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Liu F, Smith AD, Wang TTY, Pham Q, Hou P, Cheung L, Yang H, Li RW. Phospholipid-rich krill oil promotes intestinal health by strengthening beneficial gut microbial interactions in an infectious colitis model. Food Funct 2024; 15:2604-2615. [PMID: 38356343 DOI: 10.1039/d3fo04980a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Krill oil (KO) is rich in bioactive ingredients including phospholipids, omega-3 fatty acids, and astaxanthin. While health benefits and roles of KO in modulating lipid metabolism are well documented, its ability to alleviate symptoms related to infectious colitis and modulate gut microbial interactions is still largely unknown. Here we used a multi-omics approach, including transcriptome, microbiome, and metabolome analyses, to understand how KO mediates gut microbial interactions and promotes epithelial healing in an infectious colitis model. KO reversed the infection-induced intestinal hyperplasia to baseline. KO dampened intestinal inflammation via multiple targets, mediating several proinflammatory pathways, including IL17 signaling, and reducing luminal histamine levels. KO supplementation enriched butyrate-producing bacteria, including Roseburia and Clostridium, and strengthened beneficial microbial interactions in the gut microbial community. Supplementation with phospholipid-rich KO also increased microbial phylogenetic diversity. KO enhanced mucosal barrier function by increasing the production of Muc6 and the antimicrobial peptide, Leap2. KO played an active role during epithelial healing by inhibiting the expression of granzyme K while increasing the expression of a colitis protective factor, Dclk1. Together, our findings demonstrate that KO rich in omega-3 phospholipids can play a protective role in infectious colitis and should be considered a dietary option for promoting gut health.
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Affiliation(s)
- Fang Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China.
| | - Allen D Smith
- USDA-ARS, Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | - Thomas T Y Wang
- USDA-ARS, Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | - Quynhchi Pham
- USDA-ARS, Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | - Pengfen Hou
- Affilated Hospital of Qingdao Binhai University, Qingdao, China
| | - Lumei Cheung
- USDA-ARS, Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou, China.
| | - Robert W Li
- USDA-ARS, Animal Parasitic Diseases Laboratory, Beltsville, MD, USA
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2
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Wu Y, Xin M, Pham Q, Gao Y, Huang H, Jiang X, Li RW, Yu L, Luo Y, Wang J, Wang TTY. Red Cabbage Modulates Composition and Co-Occurrence Networks of Gut Microbiota in a Rodent Diet-Induced Obesity Model. Foods 2023; 13:85. [PMID: 38201113 PMCID: PMC10778922 DOI: 10.3390/foods13010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/20/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024] Open
Abstract
Red cabbage (RC), a cruciferous vegetable rich in various bioactive substances, can significantly reduce the risk factors of several non-communicable diseases, but the mechanism underlying the biological effects of RC remains unclear. Furthermore, mechanisms that operate through the regulation of gut microbiota also are not known. Given the relationships between diet, gut microbiota, and health, a diet-induced mice obesity model was used to elucidate the influence of RC on gut microbial composition and bacteria-bacteria interactions in mice. After 24 h of dietary intervention, a high-fat (HF) diet with the intake of RC led to increased Firmicutes/Bacteroidetes (F/B) ratios in the feces of mice. RC also reduced the relative abundance of Bifidobacteria, Lactobacillus, and Akkermansia muciniphila in mice fed a low-fat (LF) diet. After 8-weeks of dietary intervention, RC significantly changed the structure and the ecological network of the gut microbial community. Particularly, RC inhibited an HF-diet-induced increase in AF12 in mice, and this genus was positively correlated with body weight, low-density lipoprotein level, and fecal bile acid of mice. Unclassified Clostridiales, specifically increased via RC consumption, were also found to negatively correlate with hepatic free cholesterol levels in mice. Overall, our results demonstrated that RC modulating gut microbial composition and interactions are associated with the attenuation of HF-diet-induced body weight gain and altered cholesterol metabolism in mice.
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Affiliation(s)
- Yanbei Wu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100084, China; (Y.W.); (M.X.); (Y.G.); (J.W.)
| | - Mengmeng Xin
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100084, China; (Y.W.); (M.X.); (Y.G.); (J.W.)
| | - Quynhchi Pham
- Diet Genomics and Immunology Laboratory, BHNRC, ARS, USDA, Beltsville, MD 20705, USA;
| | - Yu Gao
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100084, China; (Y.W.); (M.X.); (Y.G.); (J.W.)
| | - Haiqiu Huang
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA (X.J.); (L.Y.)
| | - Xiaojing Jiang
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA (X.J.); (L.Y.)
| | - Robert W. Li
- Animal Parasitic Diseases Laboratory, BARC, ARS, USDA, Beltsville, MD 20705, USA;
| | - Liangli Yu
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA (X.J.); (L.Y.)
| | - Yaguang Luo
- Food Quality Laboratory, BARC, ARS, USDA, Beltsville, MD 20705, USA;
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100084, China; (Y.W.); (M.X.); (Y.G.); (J.W.)
| | - Thomas T. Y. Wang
- Diet Genomics and Immunology Laboratory, BHNRC, ARS, USDA, Beltsville, MD 20705, USA;
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3
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Lin Y, Jung H, Bulman CA, Ng J, Vinck R, O'Beirne C, Zhong S, Moser MS, Tricoche N, Peguero R, Li RW, Urban JF, Le Pape P, Pagniez F, Moretto M, Weil T, Lustigman S, Cariou K, Mitreva M, Sakanari JA, Gasser G. Discovery of New Broad-Spectrum Anti-Infectives for Eukaryotic Pathogens Using Bioorganometallic Chemistry. J Med Chem 2023; 66:15867-15882. [PMID: 38009931 DOI: 10.1021/acs.jmedchem.3c01333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Drug resistance observed with many anti-infectives clearly highlights the need for new broad-spectrum agents to treat especially neglected tropical diseases (NTDs) caused by eukaryotic parasitic pathogens, including fungal infections. Herein, we show that the simple modification of one of the most well-known antifungal drugs, fluconazole, with organometallic moieties not only improves the activity of the parent drug but also broadens the scope of application of the new derivatives. These compounds were highly effective in vivo against pathogenic fungal infections and potent against parasitic worms such as Brugia, which causes lymphatic filariasis and Trichuris, one of the soil-transmitted helminths that infects millions of people globally. Notably, the identified molecular targets indicate a mechanism of action that differs greatly from that of the parental antifungal drug, including targets involved in biosynthetic pathways that are absent in humans, offering great potential to expand our armamentarium against drug-resistant fungal infections and neglected tropical diseases (NTDs) targeted for elimination by 2030.
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Affiliation(s)
- Yan Lin
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Hyeim Jung
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States
| | - Christina A Bulman
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - James Ng
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Robin Vinck
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Cillian O'Beirne
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Shuai Zhong
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Matthew S Moser
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Nancy Tricoche
- Molecular Parasitology, New York Blood Center, Lindsley F. Kimball Research Institute, New York, New York 10065, United States
| | - Ricardo Peguero
- Molecular Parasitology, New York Blood Center, Lindsley F. Kimball Research Institute, New York, New York 10065, United States
| | - Robert W Li
- United States Department of Agricultural Research Service (USDA-ARS), Animal Parasitic Diseases Laboratory, Beltsville, Maryland 20705, United States
| | - Joseph F Urban
- United States Department of Agriculture, Diet, Genomics and Immunology Laboratory, Beltsville, Maryland 20705, United States
| | - Patrice Le Pape
- Nantes Université, CHU de Nantes, Cibles et Médicaments des Infections et de l'Immunité, IICiMed, UR 1155, F-44000 Nantes, France
| | - Fabrice Pagniez
- Nantes Université, CHU de Nantes, Cibles et Médicaments des Infections et de l'Immunité, IICiMed, UR 1155, F-44000 Nantes, France
| | - Marco Moretto
- Fondazione Edmund Mach Via E. Mach 1, Research and Innovation Centre, Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Tobias Weil
- Fondazione Edmund Mach Via E. Mach 1, Research and Innovation Centre, Via E. Mach 1, 38010 San Michele all'Adige, Italy
| | - Sara Lustigman
- Molecular Parasitology, New York Blood Center, Lindsley F. Kimball Research Institute, New York, New York 10065, United States
| | - Kevin Cariou
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Makedonka Mitreva
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri 63110, United States
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, United States
| | - Judy A Sakanari
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
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4
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Fleming DS, Liu F, Li RW. Differential Correlation of Transcriptome Data Reveals Gene Pairs and Pathways Involved in Treatment of Citrobacter rodentium Infection with Bioactive Punicalagin. Molecules 2023; 28:7369. [PMID: 37959788 PMCID: PMC10650703 DOI: 10.3390/molecules28217369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023] Open
Abstract
This study is part of the work investigating bioactive fruit enzymes as sustainable alternatives to parasite anthelmintics that can help reverse the trend of lost efficacy. The study looked to define biological and molecular interactions that demonstrate the ability of the pomegranate extract punicalagin against intracellular parasites. The study compared transcriptomic reads of two distinct conditions. Condition A was treated with punicalagin (PA) and challenged with Citrobacter rodentium, while condition B (CM) consisted of a group that was challenged and given mock treatment of PBS. To understand the effect of punicalagin on transcriptomic changes between conditions, a differential correlation analysis was conducted. The analysis examined the regulatory connections of genes expressed between different treatment conditions by statistically querying the relationship between correlated gene pairs and modules in differing conditions. The results indicated that punicalagin treatment had strong positive correlations with the over-enriched gene ontology (GO) terms related to oxidoreductase activity and lipid metabolism. However, the GO terms for immune and cytokine responses were strongly correlated with no punicalagin treatment. The results matched previous studies that showed punicalagin to have potent antioxidant and antiparasitic effects when used to treat parasitic infections in mice and livestock. Overall, the results indicated that punicalagin enhanced the effect of tissue-resident genes.
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Affiliation(s)
- Damarius S. Fleming
- USDA-ARS, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705, USA;
| | - Fang Liu
- Zhengzhou University, Zhengzhou 450001, China;
| | - Robert W. Li
- USDA-ARS, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705, USA;
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Xiong CZ, Zhang L, Zhang Y, Li RW, Sun Y, Liu YH. [Ferroptosis is involved in testicular injury induced by TDCIPP in adolescent male mice]. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi 2023; 41:562-568. [PMID: 37667150 DOI: 10.3760/cma.j.cn121094-20220512-00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Objective: To investigate the role of ferroptosis in testicular injury in adolescent male mice induced by TDCIPP. Methods: In December 2021, 30 healthy 3-week-old male C57BL/6 mice, with a body weight of (13±2) g, were selected and fed adaptive for one week. They were divided into control group, low-dose group, medium-dose group, high-dose group and iron death inhibitor group according to a random number table, with 6 mice in each group. Mice in low, medium and high dose groups were treated with 5, 25 and 125 mg/ (kg·d) TDCIPP for 28 days, respectively, while the control group was treated with the same amount of corn oil for 28 days. The iron death inhibitor group was given 125 mg/ (kg·d) TDCIPP intragastric administration for 28 days, and 30 mg/kg DFO saline solution was intraperitoneally injected three times a week. After the treatment, the mice were killed, the epididymis was separated, and sperm count was performed. HE staining was used to observe the morphological changes of mouse testis, and iron content in testis was detected by tissue iron detection kit. The level of reactive cxygen species, MDA content, and the mitochondrial membrane potential level of mice were detected. Western blot analysis of testicular glutathione peroxidase (GPX4) and internal cyclooxygenase-2 (COX2) protein expression. Results: Compared with the control group, the spermatogenic cells in the testes of mice treated with medium-and high-dose of TDCIPP were disorderly arranged, showing a vacuolar structure. the number of sperm in the epididymis was significantly reduced (P=0.009, 0.004), while the sperm deformity rate was significantly increased (P=0.010, 0.000). Moreover, the content of ROS, iron ion and MDA in the testes increased significantly (P<0.05), and the mitochondrial membrane potential of mouse testicular cells decreased significantly (P<0.05). The expression of GPX4 proteins decreased (P<0.05). while the expression of COX2 increased significantly (P<0.01). Compared with high-dose group group, spermatogenic cells in ferroptosis inhibitor group were closely arranged and normal, and ROS and Fe contents in testicular tissue were significantly decreased (P<0.01) ; GPX4 protein expression was significantly increased while COX2 protein expression was significantly decreased (P<0.05) . Conclusion: Ferroptosis is involved in TDCIPP-induced testicular damage in male pubertal mice.
