic xylo-oligosaccharides (XOS) increased beneficial gut microbiota (GM) and prevented high fat diet-induced hepatic steatosis, but the mechanisms associated with these effects are not clear. We studied whether XOS affects adipose tissue inflammation and insulin signaling, and whether the GM and fecal metabolome explain associated patterns. XOS was supplemented or not with high (HFD) or low (LFD) fat diet for 12 weeks in male Wistar rats (n = 10/group). Previously analyzed GM and fecal metabolites were biclustered to reduce data dimensionality and identify interpretable groups of co-occurring genera and metabolites. Based on our findings, biclustering provides a useful algorithmic method for capturing such joint signatures. On the HFD, XOS-supplemented rats showed lower number of adipose tissue crown-like structures, increased phosphorylation of AKT in liver and adipose tissue as well as lower expression of hepatic miRNAs. XOS-supplemented rats had more fecal glycine and less hypoxanthine, isovalerate, branched chain amino acids and aromatic amino acids. Several bacterial genera were associated with the metabolic signatures. In conclusion, the beneficial effects of XOS on hepatic steatosis involved decreased adipose tissue inflammation and likely improved insulin signaling, which were further associated with fecal metabolites and GM.
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Affiliation(s)
- Jukka Hintikka
- Faculty of Sport and Health Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland; (S.L.); (E.M.); (S.K.); (M.H.); (S.P.)
| | - Sanna Lensu
- Faculty of Sport and Health Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland; (S.L.); (E.M.); (S.K.); (M.H.); (S.P.)
- Department of Psychology, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Elina Mäkinen
- Faculty of Sport and Health Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland; (S.L.); (E.M.); (S.K.); (M.H.); (S.P.)
| | - Sira Karvinen
- Faculty of Sport and Health Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland; (S.L.); (E.M.); (S.K.); (M.H.); (S.P.)
| | - Marjaana Honkanen
- Faculty of Sport and Health Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland; (S.L.); (E.M.); (S.K.); (M.H.); (S.P.)
| | - Jere Lindén
- Veterinary Pathology and Parasitology and Finnish Centre for Laboratory Animal Pathology/HiLIFE, University of Helsinki, FIN-00014 Helsinki, Finland;
| | - Tim Garrels
- Department of Computing, University of Turku, FI-20014 Turku, Finland; (T.G.); (L.L.)
| | - Satu Pekkala
- Faculty of Sport and Health Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland; (S.L.); (E.M.); (S.K.); (M.H.); (S.P.)
- Department of Clinical Microbiology, Turku University Hospital, FI-20521 Turku, Finland
| | - Leo Lahti
- Department of Computing, University of Turku, FI-20014 Turku, Finland; (T.G.); (L.L.)
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Barbuti RC, Schiavon LL, Oliveira CP, Alvares-DA-Silva MR, Sassaki LY, Passos MDCF, Farias AQ, Barros LL, Barreto BP, Albuquerque GBDMLD, Alves AM, Navarro-Rodriguez T, Bittencourt PL. GUT MICROBIOTA, PREBIOTICS, PROBIOTICS, AND SYNBIOTICS IN GASTROINTESTINAL AND LIVER DISEASES: PROCEEDINGS OF A JOINT MEETING OF THE BRAZILIAN SOCIETY OF HEPATOLOGY (SBH), BRAZILIAN NUCLEUS FOR THE STUDY OF HELICOBACTER PYLORI AND MICROBIOTA (NBEHPM), AND BRAZILIAN FEDERATION OF GASTROENTEROLOGY (FBG). ARQUIVOS DE GASTROENTEROLOGIA 2021; 57:381-398. [PMID: 33331485 DOI: 10.1590/s0004-2803.202000000-72] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 04/06/2020] [Indexed: 02/07/2023]
Abstract
Over the last years, there is growing evidence that microorganisms are involved in the maintenance of our health and are related to various diseases, both intestinal and extraintestinal. Changes in the gut microbiota appears to be a key element in the pathogenesis of hepatic and gastrointestinal disorders, including non-alcoholic fatty liver disease, alcoholic liver disease, liver cirrhosis, inflammatory bowel disease, irritable bowel syndrome, and Clostridium difficile - associated diarrhea. In 2019, the Brazilian Society of Hepatology (SBH) in cooperation with the Brazilian Nucleus for the Study of Helicobacter Pylori and Microbiota (NBEHPM), and Brazilian Federation of Gastroenterology (FBG) sponsored a joint meeting on gut microbiota and the use of prebiotics, probiotics, and synbiotics in gastrointestinal and liver diseases. This paper summarizes the proceedings of the aforementioned meeting. It is intended to provide practical information about this topic, addressing the latest discoveries and indicating areas for future studies.
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Affiliation(s)
- Ricardo Correa Barbuti
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, São Paulo, SP, Brasil
| | - Leonardo Lucca Schiavon
- Universidade Federal de Santa Catarina, Faculdade de Medicina, Departamento de Clínica Médica, Florianópolis, SC, Brasil
| | - Cláudia P Oliveira
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, São Paulo, SP, Brasil
| | - Mário Reis Alvares-DA-Silva
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Medicina Interna, Porto Alegre, RS, Brasil
| | | | | | - Alberto Queiroz Farias
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, São Paulo, SP, Brasil
| | - Luisa Leite Barros
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, São Paulo, SP, Brasil
| | - Bruno Paes Barreto
- Universidade do Estado do Pará, Centro de Ciências Biológicas e da Saúde, Belém, PA, Brasil.,Centro Universitário do Estado do Pará (CESUPA), Belém, PA, Brasil
| | | | - Amanda Mandarino Alves
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, São Paulo, SP, Brasil
| | - Tomás Navarro-Rodriguez
- Universidade de São Paulo, Faculdade de Medicina, Departamento de Gastroenterologia, São Paulo, SP, Brasil
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Vascular Adhesion Protein 1 Mediates Gut Microbial Flagellin-Induced Inflammation, Leukocyte Infiltration, and Hepatic Steatosis. SCI 2021. [DOI: 10.3390/sci3010013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] Open
Abstract
Toll-like receptor 5 ligand, flagellin, and vascular adhesion protein 1 (VAP-1) are involved in non-alcoholic fatty liver disease. This study aimed to determine whether VAP-1 mediates flagellin-induced hepatic fat accumulation. The effects of flagellin on adipocyte VAP-1 expression were first studied in vitro. Then, flagellin (100 ng/mouse) or saline was intraperitoneally injected into C57BL/6J (WT) and C57BL/6-Aoc3-/- (VAP-1 KO) mice on a high-fat diet twice a week every 2 weeks for 10 weeks. After that, the effects on inflammation, insulin signaling, and metabolism were studied in liver and adipose tissues. Hepatic fat was quantified histologically and biochemically. Because flagellin challenge increased VAP-1 expression in human adipocytes, we used VAP-1 KO mice to determine whether VAP-1 regulates the inflammatory and metabolic effects of flagellin in vivo. In mice, VAP-1 mediated flagellin-induced inflammation, leukocyte infiltration, and lipolysis in visceral adipose tissue. Consequently, an increased release of glycerol led to hepatic steatosis in WT, but not in KO mice. Flagellin-induced hepatic fibrosis was not mediated by VAP-1. VAP-1 KO mice harbored more inflammation-related microbes than WT mice, while flagellin did not affect the gut microbiota. Our results suggest that by acting on visceral adipose tissue, flagellin increased leukocyte infiltration that induced lipolysis. Further, the released glycerol participated in hepatic fat accumulation. In conclusion, the results describe that gut microbial flagellin through VAP-1 induced hepatic steatosis.