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Affiliation(s)
- C Z Xiong
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identifiction and Control, Medical College, Wuhan University of Science and Technolgy, Wuhan 430065, China
| | - L Zhang
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identifiction and Control, Medical College, Wuhan University of Science and Technolgy, Wuhan 430065, China
| | - Y Zhang
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identifiction and Control, Medical College, Wuhan University of Science and Technolgy, Wuhan 430065, China
| | - R W Li
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identifiction and Control, Medical College, Wuhan University of Science and Technolgy, Wuhan 430065, China
| | - Y Sun
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identifiction and Control, Medical College, Wuhan University of Science and Technolgy, Wuhan 430065, China
| | - Y H Liu
- School of Public Health, Hubei Province Key Laboratory of Occupational Hazard Identifiction and Control, Medical College, Wuhan University of Science and Technolgy, Wuhan 430065, China
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Wu Y, Pham Q, Wang Y, Huang H, Jiang X, Li RW, Yu L, Luo Y, Wang J, Wang TTY. Red cabbage microgreen modulation of gut microbiota is associated with attenuation of diet-induced obesity risk factors in a mouse model. Food Funct 2023. [PMID: 37401724 DOI: 10.1039/d3fo01249b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Cruciferous vegetable microgreens, such as red cabbage microgreens (RCMG), are of special interest due to their well-documented health-promoting effects compared to their mature counterparts. However, little is known of the biological effects of microgreens. The present study used a rodent diet-induced obesity model to investigate the effect of consuming RCMG on the gut microbiota. We found that the consumption of RCMG exerted profound impacts on the microbial composition in mice. Specifically, the species diversity of mice on both low fat (LF) and high fat (HF) diets was significantly increased by the consumption of RCMG. In comparison with the LF control group, the intake of RCMG increased the gut Firmicutes/Bacteroidetes (F/B) ratio. Furthermore, an unidentified species of the Clostridiales order, increased by RCMG, was found to be negatively correlated with the hepatic cholesterol ester level in mice (r = -0.43, p < 0.05). In addition, RCMG significantly inhibited HF diet-induced elevation of the genus AF12, of which the abundance was positively correlated with the body weight gain (r = 0.52, p < 0.01) and fecal bile acid in mice (r = 0.59, p < 0.01). Overall, our results demonstrated that the consumption of RCMG in the diet can alter the gut microbiota, and attenuation of HF diet-induced body weight gain and altered cholesterol metabolism may be mediated through regulation of the gut microbiota.
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Affiliation(s)
- Yanbei Wu
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100048, PR China
| | - Quynhchi Pham
- Diet Genomics and Immunology Laboratory, BHNRC, ARS, USDA, Beltsville, MD 20705, USA.
| | - Yali Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100048, PR China
| | - Haiqiu Huang
- Diet Genomics and Immunology Laboratory, BHNRC, ARS, USDA, Beltsville, MD 20705, USA.
| | - Xiaojing Jiang
- Diet Genomics and Immunology Laboratory, BHNRC, ARS, USDA, Beltsville, MD 20705, USA.
| | - Robert W Li
- Animal Parasitic Diseases Laboratory, BARC, ARS, USDA, Beltsville, MD 20705, USA
| | - Liangli Yu
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA
| | - Yaguang Luo
- Food Quality Laboratory, BARC, ARS, USDA, Beltsville, MD 20705, USA
| | - Jing Wang
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology & Business University, Beijing 100048, PR China
| | - Thomas T Y Wang
- Diet Genomics and Immunology Laboratory, BHNRC, ARS, USDA, Beltsville, MD 20705, USA.
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7
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Lin Y, Jung H, Bulman CA, Ng J, Vinck R, O'Beirne C, Moser MS, Tricoche N, Peguero R, Li RW, Urban JF, Pape PL, Pagniez F, Moretto M, Weil T, Lustigman S, Cariou K, Mitreva M, Sakanari JA, Gasser G. Discovery of New Broad-Spectrum Anti-Infectives for Eukaryotic Pathogens Using Bioorganometallic Chemistry. bioRxiv 2023:2023.06.28.546819. [PMID: 37425761 PMCID: PMC10327022 DOI: 10.1101/2023.06.28.546819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Drug resistance observed with many anti-infectives clearly highlights the need for new broad-spectrum agents to treat especially neglected tropical diseases (NTDs) caused by eukaryotic parasitic pathogens including fungal infections. Since these diseases target the most vulnerable communities who are disadvantaged by health and socio-economic factors, new agents should be, if possible, easy-to-prepare to allow for commercialization based on their low cost. In this study, we show that simple modification of one of the most well-known antifungal drugs, fluconazole, with organometallic moieties not only improves the activity of the parent drug but also broadens the scope of application of the new derivatives. These compounds were highly effective in vivo against pathogenic fungal infections and potent against parasitic worms such as Brugia, which causes lymphatic filariasis and Trichuris, one of the soil-transmitted helminths that infects millions of people globally. Notably, the identified molecular targets indicate a mechanism of action that differs greatly from the parental antifungal drug, including targets involved in biosynthetic pathways that are absent in humans, offering great potential to expand our armamentarium against drug-resistant fungal infections and NTDs targeted for elimination by 2030. Overall, the discovery of these new compounds with broad-spectrum activity opens new avenues for the development of treatments for several current human infections, either caused by fungi or by parasites, including other NTDs, as well as newly emerging diseases. ONE-SENTENCE SUMMARY Simple derivatives of the well-known antifungal drug fluconazole were found to be highly effective in vivo against fungal infections, and also potent against the parasitic nematode Brugia, which causes lymphatic filariasis and against Trichuris, one of the soil-transmitted helminths that infects millions of people globally.
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8
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Li RW, Moon CD, Morgavi DP. Editorial: Rumen microbiome dynamics and their implications in health and environment. Front Microbiol 2023; 14:1223885. [PMID: 37346751 PMCID: PMC10280159 DOI: 10.3389/fmicb.2023.1223885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/23/2023] Open
Affiliation(s)
- Robert W. Li
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Beltsville, MD, United States
| | - Christina D. Moon
- AgResearch Ltd., Grassland Research Centre, Palmerston North, New Zealand
| | - Diego P. Morgavi
- INRAE, Clermont-Auvergne-Rhône-Alpes, Saint-Genès-Champanelle, France
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9
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Truscott J, Guan X, Fury H, Atagozli T, Metwali A, Liu W, Li Y, Li RW, Elliott DE, Blazar BR, Ince MN. After Bone Marrow Transplantation, the Cell-Intrinsic Th2 Pathway Promotes Recipient T Lymphocyte Survival and Regulates Graft-versus-Host Disease. Immunohorizons 2023; 7:442-455. [PMID: 37294277 PMCID: PMC10580113 DOI: 10.4049/immunohorizons.2300021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 06/10/2023] Open
Abstract
Recipient T cells can aggravate or regulate lethal and devastating graft-versus-host disease (GVHD) after bone marrow transplantation (BMT). In this context, we have shown before that intestinal immune conditioning with helminths is associated with survival of recipient T cells and Th2 pathway-dependent regulation of GVHD. We investigated the mechanism of survival of recipient T cells and their contribution to GVHD pathogenesis in this helminth infection and BMT model after myeloablative preparation with total body irradiation in mice. Our results indicate that the helminth-induced Th2 pathway directly promotes the survival of recipient T cells after total body irradiation. Th2 cells also directly stimulate recipient T cells to produce TGF-β, which is required to regulate donor T cell-mediated immune attack of GVHD and can thereby contribute to recipient T cell survival after BMT. Moreover, we show that recipient T cells, conditioned to produce Th2 cytokines and TGF-β after helminth infection, are fundamentally necessary for GVHD regulation. Taken together, reprogrammed or immune-conditioned recipient T cells after helminth infection are crucial elements of Th2- and TGF-β-dependent regulation of GVHD after BMT, and their survival is dependent on cell-intrinsic Th2 signaling.
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Affiliation(s)
- Jamie Truscott
- Department of Pediatrics, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Xiaoqun Guan
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
- Veterans Administration Medical Center, Iowa City, IA
| | - Hope Fury
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
- Veterans Administration Medical Center, Iowa City, IA
| | - Tyler Atagozli
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
- Veterans Administration Medical Center, Iowa City, IA
| | - Ahmed Metwali
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
- Veterans Administration Medical Center, Iowa City, IA
| | - Weiren Liu
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
- Veterans Administration Medical Center, Iowa City, IA
| | - Yue Li
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
- Veterans Administration Medical Center, Iowa City, IA
| | - Robert W. Li
- Animal Parasitic Diseases Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD
| | - David E. Elliott
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
- Veterans Administration Medical Center, Iowa City, IA
- Holden Comprehensive Cancer Center, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Bruce R. Blazar
- Division of Blood and Marrow Transplantation & Cellular Therapy, Department of Pediatrics, University of Minnesota, Minneapolis, MN
| | - M. Nedim Ince
- Department of Internal Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA
- Veterans Administration Medical Center, Iowa City, IA
- Holden Comprehensive Cancer Center, Carver College of Medicine, University of Iowa, Iowa City, IA
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10
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Liu F, Smith AD, Wang TTY, Pham Q, Yang H, Li RW. Multi-omics analysis detected multiple pathways by which pomegranate punicalagin exerts its biological effects in modulating host-microbiota interactions in murine colitis models. Food Funct 2023; 14:3824-3837. [PMID: 37013611 DOI: 10.1039/d3fo00286a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
As one of the key bioactive food ingredients in pomegranate, punicalagin (PA) possesses wide-ranging functional activities. However, the knowledge on PA-modulated microbial interactions and their physiological relevance in the gastrointestinal tract is limited. In this study, the modulating effects of PA on host-microbiota interactions were examined using multi-omics approaches in two colitis models. In a chemical colitis model, PA ingestion dampened intestinal inflammation and repressed gut microbial diversity. PA significantly reversed multiple lipids and γ-glutamyl amino acids from elevated levels in colitis mice to the baseline. Anti-inflammatory and microbiota-modulating effects of PA were further validated in an infectious colitis model induced by Citrobacter rodentium, in which PA also restored the microbial dysbiosis index to the baseline and promoted microbial interactions. Multiple microbial signatures with high predictive accuracy for key colitis pathophysiological parameters were identified, which can be developed as biomarkers for monitoring the efficacy of PA-containing functional foods in promoting gut health. Our findings should facilitate the exploitation of dual applications of PA as a bioactive food ingredient and a therapeutic agent.
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Affiliation(s)
- Fang Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China.
| | - Allen D Smith
- USDA-ARS, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
| | - Thomas T Y Wang
- USDA-ARS, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
| | - Quynhchi Pham
- USDA-ARS, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou, China.
| | - Robert W Li
- USDA-ARS, Animal Parasitic Diseases Laboratory, Beltsville, MD, USA.
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11
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Liu F, Smith AD, Wang TTY, Pham Q, Yang H, Li RW. Ellagitannin Punicalagin Disrupts the Pathways Related to Bacterial Growth and Affects Multiple Pattern Recognition Receptor Signaling by Acting as a Selective Histone Deacetylase Inhibitor. J Agric Food Chem 2023; 71:5016-5026. [PMID: 36917202 DOI: 10.1021/acs.jafc.2c08738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Punicalagin (PA) is a key ellagitannin abundant in pomegranate with wide-ranging biological activities. In this study, we examined the biological processes by which PA regulates bacterial growth and inflammation in human cells using multiomics and molecular docking approaches. PA promoted macrophage-mediated bacterial killing and inhibited the growth of Citrobacter rodentium by inducing a distinct metabolome pattern. PA acted as a selective regulator of histone deacetylases (HDACs) and affected 37 pathways in macrophages, including signaling mediated by pattern recognition receptors, such as Toll-like and NOD-like receptors. In silico simulation showed that PA can bind with high affinity to HDAC7. PA downregulated HDAC7 at both mRNA and protein levels and resulted in a decrease in the level of histone 3 lysine 27 acetylation. Our findings provide evidence that PA exerts its biological effects via multiple pathways, which can be exploited in the development of this bioactive food ingredient for disease management.
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Affiliation(s)
- Fang Liu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Allen D Smith
- Diet, Genomics and Immunology Laboratory, USDA-ARS, Beltsville, Maryland 20705, United States
| | - Thomas T Y Wang
- Diet, Genomics and Immunology Laboratory, USDA-ARS, Beltsville, Maryland 20705, United States
| | - Quynhchi Pham
- Diet, Genomics and Immunology Laboratory, USDA-ARS, Beltsville, Maryland 20705, United States
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Robert W Li
- Animal Parasitic Diseases Laboratory, USDA-ARS, Beltsville, Maryland 20705, United States
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12
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Liu F, Smith AD, Wang TTY, Pham Q, Cheung L, Yang H, Li RW. Biological pathways via which the anthocyanin malvidin alleviated the murine colitis induced by Citrobacter rodentium. Food Funct 2023; 14:1048-1061. [PMID: 36562464 DOI: 10.1039/d2fo02873e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Enteropathogenic E. coli (EPEC) is a causal agent for diarrheal diseases and contributes to morbidity and mortality in children under the age of five years. The emergence and rapid spread of antibiotic resistant EPEC strains necessitate the search for novel alternatives to antibiotics. In this study, we used Citrobacter rodentium, a natural mouse pathogen that mimics many aspects of human EPEC infections, to investigate the antimicrobial properties of the blueberry anthocyanin malvidin 3-glucoside (MG) using a multi-omics approach. MG supplementation reversed the bodyweight loss induced by C. rodentium infection and improved colonic hyperplasia and histopathological scores. In the colon tissue, MG supplementation significantly increased the expression of Hace1, a key regulator of TNFα-driven signaling, and impacted multiple pathways, such as TGFβ signaling. MG partially restored C. rodentium-induced microbial dysbiosis and significantly enhanced the abundance of the probiotic Bifidobacterium animalis. Moreover, MG disrupted the interactions of E. coli with other gut microbes. MG significantly mediated several host- and microbiota-derived metabolites, such as cytosine, ureidopropionic acid, and glutaric acid. MG normalized the bioactive lipid oleoylethanolamine, a member of the endocannabinoid system, from the dysregulated level in infected mice, directly contributing to its overall beneficial effects. Our findings provided novel insights into molecular processes via which the flavonoid malvidin exerts its biological effects in the gastrointestinal tract.
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Affiliation(s)
- Fang Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China.
| | - Allen D Smith
- USDA-ARS, Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | - Thomas T Y Wang
- USDA-ARS, Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | - Quynhchi Pham
- USDA-ARS, Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | - Lumei Cheung
- USDA-ARS, Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou, China.
| | - Robert W Li
- USDA-ARS, Animal Parasitic Diseases Laboratory, Beltsville, MD, USA.
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13
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Abstract
As one of the major short-chain fatty acids produced via microbial fermentation, butyrate serves as not only a preferred energy substrate but also an important signaling molecule. Butyrate concentrations in circulation, tissues, and gut luminal contents have important pathophysiological implications. The genetic capacity of butyrate biosynthesis by the gut microbiota is frequently compromised during aging and various disorders, such as inflammatory bowel disease, metabolic disorders and colorectal cancer. Substantial efforts have been made to identify potent butyrogenic substrates and butyrate-hyperproducing bacteria to compensate for butyrate deficiency. Interindividual butyrogenic responses exist, which are more strongly predicted by heterogeneity in the gut microbiota composition than by ingested prebiotic substrates. In this review, we catalog major food types rich in butyrogenic substrates. We also discuss the potential of butyrogenic foods with proven properties for promoting gut health and disease management using findings from clinical trials. Potential limitations and constraints in the current research are highlighted. We advocate a precise nutrition approach in designing future clinical trials by prescreening individuals for key gut microbial signatures when recruiting study volunteers. The information provided in this review will be conducive to the development of microbiota engineering approaches for enhancing the sustained production of butyrate.
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Affiliation(s)
- Miao Zhang
- College of Agriculture, Henan Provincial Key Laboratory of Ion Beam Bioengineering, Zhengzhou University, Zhengzhou, China
| | - Robert W Li
- Animal Parasitic Diseases Laboratory, USDA-ARS, Beltsville, Maryland, USA
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Zhongfang Tan
- College of Agriculture, Henan Provincial Key Laboratory of Ion Beam Bioengineering, Zhengzhou University, Zhengzhou, China
| | - Fang Liu
- College of Public Health, Zhengzhou University, Zhengzhou, China
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14
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Liu J, Bai Y, Liu F, Kohn RA, Tadesse DA, Sarria S, Li RW, Song J. Rumen Microbial Predictors for Short-Chain Fatty Acid Levels and the Grass-Fed Regimen in Angus Cattle. Animals (Basel) 2022; 12:2995. [PMID: 36359118 PMCID: PMC9656057 DOI: 10.3390/ani12212995] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/13/2022] [Accepted: 10/20/2022] [Indexed: 10/12/2023] Open
Abstract
The health benefits of grass-fed beef are well documented. However, the rumen microbiome features in beef steers raised in a grass-fed regimen have yet to be identified. This study examined the rumen microbiome profile in the feeding regimes. Our findings show that the rumen microbiome of the grass-fed cattle demonstrated greater species diversity and harbored significantly higher microbial alpha diversity, including multiple species richness and evenness indices, than the grain-fed cattle. Global network analysis unveiled that grass-fed cattle's rumen microbial interaction networks had higher modularity, suggesting a more resilient and stable microbial community under this feeding regimen. Using the analysis of compositions of microbiomes with a bias correction (ANCOM-BC) algorithm, the abundance of multiple unclassified genera, such as those belonging to Planctomycetes, LD1-PB3, SR1, Lachnospira, and Sutterella, were significantly enriched in the rumen of grass-fed steers. Sutterella was also the critical genus able to distinguish the two feeding regimens by Random Forest. A rumen microbial predictor consisting of an unclassified genus in the candidate division SR1 (numerator) and an unclassified genus in the order Bacteroidales (denominator) accurately distinguished the two feeding schemes. Multiple microbial signatures or balances strongly correlated with various levels of SCFA in the rumen. For example, a balance represented by the log abundance ratio of Sutterella to Desulfovibrio was strongly associated with acetate-to-propionate proportions in the rumen (R2 = 0.87), which could be developed as a valuable biomarker for optimizing milk fat yield and cattle growth. Therefore, our findings provided novel insights into microbial interactions in the rumen under different feed schemes and their ecophysiological implications. These findings will help to develop rumen manipulation strategies to improve feed conversion ratios and average daily weight gains for grass- or pasture-fed cattle production.
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Affiliation(s)
- Jianan Liu
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Ying Bai
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan 056038, China
| | - Fang Liu
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Richard A. Kohn
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Daniel A. Tadesse
- Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD 20708, USA
| | - Saul Sarria
- Food and Drug Administration, Center for Veterinary Medicine, Office of Research, Laurel, MD 20708, USA
| | - Robert W. Li
- United States Department of Agriculture, Agriculture Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Jiuzhou Song
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD 20742, USA
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15
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Gao Y, Yuan S, Chen Y, Liu F, Wei Z, Cao W, Li RW, Xu J, Xue C, Tang Q. The improvement effect of astaxanthin-loaded emulsions on obesity is better than that of astaxanthin in the oil phase. Food Funct 2022; 13:3720-3731. [PMID: 35266464 DOI: 10.1039/d1fo03185f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Emulsion-based delivery systems have been reported to improve the solubility, stability and bioavailability of astaxanthin. In this study, the ability of astaxanthin-loaded emulsions (AL) to ameliorate obesity induced by a high-fat and high-sucrose diet was explored, using astaxanthin in the oil phase (ASTA) as a comparison. After the administration of AL, ASTA (30 mg per kg body weight), or saline on normal or obese mice for 4 weeks, the body fat accumulation levels, hepatic lipid contents and hepatic fatty acid profiles were detected, and AL showed better anti-obesity properties than ASTA. In an acute feeding experiment, it was first observed that the astaxanthin concentration of AL was higher than that of ASTA in the blood and liver of obese mice. What's more, AL altered the microbial co-occurrence patterns in obese mice. Some gut microbial modules that were significantly correlated with obesity-related physiological parameters were identified. Overall, the improvement effect of AL on obesity is better than that of ASTA due to their higher oral absorbability and modulating effects on the gut microbiota, and we suggest AL as a more suitable astaxanthin product type for obese bodies.
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Affiliation(s)
- Yuan Gao
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Shihan Yuan
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Yuze Chen
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Fang Liu
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Zihao Wei
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Wanxiu Cao
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Robert W Li
- Laboratory of Animal Genomics and Improvement, United States Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD 20705, USA
| | - Jie Xu
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
| | - Changhu Xue
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China. .,Laboratory of Marine Drugs and Biological Products, Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong 266235, China
| | - Qingjuan Tang
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China.