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Lv XC, Chen M, Huang ZR, Guo WL, Ai LZ, Bai WD, Yu XD, Liu YL, Rao PF, Ni L. Potential mechanisms underlying the ameliorative effect of Lactobacillus paracasei FZU103 on the lipid metabolism in hyperlipidemic mice fed a high-fat diet. Food Res Int 2021; 139:109956. [DOI: 10.1016/j.foodres.2020.109956] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022]
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32
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Floreani A, De Martin S, Ikeura T, Okazaki K, Gershwin ME. Gut microbial profiling as a therapeutic and diagnostic target for managing primary biliary cholangitis. Expert Opin Orphan Drugs 2020. [DOI: 10.1080/21678707.2020.1865917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Annarosa Floreani
- Scientific Consultant, IRCCS Negrar, Verona, Italy
- Studiosa Senior, University of Padova, Padova, Italy
| | - Sara De Martin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | - Tsukasa Ikeura
- Department of Gastroenterology and Hepatology, Kansai Medical University, Osaka, Japan
| | - Kazuichi Okazaki
- Department of Gastroenterology and Hepatology, Kansai Medical University, Osaka, Japan
| | - Merrill Eric Gershwin
- Division of Rheumatology Allergy and Clinical Immunology, University of California at Davis School of Medicine, Davis, CA, USA
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Lensu S, Pariyani R, Mäkinen E, Yang B, Saleem W, Munukka E, Lehti M, Driuchina A, Lindén J, Tiirola M, Lahti L, Pekkala S. Prebiotic Xylo-Oligosaccharides Ameliorate High-Fat-Diet-Induced Hepatic Steatosis in Rats. Nutrients 2020; 12:nu12113225. [PMID: 33105554 PMCID: PMC7690286 DOI: 10.3390/nu12113225] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/12/2020] [Accepted: 10/20/2020] [Indexed: 12/12/2022] Open
Abstract
Understanding the importance of the gut microbiota (GM) in non-alcoholic fatty liver disease (NAFLD) has raised the hope for therapeutic microbes. We have shown that high hepatic fat content associated with low abundance of Faecalibacterium prausnitzii in humans and, further, the administration of F. prausnitzii prevented NAFLD in mice. Here, we aimed at targeting F. prausnitzii by prebiotic xylo-oligosaccharides (XOS) to treat NAFLD. First, the effect of XOS on F. prausnitzii growth was assessed in vitro. Then, XOS was supplemented or not with high (HFD, 60% of energy from fat) or low (LFD) fat diet for 12 weeks in Wistar rats (n = 10/group). XOS increased F. prausnitzii growth, having only a minor impact on the GM composition. When supplemented with HFD, XOS ameliorated hepatic steatosis. The underlying mechanisms involved enhanced hepatic β-oxidation and mitochondrial respiration. Nuclear magnetic resonance (1H-NMR) analysis of cecal metabolites showed that, compared to the HFD, the LFD group had a healthier cecal short-chain fatty acid profile and on the HFD, XOS reduced cecal isovalerate and tyrosine, metabolites previously linked to NAFLD. Cecal branched-chain fatty acids associated positively and butyrate negatively with hepatic triglycerides. In conclusion, XOS supplementation can ameliorate NAFLD by improving hepatic oxidative metabolism and affecting GM.
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Affiliation(s)
- Sanna Lensu
- Faculty of Sport and Health Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland; (S.L.); (E.M.); (M.L.); (A.D.)
| | - Raghunath Pariyani
- Food Chemistry and Food Development, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland; (R.P.); (B.Y.)
| | - Elina Mäkinen
- Faculty of Sport and Health Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland; (S.L.); (E.M.); (M.L.); (A.D.)
| | - Baoru Yang
- Food Chemistry and Food Development, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland; (R.P.); (B.Y.)
| | - Wisam Saleem
- Department of Future Technologies, University of Turku, FI-20014 Turku, Finland; (W.S.); (L.L.)
| | - Eveliina Munukka
- Institute of Biomedicine, University of Turku, FI-20014 Turku, Finland;
- Department of Clinical Microbiology, Turku University Hospital, FI-20521 Turku, Finland
| | - Maarit Lehti
- Faculty of Sport and Health Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland; (S.L.); (E.M.); (M.L.); (A.D.)
| | - Anastasiia Driuchina
- Faculty of Sport and Health Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland; (S.L.); (E.M.); (M.L.); (A.D.)
| | - Jere Lindén
- Veterinary Pathology and Parasitology, University of Helsinki, FIN-00014 Helsinki, Finland;
| | - Marja Tiirola
- Department of Environmental and Biological Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland;
| | - Leo Lahti
- Department of Future Technologies, University of Turku, FI-20014 Turku, Finland; (W.S.); (L.L.)
| | - Satu Pekkala
- Faculty of Sport and Health Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland; (S.L.); (E.M.); (M.L.); (A.D.)