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16
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Cao W, Liu F, Li RW, Chin Y, Wang Y, Xue C, Tang Q. Docosahexaenoic acid-rich fish oil prevented insulin resistance by modulating gut microbiome and promoting colonic peptide YY expression in diet-induced obesity mice. Food Science and Human Wellness 2022. [DOI: 10.1016/j.fshw.2021.07.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Gao Y, Liu F, Li RW, Li C, Xue C, Tang Q. Microbial Composition and Co-occurrence Patterns in the Gut Microbial Community of Normal and Obese Mice in Response to Astaxanthin. Front Microbiol 2021; 12:671271. [PMID: 34552567 PMCID: PMC8450573 DOI: 10.3389/fmicb.2021.671271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/10/2021] [Indexed: 12/02/2022] Open
Abstract
The changes and interaction of gut microbiota, which respond to dietary supplements, play critical roles on improving human health. The modulating effect of astaxanthin on gut microbiota has been reported. However, little is known about the co-occurrence patterns among microbial taxa in response to astaxanthin. In this study, the gut microbial composition, co-occurrence patterns, and microbial correlations with physiological parameters in astaxanthin-fed normal and obese mice were studied. Astaxanthin altered the microbial composition and co-occurrence patterns in normal and obese mice. Furthermore, astaxanthin gave more profound impacts on microbiota in obesity when compared with normal mice. In group A (normal or obese mice supplemented with astaxanthin), the abundance of Acinetobacter was decreased, and Alistipes was increased by astaxanthin, which also occurred in the MA group (obese mice supplemented with astaxanthin). An operational taxonomic unit (OTU) (GreenGeneID# 4029632) assigned to the genus Bacteroides acted as a connector in the global network of A and MA groups. It may play critical roles in bridging intimate interactions between the host and other bacteria intervened by astaxanthin. Several modules correlated with physiological parameters were detected. For example, modules A12 and MA10 were significantly and negatively correlated with lipopolysaccharide (LPS) and fasting blood glucose (FBG) levels, respectively. A positive correlation was found between the node connectivity of the OTUs belonging to Clostridiaceae with LPS in obese mice, which indicated the role of Clostridiales as a potential pathological marker. Our findings provided a new interpretation of the role of astaxanthin in health and may contribute to further research on microbial community engineering.
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Affiliation(s)
- Yuan Gao
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Fang Liu
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Robert W Li
- Laboratory of Animal Genomics and Improvement, United States Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD, United States
| | - Chunjun Li
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory of Marine Drugs and Biological Products, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qingjuan Tang
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, China
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18
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Cao W, Liu F, Li RW, Yang R, Wang Y, Xue C, Tang Q. Triacylglycerol rich in docosahexaenoic acid regulated appetite via the mediation of leptin and intestinal epithelial functions in high-fat, high-sugar diet-fed mice. J Nutr Biochem 2021; 99:108856. [PMID: 34517098 DOI: 10.1016/j.jnutbio.2021.108856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/25/2021] [Accepted: 08/10/2021] [Indexed: 12/13/2022]
Abstract
High-fat, high-sugar diet (HFHS) induced leptin resistance and intestinal epithelial dysfunction is implicated in hyperphagia and metabolic disorders. Numerous studies have demonstrated the efficacy of dietary interventions for reducing appetite. This study aims to investigate whether triacylglycerol rich in DHA (DHA-TG) could regulate appetite in mice fed with a HFHS diet and the mechanism by which it achieves that. DHA-TG could reduce food intake and regulate neuropeptides (POMC, AgRP, and NPY) expression in HFHS diet-fed mice. Hypothalamic transcriptome analysis reveals that these effects might be attributed to the role of DHA-TG in modulating hormone secretion and digestive system process. According to ELISA and RT-qPCR analysis, DHA-TG ameliorated leptin secretion and attenuated central leptin resistance induced by HFHS diet feeding. Besides, DHA-TG prevented the damage of intestinal epithelial barrier in nutritive obese mice by improving leptin sensitivity. Based on jejunal transcriptome analysis, DHA-TG also protected intestinal endocrine function, especially the secretion of another anorectic hormone, cholecystokinin (CCK), in HFHS diet-fed mice. Furthermore, DHA-TG was ineffective in repressing appetite, and improving gut leakage in leptin-deficient mice (ob/ob mice). In conclusion, DHA-TG has a potential to regulate appetite with the action of leptin, and intestinal epithelial functions in HFHS diet-fed mice.
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Affiliation(s)
- Wanxiu Cao
- College of Food Science and Engineering, Ocean University of China, Qingdao, China; Marine Biomedical Research Institute of Qingdao, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Fang Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Robert W Li
- United States Department of Agriculture, Agriculture Research Service (USDA-ARS), Animal Genomics and Improvement Laboratory, Beltsville, Maryland, USA
| | - Ruili Yang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yuming Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qingjuan Tang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.
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19
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Wan J, Wu Y, Pham Q, Li RW, Yu L, Chen MH, Boue SM, Yokoyama W, Li B, Wang TTY. Effects of Differences in Resistant Starch Content of Rice on Intestinal Microbial Composition. J Agric Food Chem 2021; 69:8017-8027. [PMID: 34236836 DOI: 10.1021/acs.jafc.0c07887] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The aim of this study was to evaluate the effects of resistant starch (RS) and fat levels on the gut microbiome in C57BL/6 mice. Three levels of RS from three varieties of rice were the major source of carbohydrates and fat levels were low (10%) and high (39%). We confirmed that RS decreased the Firmicutes to Bacteroidetes ratio, increased SCFA production by higher Bacteroidaceae and S24-7 abundance, and enriched predicted gene families of glycosidases and functional pathways associated with carbohydrate and glycan metabolism. We also found correlations between microbial taxa and tissue gene expression related to carbohydrate and lipid metabolism. Moreover, increasing RS levels resulted in a molecular ecological network with enhanced modularity and interspecific synergy, which is less sensitive to high fat intervention. Overall, RS as low as 0.44% from cooked rice can modulate gut microbiome in mice, which correlated to a protective effect against deleterious effects of an obesogenic diet.
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Affiliation(s)
- Jiawei Wan
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
- Diet Genomics and Immunology Laboratory, BHNRC, ARS, USDA, Beltsville, Maryland 20705, United States
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland 20742, United States
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Yanbei Wu
- Diet Genomics and Immunology Laboratory, BHNRC, ARS, USDA, Beltsville, Maryland 20705, United States
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland 20742, United States
- China-Canada Joint Lab of Food Nutrition and Health (Beijing), Beijing Technology &Business University, Beijing 100084, PR China
| | - Quynhchi Pham
- Diet Genomics and Immunology Laboratory, BHNRC, ARS, USDA, Beltsville, Maryland 20705, United States
| | - Robert W Li
- Animal Parasitic Diseases Laboratory, ARS, USDA, Beltsville, Maryland 20705, United States
| | - Liangli Yu
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland 20742, United States
| | - Ming-Hsuan Chen
- Dale Bumpers National Rice Research Center, ARS, USDA, Stuttgart, Arkansas 72160, United States
| | - Stephen M Boue
- Southern Regional Research Center, ARS, USDA, New Orleans, Louisiana 70124, United States
| | - Wallace Yokoyama
- Healthy Processed Foods Research Unit, WRRC, ARS, USDA, Albany, California 94710, United States
| | - Bin Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, PR China
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Thomas T Y Wang
- Diet Genomics and Immunology Laboratory, BHNRC, ARS, USDA, Beltsville, Maryland 20705, United States
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20
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Liu F, Hou P, Zhang H, Tang Q, Xue C, Li RW. Food-grade carrageenans and their implications in health and disease. Compr Rev Food Sci Food Saf 2021; 20:3918-3936. [PMID: 34146449 DOI: 10.1111/1541-4337.12790] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/22/2021] [Accepted: 05/13/2021] [Indexed: 12/19/2022]
Abstract
Food additives, often used to guarantee the texture, shelf-life, taste, and appearance of processed foods, have gained widespread attention due to their increased link to the growing incidence of chronic diseases. As one of the most common additives, carrageenans have been used in human diets for hundreds of years. While classified as generally recognized as safe (GRAS) for human consumption, numerous studies since the 1980s have suggested that carrageenans, particularly those with random coil conformations, may have adverse effects on gastrointestinal health, including aggravating intestinal inflammation. While these studies have provided some evidence of adverse effects, the topic is still controversial. Some have suggested that the negative consequence of the consumption of carrageenans may be structure dependent. Furthermore, pre-existing conditions may predispose individuals to varied outcomes of carrageenan intake. In this review, structure-function relationships of various carrageenans in the context of food safety are discussed. We reviewed the molecular mechanisms by which carrageenans exert their biological effects. We summarized the findings associated with carrageenan intake in animal models and clinical trials. Moreover, we examined the interactions between carrageenans and the gut microbiome in the pathogenesis of gastrointestinal disorders. This review argues for personalized guidance on carrageenan intake based on individuals' health status. Future research efforts that aim to close the knowledge gap on the effect of low-dose and chronic carrageenan intake as well as interactions among food additives should be conducive to the improved safety profile of carrageenans in processed food products.
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Affiliation(s)
- Fang Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Pengfen Hou
- Affiliated Hospital of Qingdao Binhai University, Qingdao, China
| | - Hui Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Qingjuan Tang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.,Laboratory of Marine Drugs and Biological Products, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Robert W Li
- USDA-ARS Animal Genomics and Improvement Laboratory, Beltsville, Maryland, USA
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21
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Cao W, Li RW, Chin Y, Wang Y, Xue C, Tang Q. Transcriptome analysis reveals the protective role of fructo-oligosaccharide in colonic mucosal barriers in exercise-induced stressed mice. Food Funct 2021; 12:4484-4495. [PMID: 33885098 DOI: 10.1039/d0fo02556a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Most athletes continually endure mental and physical stress from intense exercise. Fructo-oligosaccharide (FOS) can reduce physical exhaustion, but the concrete mechanism behind it still needs further research. In this study, the effect of FOS on colonic mucosal barriers was investigated using an exercise-induced stress mouse model. Except for control individuals, mice were subject to cycles of 2-day exercise (at 20 rpm) interleaved by 5-day rest. The mice experienced a total of 6 days of exercise during the feeding period. FOS improved common indicators of exhaustion, such as glycogen storage in muscle. 16S rRNA data supported that changes in the gut microbiome were also closely related to stress status. Notably, Anaerotruncus was increased in mice under stress, while FOS facilitated the growth of Dorea, which is negatively associated with exhaustion. The RNA-seq analysis revealed that FOS could maintain the integrity of colonic epithelial barriers. For example, FOS significantly restored the expression of tight junctions (Occludin and Zonula occludens-1) in the colon, which was impaired under a stress state. Besides, the NOD-like receptor family pyrin domain containing 6 (NLRP6) inflammasome might contribute to the protection of the colonic mucosa by promoting the secretion of IL-18, Mucin2 (Muc2) and intestine lectin 1 (Itln1) in FOS-treated individuals. In short, FOS administration attenuated the damage of colonic mucosal barriers in exercise-induced stressed mice.
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Affiliation(s)
- Wanxiu Cao
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.