- Department of Clinical Microbiology, Turku University Hospital, FI-20521 Turku, Finland
- Correspondence: ; Tel.: +358-45-358-28-98
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Castillo-Dela Cruz P, Wanek AG, Kumar P, An X, Elsegeiny W, Horne W, Fitch A, Burr AHP, Gopalakrishna KP, Chen K, Methé BA, Canna SW, Hand TW, Kolls JK. Intestinal IL-17R Signaling Constrains IL-18-Driven Liver Inflammation by the Regulation of Microbiome-Derived Products. Cell Rep 2020; 29:2270-2283.e7. [PMID: 31747600 PMCID: PMC6886715 DOI: 10.1016/j.celrep.2019.10.042] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 09/04/2019] [Accepted: 10/10/2019] [Indexed: 12/18/2022] Open
Abstract
Interleukin (IL)-17 signaling to the intestinal epithelium regulates the intestinal microbiome. Given the reported links between intestinal dysbiosis, bacterial translocation, and liver disease, we hypothesize that intestinal IL-17R signaling plays a critical role in mitigating hepatic inflammation. To test this, we study intestinal epithelium-specific IL-17RA-deficient mice in an immune-driven hepatitis model. At the naive state, these mice exhibit microbiome dysbiosis and increased translocation of bacterial products (CpG DNA), which drives liver IL-18 production. Upon disease induction, absence of enteric IL-17RA signaling exacerbates hepatitis and hepatocyte cell death. IL-18 is necessary for disease exacerbation and is associated with increased activated hepatic lymphocytes based on Ifng and Fasl expression. Thus, intestinal IL-17R regulates translocation of TLR9 ligands and constrains susceptibility to hepatitis. These data connect enteric Th17 signaling and the microbiome in hepatitis, with broader implications on the effects of impaired intestinal immunity and subsequent release of microbial products observed in other extra-intestinal pathologies. Castillo-dela Cruz et al. describe a unique protective role of intestinal IL-17RA in hepatitis. Disruption of intestinal IL-17RA signaling results in microbiome dysbiosis and translocation of bacterial products, specifically unmethylated CpG DNA, to the liver. This promotes IL-18 production and subsequent lymphocyte activation and cell death to exacerbate liver inflammation.
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Affiliation(s)
- Patricia Castillo-Dela Cruz
- Richard King Mellon Foundation Institute for Pediatric Research, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Alanna G Wanek
- Departments of Medicine and Pediatrics, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Pawan Kumar
- Richard King Mellon Foundation Institute for Pediatric Research, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Xiaojing An
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Waleed Elsegeiny
- Richard King Mellon Foundation Institute for Pediatric Research, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - William Horne
- Richard King Mellon Foundation Institute for Pediatric Research, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Adam Fitch
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Center for Medicine and the Microbiome, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Ansen H P Burr
- Richard King Mellon Foundation Institute for Pediatric Research, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Kathyayini P Gopalakrishna
- Richard King Mellon Foundation Institute for Pediatric Research, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA 15213, USA
| | - Kong Chen
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Barbara A Methé
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; Center for Medicine and the Microbiome, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Scott W Canna
- Richard King Mellon Foundation Institute for Pediatric Research, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Timothy W Hand
- Richard King Mellon Foundation Institute for Pediatric Research, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Jay K Kolls
- Richard King Mellon Foundation Institute for Pediatric Research, Department of Pediatrics, UPMC Children's Hospital of Pittsburgh, Pittsburgh, PA 15224, USA; Departments of Medicine and Pediatrics, Center for Translational Research in Infection and Inflammation, Tulane University School of Medicine, New Orleans, LA 70112, USA.
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Abstract
The gut microbiome is an exciting new area of research in chronic liver disease. It has shown promise in expanding our understanding of these complicated disease processes and has opened up new treatment modalities. The aim of this review is to increase understanding of the microbiome and explain the collection and analysis process in the context of liver disease. It also looks at our current understanding of the role of the microbiome in the wide spectrum of chronic liver diseases and how it is being used in current therapies and treatments.
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Affiliation(s)
- Bradley Reuter
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University, McGuire VA Medical Center, 1201 Broad Rock Boulevard, Richmond, VA 23249, USA
| | - Jasmohan S Bajaj
- Division of Gastroenterology, Hepatology and Nutrition, Virginia Commonwealth University, McGuire VA Medical Center, 1201 Broad Rock Boulevard, Richmond, VA 23249, USA.
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36
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Li Y, Long S, Liu Q, Ma H, Li J, Xiaoqing W, Yuan J, Li M, Hou B. Gut microbiota is involved in the alleviation of loperamide-induced constipation by honey supplementation in mice. Food Sci Nutr 2020; 8:4388-4398. [PMID: 32884719 PMCID: PMC7455974 DOI: 10.1002/fsn3.1736] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/02/2020] [Accepted: 06/06/2020] [Indexed: 12/12/2022] Open
Abstract
Constipation is one of the most common functional gastrointestinal disorders accompanied with intestinal dysbiosis. Laxatives for constipation usually have side effects. Bee honey is a natural food with unique composition, antimicrobial properties, and bifidogenic effect. In order to assess whether honey can ameliorate loperamide-induced constipation in BALB/c mice through the alteration of the gut microbiota, the present study was undertaken. Mice were given Jarrah honey (7.5 g/kg body weight) by gavage once per day for 5 days. Fecal water content, intestinal transit rate together with the colon concentrations of substance P (SP), vasoactive intestinal peptide (VIP), and serotonin (5-hydroxytryptamine; 5-HT) were evaluated. Furthermore, we determined the effect of honey treatment on gut microbiota in mice using stool genomic 16S rRNA sequencing. As a result, honey showed an obvious improvement in fecal water content and alleviated constipation by modulating the microbial composition of the microbiota, and this was highly associated with a proportional decrease in gut Desulfovibrio. In addition, we found that the colon level of neurotransmitters SP and VIP was significantly related to microbial variations. Our results indicate that gut microbiota is involved in the alleviation of loperamide-induced constipation by honey supplementation in mice, and it could be considered as an evaluating parameter in constipation therapy strategies.