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22
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Urban JF, Nielsen MK, Gazzola D, Xie Y, Beshah E, Hu Y, Li H, Rus F, Flanagan K, Draper A, Vakalapudi S, Li RW, Ostroff GR, Aroian RV. An inactivated bacterium (paraprobiotic) expressing Bacillus thuringiensis Cry5B as a therapeutic for Ascaris and Parascaris spp. infections in large animals. One Health 2021; 12:100241. [PMID: 33889707 PMCID: PMC8048022 DOI: 10.1016/j.onehlt.2021.100241] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023] Open
Abstract
Ascaris and Parascaris are important parasites in the family Ascarididae, large, ubiquitous intestinal-dwelling nematodes infecting all classes of vertebrates. Parasitic nematode drug resistance in veterinary medicine and drug recalcitrance in human medicine are increasing worldwide, with few if any new therapeutic classes on the horizon. Some of these parasites are zoonotic, e.g., Ascaris is passed from humans to pigs and vice versa. The development of new therapies against this family of parasites would have major implications for both human and livestock health. Here we tested the therapeutic ability of a paraprobiotic or dead probiotic that expresses the Bacillus thuringiensis Cry5B protein with known anthelmintic properties, against zoonotic Ascaris suum and Parascaris spp. This paraprobiotic, known as IBaCC, intoxicated A. suum larvae in vitro and was highly effective in vivo against intestinal A. suum infections in a new mouse model for this parasite. Fermentation was scaled up to 350 l to treat pigs and horses. Single dose Cry5B IBaCC nearly completely cleared A. suum infections in pigs. Furthermore, single dose Cry5B IBaCC drove fecal egg counts in Parascaris-infected foals to zero, showing at least parity with, and potential superiority to, current efficacy of anthelmintics used against this parasite. Cry5B IBaCC therefore represents a new, paraprobiotic One Health approach towards targeting Ascarididae that is safe, effective, massively scalable, stable, and useful in human and veterinary medicine in both the developed and developing regions of the world. IBaCC is Bacillus thuringiensis Cry5B protein crystals trapped inside dead bacteria. IBaCC intoxicates Ascaris suum intestinal parasitic nematodes in vitro. IBaCC is highly effective against A. suum parasites in vivo in mice and pigs. IBaCC is highly effective against related Parascaris parasites in foals. IBaCC represents a new paradigm for treating ascarid parasites of humans and animals.
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Affiliation(s)
- Joseph F Urban
- U. S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal and Parasitic Diseases Laboratory, Beltsville, MD, United States of America.,U. S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, United States of America
| | - Martin K Nielsen
- M.H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, United States of America
| | - David Gazzola
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Yue Xie
- U. S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal and Parasitic Diseases Laboratory, Beltsville, MD, United States of America.,U. S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, United States of America.,Department of Parasitology, College of Veterinary Medicine, Sichuan Agricultural University, Sichuan, China
| | - Ethiopia Beshah
- U. S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal and Parasitic Diseases Laboratory, Beltsville, MD, United States of America.,U. S. Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, United States of America
| | - Yan Hu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Hanchen Li
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Florentina Rus
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Kelly Flanagan
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Austin Draper
- Synthetic Biomanufacturing Facility, Utah State University, Logan, UT, United States of America
| | - Sridhar Vakalapudi
- Synthetic Biomanufacturing Facility, Utah State University, Logan, UT, United States of America
| | - Robert W Li
- U. S. Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal and Parasitic Diseases Laboratory, Beltsville, MD, United States of America
| | - Gary R Ostroff
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States of America
| | - Raffi V Aroian
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, United States of America
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23
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Abstract
Dynamic studies in time course experimental designs and clinical approaches have been widely used by the biomedical community. These applications are particularly relevant in stimuli-response models under environmental conditions, characterization of gradient biological processes in developmental biology, identification of therapeutic effects in clinical trials, disease progressive models, cell-cycle, and circadian periodicity. Despite their feasibility and popularity, sophisticated dynamic methods that are well validated in large-scale comparative studies, in terms of statistical and computational rigor, are less benchmarked, comparing to their static counterparts. To date, a number of novel methods in bulk RNA-Seq data have been developed for the various time-dependent stimuli, circadian rhythms, cell-lineage in differentiation, and disease progression. Here, we comprehensively review a key set of representative dynamic strategies and discuss current issues associated with the detection of dynamically changing genes. We also provide recommendations for future directions for studying non-periodical, periodical time course data, and meta-dynamic datasets.
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Affiliation(s)
- Vera-Khlara S. Oh
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA;
- Department of Computer Science and Statistics, College of Natural Sciences, Jeju National University, Jeju City 63243, Korea
| | - Robert W. Li
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA;
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24
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Andrade FDO, Liu F, Zhang X, Rosim MP, Dani C, Cruz I, Wang TTY, Helferich W, Li RW, Hilakivi-Clarke L. Genistein Reduces the Risk of Local Mammary Cancer Recurrence and Ameliorates Alterations in the Gut Microbiota in the Offspring of Obese Dams. Nutrients 2021; 13:nu13010201. [PMID: 33440675 PMCID: PMC7827465 DOI: 10.3390/nu13010201] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 12/29/2020] [Accepted: 01/05/2021] [Indexed: 02/06/2023] Open
Abstract
The risk of recurrence of estrogen receptor-positive breast cancer remains constant, even 20 years after diagnosis. Recurrence may be more likely in patients pre-programmed for it already in the womb, such as in the daughters born to obese mothers. Maternal obesity persistently alters offspring’s gut microbiota and impairs tumor immune responses. To investigate if the gut dysbiosis is linked to increased risk of mammary cancer recurrence in the offspring of obese rat dams, we fed adult offspring genistein which is known to have beneficial effects on the gut bacteria. However, the effects of genistein on breast cancer remain controversial. We found that genistein intake after tamoxifen response prevented the increased risk of local recurrence in the offspring of obese dams but had no effect on the control offspring. A significant increase in the abundance of inflammatory Prevotellaceae and Enterobacteriaceae, and a reduction in short-chain fatty acid producing Clostridiaceae was observed in the offspring of obese dams. Genistein supplementation reversed these changes as well as reversed increased gut metabolite N-acetylvaline levels which are linked to increased all-cause mortality. Genistein supplementation also reduced genotoxic tyramine levels, increased metabolites improving pro-resolving phase of inflammation, and reversed the elevated tumor mRNA expression of multiple immunosuppressive genes in the offspring of obese dams. If translatable to breast cancer patients, attempts to prevent breast cancer recurrences might need to focus on dietary modifications which beneficially modify the gut microbiota.
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Affiliation(s)
- Fabia de Oliveira Andrade
- Department of Oncology, Georgetown University, Washington, DC 20057, USA; (F.d.O.A.); (X.Z.); (M.P.R.); (C.D.); (I.C.)
| | - Fang Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266555, China;
| | - Xiyuan Zhang
- Department of Oncology, Georgetown University, Washington, DC 20057, USA; (F.d.O.A.); (X.Z.); (M.P.R.); (C.D.); (I.C.)
| | - Mariana Papaleo Rosim
- Department of Oncology, Georgetown University, Washington, DC 20057, USA; (F.d.O.A.); (X.Z.); (M.P.R.); (C.D.); (I.C.)
| | - Caroline Dani
- Department of Oncology, Georgetown University, Washington, DC 20057, USA; (F.d.O.A.); (X.Z.); (M.P.R.); (C.D.); (I.C.)
| | - Idalia Cruz
- Department of Oncology, Georgetown University, Washington, DC 20057, USA; (F.d.O.A.); (X.Z.); (M.P.R.); (C.D.); (I.C.)
| | - Thomas T. Y. Wang
- United States Department of Agriculture, Beltsville Human Nutrition Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD 20705, USA;
| | - William Helferich
- Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, IL 1801, USA;
| | - Robert W. Li
- United States Department of Agriculture, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA;
| | - Leena Hilakivi-Clarke
- Department of Oncology, Georgetown University, Washington, DC 20057, USA; (F.d.O.A.); (X.Z.); (M.P.R.); (C.D.); (I.C.)
- Correspondence:
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25
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Sanders J, Xie Y, Gazzola D, Li H, Abraham A, Flanagan K, Rus F, Miller M, Hu Y, Guynn S, Draper A, Vakalapudi S, Petersson KH, Zarlenga D, Li RW, Urban JF, Ostroff GR, Zajac A, Aroian RV. A new paraprobiotic-based treatment for control of Haemonchus contortus in sheep. Int J Parasitol Drugs Drug Resist 2020; 14:230-236. [PMID: 33242790 PMCID: PMC7695930 DOI: 10.1016/j.ijpddr.2020.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 12/21/2022]
Abstract
Haemonchus contortus is a critical parasite of goats and sheep. Infection by this blood-feeding gastrointestinal nematode (GIN) parasite has significant health consequences, especially in lambs and kids. The parasite has developed resistance to virtually all known classes of small molecule anthelmintics used to treat it, giving rise in some areas to multidrug resistant parasites that are very difficult to control. Thus, new anthelmintics are urgently needed. Bacillus thuringiensis (Bt) crystal protein 5B (Cry5B), a naturally occurring protein made by a bacterium widely and safely used around the world as a bioinsecticide, represents a new non-small molecule modality for treating GINs. Cry5B has demonstrated anthelmintic activities against parasites of monogastric animals, including some related to those that infect humans, but has not yet been studied in a ruminant. Here we show that H. contortus adults are susceptible to Cry5B protein in vitro. Cry5B produced in its natural form as a spore-crystal lysate against H. contortus infections in goats had no significant efficacy. However, a new Active Pharmaceutical Ingredient (API) paraprobiotic form of Cry5B called IBaCC (Inactivated Bacterium with Cytosolic Crystals), in which Cry5B crystals are encapsulated in dead Bt cell wall ghosts, showed excellent efficacy in vitro against larval stages of H. contortus and relative protein stability in bovine rumen fluid. When given to sheep experimentally infected with H. contortus as three 60 mg/kg doses, Cry5B IBaCC resulted in significant reductions in fecal egg counts (90%) and parasite burdens (72%), with a very high impact on female parasites (96% reduction). These data indicate that Cry5B IBaCC is a potent new treatment tool for small ruminants in the battle against H. contortus.
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Affiliation(s)
- John Sanders
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Yue Xie
- United State Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, Immunology Laboratory, Beltsville, MD, 20705, USA
| | - David Gazzola
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Hanchen Li
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Ambily Abraham
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Kelly Flanagan
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Florentina Rus
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Melanie Miller
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yan Hu
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA; Biology Department, Worcester State University, Worcester, MA, 01602, USA
| | - Sierra Guynn
- Department of Large Animal Clinical Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Austin Draper
- Synthetic Biomanufacturing Facility, Utah State University, Logan, UT, 84341, USA
| | - Sridhar Vakalapudi
- Synthetic Biomanufacturing Facility, Utah State University, Logan, UT, 84341, USA
| | - Katherine H Petersson
- Department of Fisheries, Animal, and Veterinary Sciences, University of Rhode Island, Kingston, RI, 02881, USA
| | - Dante Zarlenga
- United State Department of Agriculture, Agricultural Research Service, Animal Parasitic Diseases Laboratory, Beltsville, MD, 20705, USA
| | - Robert W Li
- United State Department of Agriculture, Agricultural Research Service, Animal Parasitic Diseases Laboratory, Beltsville, MD, 20705, USA
| | - Joseph F Urban
- United State Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, Immunology Laboratory, Beltsville, MD, 20705, USA; United State Department of Agriculture, Agricultural Research Service, Animal Parasitic Diseases Laboratory, Beltsville, MD, 20705, USA
| | - Gary R Ostroff
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Anne Zajac
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Raffi V Aroian
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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26
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Gao Y, Yuan S, Zhang L, Yang L, Liu F, Li RW, Li C, Xue C, Xu J, Tang Q. Absorbability of Astaxanthin Was Much Lower in Obese Mice Than in Normal Mice. J Agric Food Chem 2020; 68:11161-11169. [PMID: 32914625 DOI: 10.1021/acs.jafc.0c03486] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Astaxanthin has been favored as a health food supplement by obese consumers. However, no detailed descriptions are available concerning the absorption of astaxanthin in obese individuals. In this study, we conducted acute and chronic feeding experiments in C57BL/6J mice to study the differences in astaxanthin absorption in normal and obese bodies. The obesity condition greatly decreased astaxanthin concentration in the blood and liver, its accumulation in tissues and organs, and the bioaccessibility. This may be related to the excessive intake of sucrose, fatty acids, and cholesterol, the increased gastrointestinal motility, and the disorder of gut microbiota in the obese body. Overall, our study showed that the obese body had a far less oral absorbability of astaxanthin than a normal body, and we suggest that the recommended or approved doses of astaxanthin can be properly increased for the obese body in the hope that astaxanthin will play a more active role in obese individuals.
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Affiliation(s)
- Yuan Gao
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Shihan Yuan
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Lirong Zhang
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Lu Yang
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Fang Liu
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Robert W Li
- Laboratory of Animal Genomics and Improvement, United States Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, Maryland 20705, United States
| | - Chunjun Li
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Changhu Xue
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong 266235, China
| | - Jie Xu
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
| | - Qingjuan Tang
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong 266003, China
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27
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Liu J, Liu F, Cai W, Jia C, Bai Y, He Y, Zhu W, Li RW, Song J. Diet-induced changes in bacterial communities in the jejunum and their associations with bile acids in Angus beef cattle. Anim Microbiome 2020; 2:33. [PMID: 33499973 PMCID: PMC7807434 DOI: 10.1186/s42523-020-00051-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022] Open
Abstract
Background The small intestine, while serving as the main absorption organ, also possesses a unique bacterial environment and holds the critical function of conversion of primary bile acids. Bile acids are, in turn, able to regulate bacterial composition and promote the growth of bacteria that convert primary bile acids to secondary bile acids. However, in beef cattle, few studies have explored the influence of diets on jejunal bacterial communities and examined its relationships with bile acids. Here, we examined the impact of grain- and grass-based diets on jejunal and fecal bacterial communities’ composition and investigated possible association of bacterial features with bile acids. Results We demonstrated that the influences of diets on intestinal bacteria can be observed in young beef cattle after weaning. A significantly higher level of microbial diversity was documented in feces of grass-fed cattle comparing to grain-fed cattle. Top 20 important genera identified with random forest analysis on fecal bacterial community can be good candidates for microbial biomarkers. Moreover, the jejunal bacteria of adult Angus beef cattle exhibited significant differences in microbial composition and metabolic potential under different diets. Global balances and bacteria signatures predictive of bile acids were identified, indicative of the potential association of bacterial features with bile acids. Conclusions The findings from this study provided novel insights into the relationships between jejunal bacteria and bile acids under different diets in Angus beef cattle. Our results should help us gain a better understanding of potential health benefits of grass-fed beef.
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Affiliation(s)
- Jianan Liu
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD, 20742, USA.,United States Department of Agriculture, Agriculture Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA
| | - Fang Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Wentao Cai
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Cunling Jia
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Ying Bai
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Yanghua He
- Department of Human Nutrition, Food and Animal Sciences, University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - Weiyun Zhu
- College of Animal Science, Nanjing Agricultural University, Nanjing, China
| | - Robert W Li
- United States Department of Agriculture, Agriculture Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA.
| | - Jiuzhou Song
- Department of Animal & Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
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28
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Dawson HD, Chen C, Li RW, Bell LN, Shea-Donohue T, Kringel H, Beshah E, Hill DE, Urban JF. Molecular and metabolomic changes in the proximal colon of pigs infected with Trichuris suis. Sci Rep 2020; 10:12853. [PMID: 32732949 PMCID: PMC7393168 DOI: 10.1038/s41598-020-69462-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
The pig whipworm Trichuris suis is important in swine production because of its negative effects on pig performance and, notably, to some humans with inflammatory bowel disease as a therapeutic agent that modulates inflammation. The proximal colon of T. suis-infected pigs exhibited general inflammation around day 21 after inoculation with infective eggs that is transcriptionally characterized by markers of type-2 immune activation, inflammation, cellular infiltration, tissue repair enzymes, pathways of oxidative stress, and altered intestinal barrier function. Prominent gene pathways involved the Th2-response, de novo cholesterol synthesis, fructose and glucose metabolism, basic amino acid metabolism, and bile acid transport. Upstream regulatory factor analysis implicated the bile acid/farnesoid X receptor in some of these processes. Metabolic analysis indicated changes in fatty acids, antioxidant capacity, biochemicals related to methylation, protein glycosylation, extracellular matrix structure, sugars, Krebs cycle intermediates, microbe-derived metabolites and altered metabolite transport. Close to 1,200 differentially expressed genes were modulated in the proximal colon of pigs with a persistent adult worm infection that was nearly 90% lower in pigs that had expelled worms. The results support a model to test diets that favorably alter the microbiome and improve host intestinal health in both pigs and humans exposed to Trichuris.
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Affiliation(s)
- Harry D Dawson
- United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, Beltsville, USA
| | - Celine Chen
- United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, Beltsville, USA
| | - Robert W Li
- Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD, USA
| | | | | | - Helene Kringel
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ethiopia Beshah
- United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, Beltsville, USA
| | - Dolores E Hill
- Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD, USA
| | - Joseph F Urban
- United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics, and Immunology Laboratory, Beltsville, USA. .,Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD, USA.
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29
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Liu F, Smith AD, Solano-Aguilar G, Wang TTY, Pham Q, Beshah E, Tang Q, Urban JF, Xue C, Li RW. Mechanistic insights into the attenuation of intestinal inflammation and modulation of the gut microbiome by krill oil using in vitro and in vivo models. Microbiome 2020; 8:83. [PMID: 32498703 PMCID: PMC7273679 DOI: 10.1186/s40168-020-00843-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/17/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND The anti-inflammatory property of ω-3 polyunsaturated fatty acids (PUFA) has been exploited in the management of inflammatory bowel disease (IBD) with promising results. However, it remains unclear if PUFA play a significant role in the resolution of inflammation and promotion of mucosal healing. Krill oil (KO) is a natural product rich in PUFA and the potent antioxidant, astaxanthin. In this study, we attempted to understand the mechanisms through which KO modulates the gut microbiome and metabolome using in vitro and in vivo colitis models and a multi-omics based approach. RESULTS KO significantly decreased LPS-induced IL1β and TNFα expression in human macrophages in vitro in a dose-dependent manner by regulating a broad spectrum of signaling pathways, including NF-κB and NOD-like receptor signaling, and displayed a synergistic effect with COX2 and IKK2 inhibitors in attenuating inflammatory pathways. Moreover, KO was involved in the resolution of inflammation by promoting M2 polarization and enhancing macrophage-mediated intracellular bacterial killing. Parasite-dependent intestinal mucosal damage and microbial dysbiosis induced by Trichuris suis infection in pigs were partially restored by feeding KO. KO supplementation reduced the abundance of Rickettsiales and several species of Lactobacillus, which were among the important features identified by random forests analysis contributing to classification accuracy for KO supplementation. Several microbial signatures with strong predictive power for the status of both infection and supplementation were identified. The inhibitory effect of KO on histidine metabolism was identified using untargeted metabolomics. KO supplementation reduced several key metabolites related to histamine metabolism by suppressing the expression of a gene encoding L-histidine decarboxylase in the colon mucosa and reducing histamine biosynthesis of microbial origin. Moreover, the pro-resolving properties of KO were validated using a Citrobacter rodentium-induced Th1-dependent colitis murine model. Further, microbial signatures with high prediction accuracy for colitis-related pathophysiological traits were identified in mice. CONCLUSION The findings from this study provided a mechanistic basis for optimizing microbiome-inspired alternative therapeutics in the management of IBD. The microbial signatures identified, particularly those with strong predictive accuracy for colitis phenotypes, will facilitate the development of biomarkers associated with appropriate dietary intervention to manage intestinal inflammation. Video abstract.
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Affiliation(s)
- Fang Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Allen D Smith
- United States Department of Agriculture, Beltsville Human Nutrition Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
| | - Gloria Solano-Aguilar
- United States Department of Agriculture, Beltsville Human Nutrition Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
| | - Thomas T Y Wang
- United States Department of Agriculture, Beltsville Human Nutrition Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
| | - Quynhchi Pham
- United States Department of Agriculture, Beltsville Human Nutrition Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
| | - Ethiopia Beshah
- United States Department of Agriculture, Beltsville Human Nutrition Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
| | - Qingjuan Tang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Joseph F Urban
- United States Department of Agriculture, Beltsville Human Nutrition Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China.
| | - Robert W Li
- United States Department of Agriculture, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA.
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30
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Lu M, Li RW, Zhao H, Yan X, Lillehoj HS, Sun Z, Oh S, Wang Y, Li C. Effects of Eimeria maxima and Clostridium perfringens infections on cecal microbial composition and the possible correlation with body weight gain in broiler chickens. Res Vet Sci 2020; 132:142-149. [PMID: 32575030 DOI: 10.1016/j.rvsc.2020.05.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/19/2020] [Accepted: 05/16/2020] [Indexed: 02/07/2023]
Abstract
With the voluntary and regulatory withdrawal of antibiotic growth promoters from animal feed, coccidiosis and necrotic enteritis (NE) emerge as the top two enteric poultry infectious diseases responsible for major economic loss worldwide. The objective of this study was to investigate the correlation between the cecal microbiota compositions with the growth trait after coccidiosis and NE. In this study, the effects of Eimeria maxima and/or Clostridium perfringens infections on the microbial composition and potential correlation with the body weight gain were investigated in broiler chickens using 16S rRNA gene sequencing. E. maxima and C. perfringens coinfection successfully induced NE with its typical gut lesions and significant reductions in the percentage of relative body weight gain (RBWG%). The NE challenge model did not affect cecal microbial diversity, but influenced the cecal microbial composition. KEGG enzymes in microbiota were significantly altered in abundance following dual infections. Furthermore, significant correlations between cecal microbiota modules and RBWG% were identified in the sham control, E. maxima or C. perfringens infected groups. Understanding of host-microbiota interaction in NE would enhance the development of antibiotics-independent strategies to reduce the harmful effect of NE on the gut microbiota structure, and improve the gut health and poultry production.