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Affiliation(s)
- Yuyuan Li
- Advanced Institute for Medical SciencesDalian Medical UniversityDalianChina
| | - Shangqin Long
- Department of MicroecologyCollege of Basic Medical ScienceDalian Medical UniversityDalianChina
| | - Qiaochu Liu
- Department of MicroecologyCollege of Basic Medical ScienceDalian Medical UniversityDalianChina
| | - Hong Ma
- Department of MicroecologyCollege of Basic Medical ScienceDalian Medical UniversityDalianChina
| | - Jianxin Li
- Department of MicroecologyCollege of Basic Medical ScienceDalian Medical UniversityDalianChina
| | - Wei Xiaoqing
- The Core Laboratory of Medical Molecular Biology of Liaoning ProvinceDalian Medical UniversityDalianChina
| | - Jieli Yuan
- Department of MicroecologyCollege of Basic Medical ScienceDalian Medical UniversityDalianChina
| | - Ming Li
- Department of MicroecologyCollege of Basic Medical ScienceDalian Medical UniversityDalianChina
| | - Binbin Hou
- The Second Hospital of Dalian Medical UniversityDalianChina
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37
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Long Y, Luo J, Zhang Y, Xia Y. Predicting human microbe-disease associations via graph attention networks with inductive matrix completion. Brief Bioinform 2020; 22:5876591. [PMID: 32725163 DOI: 10.1093/bib/bbaa146] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 12/13/2022] Open
Abstract
MOTIVATION human microbes play a critical role in an extensive range of complex human diseases and become a new target in precision medicine. In silico methods of identifying microbe-disease associations not only can provide a deep insight into understanding the pathogenic mechanism of complex human diseases but also assist pharmacologists to screen candidate targets for drug development. However, the majority of existing approaches are based on linear models or label propagation, which suffers from limitations in capturing nonlinear associations between microbes and diseases. Besides, it is still a great challenge for most previous methods to make predictions for new diseases (or new microbes) with few or without any observed associations. RESULTS in this work, we construct features for microbes and diseases by fully exploiting multiply sources of biomedical data, and then propose a novel deep learning framework of graph attention networks with inductive matrix completion for human microbe-disease association prediction, named GATMDA. To our knowledge, this is the first attempt to leverage graph attention networks for this important task. In particular, we develop an optimized graph attention network with talking-heads to learn representations for nodes (i.e. microbes and diseases). To focus on more important neighbours and filter out noises, we further design a bi-interaction aggregator to enforce representation aggregation of similar neighbours. In addition, we combine inductive matrix completion to reconstruct microbe-disease associations to capture the complicated associations between diseases and microbes. Comprehensive experiments on two data sets (i.e. HMDAD and Disbiome) demonstrated that our proposed model consistently outperformed baseline methods. Case studies on two diseases, i.e. asthma and inflammatory bowel disease, further confirmed the effectiveness of our proposed model of GATMDA. AVAILABILITY python codes and data set are available at: https://github.com/yahuilong/GATMDA. CONTACT luojiawei@hnu.edu.cn.
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Affiliation(s)
- Yahui Long
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410000, China.,School of Computer Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410000, China
| | - Yu Zhang
- School of Computer Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Yan Xia
- College of Computer Science and Electronic Engineering, Hunan University, Changsha 410000, China
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38
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Guo WL, Guo JB, Liu BY, Lu JQ, Chen M, Liu B, Bai WD, Rao PF, Ni L, Lv XC. Ganoderic acid A from Ganoderma lucidum ameliorates lipid metabolism and alters gut microbiota composition in hyperlipidemic mice fed a high-fat diet. Food Funct 2020; 11:6818-6833. [PMID: 32686808 DOI: 10.1039/d0fo00436g] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Ganoderic acid A (GA) is one of the most abundant triterpenoids in Ganoderma lucidum, and has been proved to possess a wide range of beneficial health effects. The aim of the current study is to investigate the amelioration effects and mechanism of GA on improving hyperlipidemia in mice fed a high-fat diet (HFD). The results showed that GA intervention significantly inhibited the abnormal growth of body weight and epididymal white adipose tissue (eWAT), prevented the hypertrophy of epididymal adipocytes, and ameliorated the biochemical parameters of serum and liver related to lipid metabolism in HFD-fed mice. Histological analysis also showed that the excessive accumulation of lipid droplets in the liver induced by HFD-feeding was greatly alleviated by GA intervention. In addition, GA intervention also increased the level of short chain fatty acids (SCFAs) in the intestine and promoted the excretion of bile acids (BAs) through feces. High-throughput sequencing of bacterial full-length 16S rDNA revealed that daily supplementation with GA made significant structural changes in the gut microbial population of mice fed with HFD, in particular modulating the relative abundance of some function related microbial phylotypes. The relationships between lipid metabolic parameters and gut microbial phylotypes were also revealed by correlation analysis based on a heatmap and network. The result showed that 46 key gut microbial phylotypes (OTUs) were markedly correlated with at least one lipid metabolic parameter. Moreover, UPLC-QTOF/MS-based liver metabolomics showed that 111 biomarkers (47 up-regulated metabolites and 64 down-regulated metabolites) were significantly changed after high-dose GA intervention (75 mg kg-1 day-1), compared with the HFD-fed hyperlipidemic mice. Metabolic pathway enrichment analysis of the differential hepatic metabolites demonstrated that GA intervention had significant regulatory effects on primary bile acid biosynthesis, fatty acid biosynthesis, amino sugar and nucleotide sugar metabolism, inositol phosphate metabolism, and so on. In addition, GA intervention regulated the mRNA levels of hepatic genes involved in fatty acid metabolism and bile acid homeostasis. These findings present new evidence supporting that GA from G. lucidum has the potential to alleviate lipid metabolic disorders and ameliorate the imbalance of gut microflora in a positive way.
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Affiliation(s)
- Wei-Ling Guo
- Institute of Food Science and Technology, College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian 350108, P. R. China.