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Affiliation(s)
- Mingmin Lu
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service (ARS), US Department of Agriculture (USDA), Beltsville, MD, USA
| | - Robert W Li
- Animal Genomics & Improvement Laboratory, ARS, USDA, Beltsville, MD, USA
| | - Hongyan Zhao
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service (ARS), US Department of Agriculture (USDA), Beltsville, MD, USA; College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Xianghe Yan
- Environment Microbial and Food Safety Laboratory, ARS, USDA, Beltsville, MD, USA
| | - Hyun S Lillehoj
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service (ARS), US Department of Agriculture (USDA), Beltsville, MD, USA
| | - Zhifeng Sun
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service (ARS), US Department of Agriculture (USDA), Beltsville, MD, USA
| | - SungTak Oh
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service (ARS), US Department of Agriculture (USDA), Beltsville, MD, USA
| | - Yueying Wang
- Animal Genomics & Improvement Laboratory, ARS, USDA, Beltsville, MD, USA; College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, China
| | - Charles Li
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service (ARS), US Department of Agriculture (USDA), Beltsville, MD, USA.
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Gao Y, Yang L, Chin Y, Liu F, Li RW, Yuan S, Xue C, Xu J, Tang Q. Astaxanthin n-Octanoic Acid Diester Ameliorates Insulin Resistance and Modulates Gut Microbiota in High-Fat and High-Sucrose Diet-Fed Mice. Int J Mol Sci 2020; 21:ijms21062149. [PMID: 32245087 PMCID: PMC7139465 DOI: 10.3390/ijms21062149] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023] Open
Abstract
Astaxanthin n-octanoic acid diester (AOD) is a type of astaxanthin connecting medium-chain fatty acids with a more stable structure. In this study, we examined the role of AOD in ameliorating insulin resistance (IR) induced by a high-fat and high-sucrose diet (HFD) as well as its effect on modulating gut microbiota in mice, with free astaxanthin (AST) as a comparison. Four groups of male C57BL/6J mice (6 weeks old; n = 10 per group) were fed with a normal control diet (NC), HFD orally administered with AOD, AST (50 mg/kg body weight), or vehicle for 8 weeks. AOD improved glucose tolerance, IR, systematic and intestinal inflammation, and intestinal integrity better than AST. Further, both AOD and AST modulated gut microbiota. A significantly higher abundance of Bacteroides and Coprococcus was found in AOD than in AST, and the predicted pathway of carbohydrate metabolism was significantly impacted by AOD. Overall, AOD may play a role in alleviating IR and inflammation with the modulating effect on microbiota in HFD-fed mice. Our findings could facilitate the development of AOD as a bioactive nutraceutical and more stable alternative to AST.
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Affiliation(s)
- Yuan Gao
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Lu Yang
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Yaoxian Chin
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Fang Liu
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Robert W. Li
- Laboratory of Animal Genomics and Improvement, United States Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD 20705, USA
| | - Shihan Yuan
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Changhu Xue
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, China
| | - Jie Xu
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Correspondence: (J.X.); (Q.T.); Tel.: +86-0532-8203-2597 (J.X. & Q.T.)
| | - Qingjuan Tang
- Laboratory of Food Science and Human Health, College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Correspondence: (J.X.); (Q.T.); Tel.: +86-0532-8203-2597 (J.X. & Q.T.)
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Liu F, Xie Y, Zajac AM, Hu Y, Aroian RV, Urban JF, Li RW. Gut microbial signatures associated with moxidectin treatment efficacy of Haemonchus contortus in infected goats. Vet Microbiol 2020; 242:108607. [PMID: 32122611 DOI: 10.1016/j.vetmic.2020.108607] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/14/2020] [Accepted: 02/05/2020] [Indexed: 12/14/2022]
Abstract
Parasitic infections are associated with profound changes in the structure and function of the gut microbiome in various host-parasite systems. Here we examined the microbial composition and function in the abomasum, proximal colon and feces of Haemonchus contortus-infected goats after a partial anthelmintic drug clearance. A single-dose treatment of H. contortus-infected goats with Cydectin (moxidectin) resulted in an 83.9 % and 61.8 % reduction in fecal egg counts (EPG) and worm burden, respectively (P < 0.01), and restored abomasal pH to a normal baseline level. The treatment significantly increased the abundance of Proteobacteria, particularly that of Campylobacter, in the proximal colon. It also significantly affected several basic pathways, including bacterial secretion, butyrate metabolism, and LPS biosynthesis, and seemingly reduced the cellulolytic capacity in the colon. Several network modules displayed a strong correlation with EPG and worm burden. The Mantel test indicated a strong correlation between treatment related network topologies of the operational taxonomic units (OTU) belonging to Actinobacteria and Rikenellaceae and EPG and worm burden levels, respectively. Furthermore, microbial signatures that may better predict anthelmintic efficacy were identified. A signature or balance represented by the log ratio of the abundance of Verrucomicrobiaceae and Camplyobacteraceae had a strong correlation with EPG (r = 0.80). These novel insights into the interactions between H. contortus and gut microbiome in the caprine host and the consequence of a partial anthelmintic clearance on animal health and well-being may facilitate the design of more effective next-generation anthelmintics.
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Affiliation(s)
- Fang Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yue Xie
- Sichuan Agricultural University, College of Veterinary Medicine, Department of Parasitology, Chengdu, Sichuan, China
| | - Anne M Zajac
- Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | - Yan Hu
- Biology Department, Worcester State University, Worcester, MA, USA
| | | | - Joseph F Urban
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD, USA; United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Immunology, and Genomics Laboratory, Beltsville, MD, USA
| | - Robert W Li
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD, USA.
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Liu F, Wang TTY, Tang Q, Xue C, Li RW, Wu VCH. Malvidin 3-Glucoside Modulated Gut Microbial Dysbiosis and Global Metabolome Disrupted in a Murine Colitis Model Induced by Dextran Sulfate Sodium. Mol Nutr Food Res 2019; 63:e1900455. [PMID: 31444937 DOI: 10.1002/mnfr.201900455] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/10/2019] [Indexed: 12/25/2022]
Abstract
SCOPE This study aims to elucidate the mechanisms of the anthocyanin malvidin 3-glucoside (MV) in alleviating gut dysbiosis using a murine colitis model induced by dextran sulfate sodium (DSS). METHODS AND RESULTS The effect of MV on the structure and function of the colon microbiome and microbial metabolism is evaluated using 16S rRNA gene sequencing, global metabolomics, and a network algorithm based on the random-matrix theory. MV ingestion improved histopathological scores and increased IL10 expression in the colon mucosa of colitis mice. While DSS has a profound effect on the gut microbiome and significantly decreases both microbial richness and evenness, MV further reduces evenness but promotes microbial interactions and restores the Firmicutes/Bacteroidetes ratio repressed by DSS. Moreover, MV reduces the abundance of pathogenic bacteria, such as Ruminococcus gnavus, in colitis mice and has a strong modulatory effect on microbial co-occurrence patterns and gut metabolites. In addition, MV reverses several key inflammatory mediators, including sphingolipid metabolites, from elevated levels in DSS colitis mice. As a bioactive ingredient, MV exerts its effect on the gut microbiome in a mechanism that differs from the whole blueberry. CONCLUSION MV ingestion ameliorates intestinal inflammation by modulating colon epithelium integrity, gut microbiome, and key inflammatory mediators.
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Affiliation(s)
- Fang Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.,Produce Safety and Microbiology Research Unit, United States Department of Agriculture, Agriculture Research Service, Albany, CA, 94706, USA
| | - Thomas T Y Wang
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, 20705, USA
| | - Qingjuan Tang
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Robert W Li
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service, Beltsville, MD, 20705, USA
| | - Vivian C H Wu
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture, Agriculture Research Service, Albany, CA, 94706, USA
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Liu F, Li Z, Wang X, Xue C, Tang Q, Li RW. Microbial Co-Occurrence Patterns and Keystone Species in the Gut Microbial Community of Mice in Response to Stress and Chondroitin Sulfate Disaccharide. Int J Mol Sci 2019; 20:ijms20092130. [PMID: 31052157 PMCID: PMC6539173 DOI: 10.3390/ijms20092130] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/21/2019] [Accepted: 04/26/2019] [Indexed: 01/10/2023] Open
Abstract
Detecting microbial interactions is essential to the understanding of the structure and function of the gut microbiome. In this study, microbial co-occurrence patterns were inferred using a random matrix theory based approach in the gut microbiome of mice in response to chondroitin sulfate disaccharide (CSD) under healthy and stressed conditions. The exercise stress disrupted the network composition and microbial co-occurrence patterns. Thirty-four Operational Taxonomic Units (OTU) were identified as module hubs and connectors, likely acting as generalists in the microbial community. Mucispirillum schaedleri acted as a connector in the stressed network in response to CSD supplement and may play a key role in bridging intimate interactions between the host and its microbiome. Several modules correlated with physiological parameters were detected. For example, Modules M02 (under stress) and S05 (stress + CSD) were strongly correlated with blood urea nitrogen levels (r = 0.90 and -0.75, respectively). A positive correlation between node connectivity of the OTUs assigned to Proteobacteria with superoxide dismutase activities under stress (r = 0.57, p < 0.05) provided further evidence that Proteobacteria can be developed as a potential pathological marker. Our findings provided novel insights into gut microbial interactions and may facilitate future endeavor in microbial community engineering.
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Affiliation(s)
- Fang Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Zhaojie Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Xiong Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Qingjuan Tang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China.
| | - Robert W Li
- United States Department of Agriculture, Agriculture Research Service (USDA-ARS), Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA.
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Li RW, Liu F, Li X, Xue C, Tang Q. Microbial Co‐occurrence Patterns and Keystone Species in the Gut Microbial Community of Mice in Response to Stress and Chondroitin Sulfate Disaccharide. FASEB J 2019. [DOI: 10.1096/fasebj.2019.33.1_supplement.lb300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Fang Liu
- Ocean Unievrsity of ChinaQingdaoPeople's Republic of China
| | - Xhaojie Li
- Ocean University of ChinaqingdaoPeople's Republic of China
| | - Changhu Xue
- Ocean University of ChinaqingdaoPeople's Republic of China
| | - Qingjuan Tang
- Ocean University of ChinaqingdaoPeople's Republic of China
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36
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Wang Y, Liu F, Urban JF, Paerewijck O, Geldhof P, Li RW. Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome. Int J Parasitol 2019; 49:247-256. [DOI: 10.1016/j.ijpara.2018.10.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/23/2018] [Accepted: 10/26/2018] [Indexed: 01/02/2023]
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37
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Wu Y, Li RW, Huang H, Fletcher A, Yu L, Pham Q, Yu L, He Q, Wang TTY. Inhibition of Tumor Growth by Dietary Indole-3-Carbinol in a Prostate Cancer Xenograft Model May Be Associated with Disrupted Gut Microbial Interactions. Nutrients 2019; 11:nu11020467. [PMID: 30813350 PMCID: PMC6413210 DOI: 10.3390/nu11020467] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 02/16/2019] [Accepted: 02/19/2019] [Indexed: 02/06/2023] Open
Abstract
Accumulated evidence suggests that the cruciferous vegetables-derived compound indole-3-carbinol (I3C) may protect against prostate cancer, but the precise mechanisms underlying its action remain unclear. This study aimed to verify the hypothesis that the beneficial effect of dietary I3C may be due to its modulatory effect on the gut microbiome of mice. Athymic nude mice (5–7 weeks old, male, Balb c/c nu/nu) with established tumor xenografts were fed a basal diet (AIN-93) with or without 1 µmoles I3C/g for 9 weeks. The effects of dietary I3C on gut microbial composition and microbial species interactions were then examined by 16s rRNA gene-based sequencing and co-occurrence network analysis. I3C supplementation significantly inhibited tumor growth (p < 0.0001) and altered the structure of gut microbiome. The abundance of the phylum Deferribacteres, more specifically, Mucispirillum schaedleri, was significantly increased by dietary I3C. Additionally, I3C consumption also changed gut microbial co-occurrence patterns. One of the network modules in the control group, consisting of seven bacteria in family S-27, was positively correlated with tumor size (p < 0.009). Moreover, dietary I3C disrupted microbial interactions and altered this association between specific microbial network and tumor development. Our results unraveled complex relationships among I3C ingestion, gut microbiota, and prostate tumor development and may provide a novel insight into the mechanism for the chemopreventive effect of dietary I3C on prostate cancer.