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40
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Yu L, Wang L, Yi H, Wu X. Beneficial effects of LRP6-CRISPR on prevention of alcohol-related liver injury surpassed fecal microbiota transplant in a rat model. Gut Microbes 2020; 11:1015-1029. [PMID: 32167008 PMCID: PMC7524294 DOI: 10.1080/19490976.2020.1736457] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Alcohol intake can modify gut microbiota composition, increase gut permeability, and promote liver fibrogenesis. LRP6 is a signal transmembrane protein and a co-receptor for the canonical Wnt signaling pathway. This study compared the curative effect of LRP6-CRISPR on alcohol-related liver injury with that of traditional fecal microbiota transplant (FMT) and investigated the alteration of the gut microbiome following the treatment. A rat model of alcohol-related liver injury was established and injected with lentiviral vectors expressing LRP6-CRISPR or administered with fecal filtrate from healthy rats, with healthy rat served as the control. Liver tissues of rats were examined by HE staining, Sirius staining, and Oil red O staining, respectively. The expression of LRP6 and fibrosis biomarkers were tested by PCR. The fecal sample of rats was collected and examined by 16S rRNA sequencing. Our data indicated that LRP6-CRISPR was more efficient in the prevention of alcohol-related liver injury than FMT. Microbiome analysis showed that alcohol-related liver injury related to gut microbiota dysbiosis, while treatment with LRP6-CRISPR or FMT increased gut microflora diversity and improved gut symbiosis. Further, bacteria specific to the disease stages were identified. Genera Romboutsia, Escherichia-Shigella, Pseudomonas, Turicibacter, and Helicobacter were prevalent in the intestine of rats with alcohol-related liver injury, while the domination of Lactobacillus was found in rats treated with LRP6-CRISPR or FMT. Besides, Lactobacillus and genera belonging to family Lachnospiraceae, Bacteroidales S24-7 group, and Ruminococcaceae were enriched in healthy rats. LRP6-CRISPR and FMT have beneficial effects on the prevention of alcohol-related liver injury, and correspondently, both treatments altered the disrupted gut microflora to a healthy one.
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Affiliation(s)
- Linghua Yu
- Center for Gastroenterology and Hepatology, Institute of Liver Diseases, Affiliated Hospital of Jiaxing College, Jiaxing, Zhejiang Province, PR China,CONTACT Linghua Yu Center for Gastroenterology and Hepatology, Affiliated Hospital of Jiaxing College, 1882 Central-South Road, Jiaxing314001, Zhejiang Province, PR China
| | - Linlin Wang
- Department of Basic Medicine Sciences School of Medicine, Zhejiang University, Hangzhou, Zhejiang Province, PR China
| | - Huixing Yi
- Intensive Care Unit, The Second Affiliated Hospital of Zhejiang University, Hangzhou, Zhejiang Province, PR China
| | - Xiaojun Wu
- Center for Gastroenterology and Hepatology, Institute of Liver Diseases, Affiliated Hospital of Jiaxing College, Jiaxing, Zhejiang Province, PR China
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41
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Liwinski T, Casar C, Ruehlemann MC, Bang C, Sebode M, Hohenester S, Denk G, Lieb W, Lohse AW, Franke A, Schramm C. A disease-specific decline of the relative abundance of Bifidobacterium in patients with autoimmune hepatitis. Aliment Pharmacol Ther 2020; 51:1417-1428. [PMID: 32383181 DOI: 10.1111/apt.15754] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 01/26/2020] [Accepted: 04/06/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND The pathogenesis of autoimmune hepatitis (AIH) is poorly understood and little is known about enteric microbiota in AIH. AIM To investigate disease-specific microbiome alterations in AIH. METHODS The V1-V2 variable regions of the 16S rRNA gene were sequenced in faecal samples from 347 patients with AIH and controls (AIH n = 72, healthy controls (HC) n = 95, primary biliary cholangitis (PBC) n = 99 and ulcerative colitis (UC) n = 81). RESULTS Biodiversity (Shannon entropy) was decreased in AIH patients compared to HC (P = 0.016), which was partially reversed by azathioprine (P = 0.011). Regarding between-sample diversity, AIH patients separated from HC, PBC and UC individuals (all P = 0.001). Compared to HC, decreased relative abundance of anaerobic genera such as Faecalibacterium and an increase of Veillonella and the facultative anaerobic genera Streptococcus and Lactobacillus were detected. Importantly, a disease-specific decline of relative abundance of Bifidobacterium was observed in AIH patients. Lack of Bifidobacterium was associated with failure to achieve remission of AIH (P < 0.001). Of potential therapeutic implication, Bifidobacterium abundance correlated with average protein intake (P < 0.001). Random forests classification between AIH and PBC on the microbiome signature yielded an area under receiver operating characteristic curve (AUC) of 0.787 in the training cohort, and an AUC of 0.849 in an external validation cohort. CONCLUSION Disease-specific faecal microbial alterations were identified in patients with AIH. Intestinal dysbiosis in AIH was characterised by a decline of Bifidobacterium, which was associated with increased disease activity. These results point to the contribution of intestinal microbiota to AIH pathogenesis and to novel therapeutic targets.
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Affiliation(s)
- Timur Liwinski
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,European Reference Network for Hepatological Diseases (ERN-RARE-LIVER), Hamburg, Germany
| | - Christian Casar
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,European Reference Network for Hepatological Diseases (ERN-RARE-LIVER), Hamburg, Germany
| | - Malte C Ruehlemann
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Marcial Sebode
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,European Reference Network for Hepatological Diseases (ERN-RARE-LIVER), Hamburg, Germany
| | - Simon Hohenester
- Department of Medicine II, Liver Center Munich, LMU Munich, University Hospital, Munich, Germany
| | - Gerald Denk
- Department of Medicine II, Liver Center Munich, LMU Munich, University Hospital, Munich, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Ansgar W Lohse
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,European Reference Network for Hepatological Diseases (ERN-RARE-LIVER), Hamburg, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Christoph Schramm
- 1st Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,European Reference Network for Hepatological Diseases (ERN-RARE-LIVER), Hamburg, Germany.,Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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42
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Wan S, Huang C, Wang A, Zhu X. Ursolic acid improves the bacterial community mapping of the intestinal tract in liver fibrosis mice. PeerJ 2020; 8:e9050. [PMID: 32355580 PMCID: PMC7185030 DOI: 10.7717/peerj.9050] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 04/02/2020] [Indexed: 12/24/2022] Open
Abstract
Liver fibrosis often appears in chronic liver disease, with extracellular matrix (ECM) deposition as the main feature. Due to the presence of the liver-gut axis, the destruction of intestinal homeostasis is often accompanied by the development of liver fibrosis. The inconsistent ecological environment of different intestinal sites may lead to differences in the microbiota. The traditional Chinese medicine ursolic acid (UA) has been proven to protect the liver from fibrosis. We investigated the changes in the microbiota of different parts of the intestine during liver fibrosis and the effect of UA on these changes based on high-throughput sequencing technology. Sequencing results suggest that the diversity and abundance of intestinal microbiota decline and the composition of the microbiota is disordered, the potentially beneficial Firmicutes bacteria are reduced, and the pathways for functional prediction are changed in the ilea and anal faeces of liver fibrosis mice compared with normal mice. However, in UA-treated liver fibrosis mice, these disorders improved. It is worth noting that the bacterial changes in the ilea and anal faeces are not consistent. In conclusion, in liver fibrosis, the microbiota of different parts of the intestines have different degrees of disorder, and UA can improve this disorder. This may be a potential mechanism for UA to achieve anti-fibrosis. This study provides theoretical guidance for the UA targeting of intestinal microbiota for the treatment of liver fibrosis.
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Affiliation(s)
- Sizhe Wan
- Department of Gastroenterology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chenkai Huang
- Department of Gastroenterology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Anjiang Wang
- Department of Gastroenterology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xuan Zhu
- Department of Gastroenterology, First Affiliated Hospital of Nanchang University, Nanchang, China
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43
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Roehlen N, Crouchet E, Baumert TF. Liver Fibrosis: Mechanistic Concepts and Therapeutic Perspectives. Cells 2020; 9:cells9040875. [PMID: 32260126 PMCID: PMC7226751 DOI: 10.3390/cells9040875] [Citation(s) in RCA: 549] [Impact Index Per Article: 137.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/28/2020] [Accepted: 04/01/2020] [Indexed: 02/06/2023] Open
Abstract
Liver fibrosis due to viral or metabolic chronic liver diseases is a major challenge of global health. Correlating with liver disease progression, fibrosis is a key factor for liver disease outcome and risk of hepatocellular carcinoma (HCC). Despite different mechanism of primary liver injury and disease-specific cell responses, the progression of fibrotic liver disease follows shared patterns across the main liver disease etiologies. Scientific discoveries within the last decade have transformed the understanding of the mechanisms of liver fibrosis. Removal or elimination of the causative agent such as control or cure of viral infection has shown that liver fibrosis is reversible. However, reversal often occurs too slowly or too infrequent to avoid life-threatening complications particularly in advanced fibrosis. Thus, there is a huge unmet medical need for anti-fibrotic therapies to prevent liver disease progression and HCC development. However, while many anti-fibrotic candidate agents have shown robust effects in experimental animal models, their anti-fibrotic effects in clinical trials have been limited or absent. Thus, no approved therapy exists for liver fibrosis. In this review we summarize cellular drivers and molecular mechanisms of fibrogenesis in chronic liver diseases and discuss their impact for the development of urgently needed anti-fibrotic therapies.
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Affiliation(s)
- Natascha Roehlen
- Université de Strasbourg, 67000 Strasbourg, France; (N.R.); (E.C.)
- Institut de Recherche sur les Maladies Virales et Hépatiques U1110, 67000 Strasbourg, France
| | - Emilie Crouchet
- Université de Strasbourg, 67000 Strasbourg, France; (N.R.); (E.C.)
- Institut de Recherche sur les Maladies Virales et Hépatiques U1110, 67000 Strasbourg, France
| | - Thomas F. Baumert
- Université de Strasbourg, 67000 Strasbourg, France; (N.R.); (E.C.)
- Institut de Recherche sur les Maladies Virales et Hépatiques U1110, 67000 Strasbourg, France
- Pôle Hepato-digestif, Institut Hopitalo-Universitaire, Hôpitaux Universitaires de Strasbourg, 67000 Strasbourg, France
- Correspondence: ; Tel.: +33-366853703
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Jin CJ, Baumann A, Brandt A, Engstler AJ, Nier A, Hege M, Schmeer C, Kehm R, Höhn A, Grune T, Witte OW, Bergheim I. Aging-related liver degeneration is associated with increased bacterial endotoxin and lipopolysaccharide binding protein levels. Am J Physiol Gastrointest Liver Physiol 2020; 318:G736-G747. [PMID: 32090603 DOI: 10.1152/ajpgi.00345.2018] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Aging is a risk factor in the development of many diseases, including liver-related diseases. The two aims of the present study were 1) to determine how aging affects liver health in mice in the absence of any interventions and 2) if degenerations observed in relation to blood endotoxin levels are critical in aging-associated liver degeneration. Endotoxin levels and markers of liver damage, mitochondrial dysfunction, insulin resistance, and apoptosis as well as the Toll-like receptor 4 (Tlr-4) signaling cascade were studied in liver tissue and blood, respectively, of 3- and 24-mo-old male C57BL/6J mice. In a second set of experiments, 3- to 4-mo-old and 14-mo-old female lipopolysaccharide-binding protein (LBP)-/- mice and littermates fed standard chow, markers of liver damage, insulin resistance, and mitochondrial dysfunction were assessed. Plasma activity of aspartate aminotransferase and histological signs of hepatic inflammation and fibrosis were significantly higher in old C57BL/6J mice than in young animals. The number of neutrophils, CD8α-positive cells, and mRNA expression of markers of apoptosis were also significantly higher in livers of old C57BL/6J mice compared with young animals, being also associated with a significant induction of hepatic Tlr-4 and LBP expression as well as higher endotoxin levels in peripheral blood. Compared with age-matched littermates, LBP-/- mice display less signs of senescence in liver. Taken together, our data suggest that, despite being fed standard chow, old mice developed liver inflammation and beginning fibrosis and that bacterial endotoxin may play a critical role herein.NEW & NOTEWORTHY Old age in mice is associated with marked signs of liver degeneration, hepatic inflammation, and fibrosis. Aging-associated liver degeneration is associated with elevated bacterial endotoxin levels and an induction of lipopolysaccharide-binding protein (LBP) and Toll-like receptor 4-dependent signaling cascades in liver tissue. Furthermore, in old aged LBP-/- mice, markers of senescence seem to be lessened, supporting the hypothesis that bacterial endotoxin levels might be critical in aging-associated decline of liver.
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Affiliation(s)
- Cheng Jun Jin
- Institute of Nutrition, SD Model Systems of Molecular Nutrition, Friedrich-Schiller-University Jena, Jena, Germany.,Clinic for Gastroenterology, Hepatology, and Infectiology, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Anja Baumann
- Institute of Nutrition, SD Model Systems of Molecular Nutrition, Friedrich-Schiller-University Jena, Jena, Germany.,Department of Nutritional Sciences, Molecular Nutritional Science, University of Vienna, Vienna, Austria
| | - Annette Brandt
- Institute of Nutrition, SD Model Systems of Molecular Nutrition, Friedrich-Schiller-University Jena, Jena, Germany.,Department of Nutritional Sciences, Molecular Nutritional Science, University of Vienna, Vienna, Austria
| | - Anna Janina Engstler
- Institute of Nutrition, SD Model Systems of Molecular Nutrition, Friedrich-Schiller-University Jena, Jena, Germany.,Department of Nutritional Sciences, Molecular Nutritional Science, University of Vienna, Vienna, Austria
| | - Anika Nier
- Institute of Nutrition, SD Model Systems of Molecular Nutrition, Friedrich-Schiller-University Jena, Jena, Germany.,Department of Nutritional Sciences, Molecular Nutritional Science, University of Vienna, Vienna, Austria
| | - Marianne Hege
- Institute of Nutrition, SD Model Systems of Molecular Nutrition, Friedrich-Schiller-University Jena, Jena, Germany
| | - Christian Schmeer
- Hans-Berger Department of Neurology, University Hospital Jena, Jena, Germany
| | - Richard Kehm
- German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
| | - Annika Höhn
- German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
| | - Tilman Grune
- German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany.,German Center for Diabetes Research, Munich-Neuherberg, Germany
| | - Otto W Witte
- Hans-Berger Department of Neurology, University Hospital Jena, Jena, Germany
| | - Ina Bergheim
- Institute of Nutrition, SD Model Systems of Molecular Nutrition, Friedrich-Schiller-University Jena, Jena, Germany.,Department of Nutritional Sciences, Molecular Nutritional Science, University of Vienna, Vienna, Austria
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Ma B, France MT, Crabtree J, Holm JB, Humphrys MS, Brotman RM, Ravel J. A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina. Nat Commun 2020; 11:940. [PMID: 32103005 PMCID: PMC7044274 DOI: 10.1038/s41467-020-14677-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 01/23/2020] [Indexed: 12/12/2022] Open
Abstract
Analysis of metagenomic and metatranscriptomic data is complicated and typically requires extensive computational resources. Leveraging a curated reference database of genes encoded by members of the target microbiome can make these analyses more tractable. In this study, we assemble a comprehensive human vaginal non-redundant gene catalog (VIRGO) that includes 0.95 million non-redundant genes. The gene catalog is functionally and taxonomically annotated. We also construct a vaginal orthologous groups (VOG) from VIRGO. The gene-centric design of VIRGO and VOG provides an easily accessible tool to comprehensively characterize the structure and function of vaginal metagenome and metatranscriptome datasets. To highlight the utility of VIRGO, we analyze 1,507 additional vaginal metagenomes, and identify a high degree of intraspecies diversity within and across vaginal microbiota. VIRGO offers a convenient reference database and toolkit that will facilitate a more in-depth understanding of the role of vaginal microorganisms in women’s health and reproductive outcomes. Reference databases are essential for studies on host-microbiota interactions. Here, the authors present the construction of VIRGO, a human vaginal non-redundant gene catalog, which represents a comprehensive resource for taxonomic and functional profiling of vaginal microbiomes from metagenomic and metatranscriptomic datasets.
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Affiliation(s)
- Bing Ma
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Michael T France
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Johanna B Holm
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Michael S Humphrys
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Rebecca M Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA. .,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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Wan S, Nie Y, Zhang Y, Huang C, Zhu X. Gut Microbial Dysbiosis Is Associated With Profibrotic Factors in Liver Fibrosis Mice. Front Cell Infect Microbiol 2020; 10:18. [PMID: 32083022 PMCID: PMC7004962 DOI: 10.3389/fcimb.2020.00018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 01/14/2020] [Indexed: 12/11/2022] Open
Abstract
Background and Aims: Continuous development will evolve into end-stage liver disease. Profibrotic factors NOX4 and RhoA participate in the activation of HSC and accelerate the development of liver fibrosis. Abnormal intrahepatic metabolism during liver fibrosis interferes with intestinal homeostasis through the liver—gut axis. Methods: Wild-type (WT), NOX4 knockout, RhoA expression inhibition C57BL/6 mice were randomly divided into 6 groups as follows: control group, CCl4 group, NOX4−/− group, AP group, RhoAi group, and FA group. Results: The results of alpha-diversity suggest that the diversity and abundance of intestinal flora in liver fibrosis mice is lower than that in normal mice, but there is some recovery in liver fibrosis mice with NOX4 or RhoA intervention. The flora structure showed that the intestinal flora of the control group, NOX4−/− group, AP group, RhoAi group, and FA group belonged to one type, while the intestinal flora of the CCl4 group belonged to another type. In addition, analysis of the composition of the flora at the level of the phylum and genus also suggested the decline in Firmicutes and Lactobacillus caused by liver fibrosis has partially restore in the liver fibrosis mice with NOX4 or RhoA intervention. In terms of functional prediction, the “Secondary metabolites biosynthesis, transport and catabolism,” “Infectious diseases,” and “Xenobiotics biodegradation and metabolism” signaling pathways are mainly enriched in liver fibrosis mice, and the “Energy production and conversion,” “Defense mechanisms,” and “Carbohydrate metabolism” signaling pathways are mainly enriched in the NOX4 and RhoA intervention groups. Conclusion: In the case of liver fibrosis, the intestinal flora is disordered, and the disorder is related to NOX4 and RhoA. This study provides theoretical support for a better understanding of the underlying mechanisms of liver fibrosis development.
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Affiliation(s)
- Sizhe Wan
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yuan Nie
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yue Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Chenkai Huang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xuan Zhu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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Chen M, Guo WL, Li QY, Xu JX, Cao YJ, Liu B, Yu XD, Rao PF, Ni L, Lv XC. The protective mechanism ofLactobacillus plantarumFZU3013 against non-alcoholic fatty liver associated with hyperlipidemia in mice fed a high-fat diet. Food Funct 2020; 11:3316-3331. [DOI: 10.1039/c9fo03003d] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Lactobacillus plantarumFZU3013, isolated from the traditional brewing process ofHongqurice wine, has beneficial effects on improving lipid metabolism disorders.
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Vascular Adhesion Protein 1 Mediates Gut Microbial Flagellin-Induced Inflammation, Leukocyte Infiltration, and Hepatic Steatosis. SCI 2019. [DOI: 10.3390/sci1030065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Toll-like receptor 5 ligand, flagellin, and Vascular Adhesion Protein-1 (VAP-1) are involved in non-alcoholic fatty liver disease (NAFLD). This study aimed to determine whether VAP-1 mediates flagellin-induced hepatic fat accumulation. The effects of flagellin on adipocyte VAP-1 expression were first studied in vitro. Then, flagellin (100 ng/mouse) or saline was intraperitoneally injected to C57BL/6J WT and C57BL/6-Aoc3-/- (VAP-1 KO) mice on high-fat diet twice a week every two weeks for 10-weeks. After that, the effects on inflammation, insulin signaling, and metabolism were studied in liver and adipose tissues. Hepatic fat was quantified histologically and biochemically. Because flagellin challenge increased VAP-1 expression in human adipocytes, we used VAP-1 KO mice to determine whether VAP-1 regulates the inflammatory and metabolic effects of flagellin in vivo. In mice, VAP-1 mediated flagellin-induced inflammation, leukocyte infiltration and lipolysis in visceral adipose tissue. Consequently, increased release of glycerol led to hepatic steatosis in WT but not KO mice. Flagellin-induced hepatic fibrosis was not mediated by VAP-1. VAP-1 KO mice harbored more inflammation-related microbes than WT, while flagellin did not affect the gut microbiota. Our results suggest that by acting on visceral adipose tissue, flagellin increased leukocyte infiltration that induced lipolysis. Further, the released glycerol participated in hepatic fat accumulation. In conclusion, the results describe that gut microbial flagellin through VAP-1 induced hepatic steatosis.
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Czaja AJ. Examining pathogenic concepts of autoimmune hepatitis for cues to future investigations and interventions. World J Gastroenterol 2019; 25:6579-6606. [PMID: 31832000 PMCID: PMC6906207 DOI: 10.3748/wjg.v25.i45.6579] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/25/2019] [Accepted: 11/29/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Multiple pathogenic mechanisms have been implicated in autoimmune hepatitis, but they have not fully explained susceptibility, triggering events, and maintenance or escalation of the disease. Furthermore, they have not identified a critical defect that can be targeted. The goals of this review are to examine the diverse pathogenic mechanisms that have been considered in autoimmune hepatitis, indicate investigational opportunities to validate their contribution, and suggest interventions that might evolve to modify their impact. English abstracts were identified in PubMed by multiple search terms. Full length articles were selected for review, and secondary and tertiary bibliographies were developed. Genetic and epigenetic factors can affect susceptibility by influencing the expression of immune regulatory genes. Thymic dysfunction, possibly related to deficient production of programmed cell death protein-1, can allow autoreactive T cells to escape deletion, and alterations in the intestinal microbiome may help overcome immune tolerance and affect gender bias. Environmental factors may trigger the disease or induce epigenetic changes in gene function. Molecular mimicry, epitope spread, bystander activation, neo-antigen production, lymphocytic polyspecificity, and disturbances in immune inhibitory mechanisms may maintain or escalate the disease. Interventions that modify epigenetic effects on gene expression, alter intestinal dysbiosis, eliminate deleterious environmental factors, and target critical pathogenic mechanisms are therapeutic possibilities that might reduce risk, individualize management, and improve outcome. In conclusion, diverse pathogenic mechanisms have been implicated in autoimmune hepatitis, and they may identify a critical factor or sequence that can be validated and used to direct future management and preventive strategies.
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Affiliation(s)
- Albert J Czaja
- Division of Gastroenterology and Hepatology, Mayo Clinic College of Medicine and Science, Rochester, MN 55905, United States
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Long Y, Luo J. WMGHMDA: a novel weighted meta-graph-based model for predicting human microbe-disease association on heterogeneous information network. BMC Bioinformatics 2019; 20:541. [PMID: 31675979 PMCID: PMC6824056 DOI: 10.1186/s12859-019-3066-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/02/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND An increasing number of biological and clinical evidences have indicated that the microorganisms significantly get involved in the pathological mechanism of extensive varieties of complex human diseases. Inferring potential related microbes for diseases can not only promote disease prevention, diagnosis and treatment, but also provide valuable information for drug development. Considering that experimental methods are expensive and time-consuming, developing computational methods is an alternative choice. However, most of existing methods are biased towards well-characterized diseases and microbes. Furthermore, existing computational methods are limited in predicting potential microbes for new diseases. RESULTS Here, we developed a novel computational model to predict potential human microbe-disease associations (MDAs) based on Weighted Meta-Graph (WMGHMDA). We first constructed a heterogeneous information network (HIN) by combining the integrated microbe similarity network, the integrated disease similarity network and the known microbe-disease bipartite network. And then, we implemented iteratively pre-designed Weighted Meta-Graph search algorithm on the HIN to uncover possible microbe-disease pairs by cumulating the contribution values of weighted meta-graphs to the pairs as their probability scores. Depending on contribution potential, we described the contribution degree of different types of meta-graphs to a microbe-disease pair with bias rating. Meta-graph with higher bias rating will be assigned greater weight value when calculating probability scores. CONCLUSIONS The experimental results showed that WMGHMDA outperformed some state-of-the-art methods with average AUCs of 0.9288, 0.9068 ±0.0031 in global leave-one-out cross validation (LOOCV) and 5-fold cross validation (5-fold CV), respectively. In the case studies, 9, 19, 37 and 10, 20, 45 out of top-10, 20, 50 candidate microbes were manually verified by previous reports for asthma and inflammatory bowel disease (IBD), respectively. Furthermore, three common human diseases (Crohn's disease, Liver cirrhosis, Type 1 diabetes) were adopted to demonstrate that WMGHMDA could be efficiently applied to make predictions for new diseases. In summary, WMGHMDA has a high potential in predicting microbe-disease associations.
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Affiliation(s)
- Yahui Long
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, 410082, China.
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