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Affiliation(s)
- Yanbei Wu
- College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, China.
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA.
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, MD 20705, USA.
| | - Robert W Li
- Animal Parasitic Diseases Laboratory, USDA-ARS, Beltsville, MD 20705, USA.
| | - Haiqiu Huang
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, MD 20705, USA.
| | - Arnetta Fletcher
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA.
- Department of Family and Consumer Sciences, Shepherd University, Shepherdstown, WV 25443, USA.
| | - Lu Yu
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA.
| | - Quynhchi Pham
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, MD 20705, USA.
| | - Liangli Yu
- Department of Nutrition and Food Science, University of Maryland, College Park, MD 20742, USA.
| | - Qiang He
- College of Light Industry, Textile and Food Engineering, Sichuan University, Chengdu 610065, China.
| | - Thomas T Y Wang
- Diet, Genomics, and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, MD 20705, USA.
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Zhang R, Liu F, Hunt P, Li C, Zhang L, Ingham A, Li RW. Transcriptome analysis unraveled potential mechanisms of resistance to Haemonchus contortus infection in Merino sheep populations bred for parasite resistance. Vet Res 2019; 50:7. [PMID: 30678719 PMCID: PMC6345051 DOI: 10.1186/s13567-019-0622-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/12/2018] [Indexed: 12/13/2022] Open
Abstract
Haemonchus contortus is one of the most pathogenic gastrointestinal nematodes in small ruminants. To understand molecular mechanisms underlying host resistance to this parasite, we used RNA-sequencing technology to compare the transcriptomic response of the abomasal tissue, the site of the host-parasite interaction, of Merino sheep bred to be either genetically resistant or susceptible to H. contortus infection. Two different selection flocks, the Haemonchus selection flock (HSF) and the Trichostrongylus selection flock (TSF), and each contains a resistant and susceptible line, were studied. The TSF flock was seemingly more responsive to both primary and repeated infections than HSF. A total of 127 and 726 genes displayed a significant difference in abundance between resistant and susceptible animals in response to a primary infection in HSF and TSF, respectively. Among them, 38 genes were significantly affected by infection in both flocks. Gene ontology (GO) enrichment of the differentially expressed genes identified in this study predicted the likely involvement of extracellular exosomes in the immune response to H. contortus infection. While the resistant lines in HSF and TSF relied on different mechanisms for the development of host resistance, adhesion and diapedesis of both agranulocytes and granulocytes, coagulation and complement cascades, and multiple pathways related to tissue repair likely played critical roles in the process. Our results offered a quantitative snapshot of changes in the host transcriptome induced by H. contortus infection and provided novel insights into molecular mechanisms of host resistance.
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Affiliation(s)
- Runfeng Zhang
- College of Life Science, Hubei Normal University, Huangshi, Hubei, China
| | - Fang Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Peter Hunt
- CSIRO Agriculture and Food, Armidale, NSW, Australia
| | - Congjun Li
- United States Department of Agriculture, Agriculture Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA
| | - Lichun Zhang
- Branch of Husbandry, Jilin Academy of Agricultural Science, Gongzhuling, Jilin, China
| | - Aaron Ingham
- CSIRO Agriculture and Food, St Lucia, Queensland, Australia.
| | - Robert W Li
- United States Department of Agriculture, Agriculture Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA.
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Liu F, Horton-Sparks K, Hull V, Li RW, Martínez-Cerdeño V. The valproic acid rat model of autism presents with gut bacterial dysbiosis similar to that in human autism. Mol Autism 2018; 9:61. [PMID: 30555669 PMCID: PMC6288876 DOI: 10.1186/s13229-018-0251-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023] Open
Abstract
Background Gut microbiota has the capacity to impact the regular function of the brain, which can in turn affect the composition of microbiota. Autism spectrum disorder (ASD) patients suffer from gastrointestinal problems and experience changes in gut microbiota; however, it is not yet clear whether the change in the microbiota associated with ASD is a cause or a consequence of the disease. Methods We have investigated the species richness and microbial composition in a valproic acid (VPA)-induced rat model autism. Fecal samples from the rectum were collected at necropsy, microbial total DNA was extracted, 16 rRNA genes sequenced using Illumina, and the global microbial co-occurrence network was constructed using a random matrix theory-based pipeline. Collected rat microbiome data were compared to available data derived from cases of autism. Results We found that VPA administration during pregnancy reduced fecal microbial richness, changed the gut microbial composition, and altered the metabolite potential of the fecal microbial community in a pattern similar to that seen in patients with ASD. However, the global network property and network composition as well as microbial co-occurrence patterns were largely preserved in the offspring of rats exposed to prenatal administration of VPA. Conclusions Our data on the microbiota of the VPA rat model of autism indicate that this model, in addition to behaviorally and anatomically mimicking the autistic brain as previously shown, also mimics the microbiome features of autism, making it one of the best-suited rodent models for the study of autism and ASD.
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Affiliation(s)
- Fang Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Kayla Horton-Sparks
- Institute for Pediatric Regenerative Medicine and Shriners Hospitals for Children Northern California, 2504 Stockton Blvd, Sacramento, CA 95817 USA
| | - Vanessa Hull
- Institute for Pediatric Regenerative Medicine and Shriners Hospitals for Children Northern California, 2504 Stockton Blvd, Sacramento, CA 95817 USA
| | - Robert W. Li
- United States Department of Agriculture, Agriculture Research Service (USDA-ARS), Animal Genomics and Improvement Laboratory, Beltsville, MD USA
| | - Verónica Martínez-Cerdeño
- Institute for Pediatric Regenerative Medicine and Shriners Hospitals for Children Northern California, 2504 Stockton Blvd, Sacramento, CA 95817 USA
- Department of Pathology and Laboratory Medicine, UC Davis School of Medicine, Sacramento, CA USA
- MIND Institute, Sacramento, CA USA
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Liao YT, Liu F, Sun X, Li RW, Wu VCH. Complete Genome Sequence of Escherichia coli Phage vB_EcoS Sa179lw, Isolated from Surface Water in a Produce-Growing Area in Northern California. Genome Announc 2018; 6:e00337-18. [PMID: 29976601 PMCID: PMC6033975 DOI: 10.1128/genomea.00337-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 05/31/2018] [Indexed: 11/20/2022]
Abstract
We report here the whole-genome sequence of a novel Escherichia coli phage, vB_EcoS Sa179lw, isolated from surface water collected in a produce-growing area. With the presence of a putative eae-like gene that was associated with previous non-O157 Shiga toxin-producing E. coli outbreaks, this phage is a candidate for the study of virulence gene transfer.
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Affiliation(s)
- Yen-Te Liao
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
| | - Fang Liu
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Xincheng Sun
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
- College of Food and Biological Engineering, Zhengzhou University of Light Industry, Zhengzhou, China
- Collaborative Innovation Center of Food Production and Safety, Zhengzhou, China
| | - Robert W Li
- Animal Genomics and Improvement Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, USA
| | - Vivian C H Wu
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, California, USA
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Baldwin RL, Li RW, Jia Y, Li CJ. Transcriptomic Impacts of Rumen Epithelium Induced by Butyrate Infusion in Dairy Cattle in Dry Period. Gene Regul Syst Bio 2018; 12:1177625018774798. [PMID: 29785087 PMCID: PMC5954180 DOI: 10.1177/1177625018774798] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 04/09/2018] [Indexed: 01/14/2023]
Abstract
The purpose of this study was to evaluate the effects of butyrate infusion on rumen epithelial transcriptome. Next-generation sequencing (NGS) and bioinformatics are used to accelerate our understanding of regulation in rumen epithelial transcriptome of cattle in the dry period induced by butyrate infusion at the level of the whole transcriptome. Butyrate, as an essential element of nutrients, is a histone deacetylase (HDAC) inhibitor that can alter histone acetylation and methylation, and plays a prominent role in regulating genomic activities influencing rumen nutrition utilization and function. Ruminal infusion of butyrate was following 0-hour sampling (baseline controls) and continued for 168 hours at a rate of 5.0 L/day of a 2.5 M solution as a continuous infusion. Following the 168-hour infusion, the infusion was stopped, and cows were maintained on the basal lactation ration for an additional 168 hours for sampling. Rumen epithelial samples were serially collected via biopsy through rumen fistulae at 0-, 24-, 72-, and 168-hour (D1, D3, D7) and 168-hour post-infusion (D14). In comparison with pre-infusion at 0 hours, a total of 3513 genes were identified to be impacted in the rumen epithelium by butyrate infusion at least once at different sampling time points at a stringent cutoff of false discovery rate (FDR) < 0.01. The maximal effect of butyrate was observed at day 7. Among these impacted genes, 117 genes were responsive consistently from day 1 to day 14, and another 42 genes were lasting through day 7. Temporal effects induced by butyrate infusion indicate that the transcriptomic alterations are very dynamic. Gene ontology (GO) enrichment analysis revealed that in the early stage of rumen butyrate infusion (on day 1 and day 3 of butyrate infusion), the transcriptomic effects in the rumen epithelium were involved with mitotic cell cycle process, cell cycle process, and regulation of cell cycle. Bioinformatic analysis of cellular functions, canonical pathways, and upstream regulator of impacted genes underlie the potential mechanisms of butyrate-induced gene expression regulation in rumen epithelium. The introduction of transcriptomic and bioinformatic technologies to study nutrigenomics in the farm animal presented a new prospect to study multiple levels of biological information to better apprehend the whole animal response to nutrition, physiological state, and their interactions. The nutrigenomics approach may eventually lead to more precise management of utilization of feed resources in a more effective approach.
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Affiliation(s)
- Ransom L Baldwin
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Robert W Li
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Yankai Jia
- Lieber Institute for Brain Development, Johns Hopkins University, Baltimore, MD, USA
| | - Cong-Jun Li
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD, USA
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Wang X, Liu F, Gao Y, Xue CH, Li RW, Tang QJ. Transcriptome analysis revealed anti-obesity effects of the Sodium Alginate in high-fat diet -induced obese mice. Int J Biol Macromol 2018; 115:861-870. [PMID: 29649537 DOI: 10.1016/j.ijbiomac.2018.04.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 03/30/2018] [Accepted: 04/09/2018] [Indexed: 02/06/2023]
Abstract
Human obesity and overweight, caused by accumulated of fat, is the most commonly phenomenon from all over the world, especially in Western countries and Chinese mainland during the past three decades. Sodium Alginate, a polysaccharide extracted from brown seaweeds, has been proved its strong ability on body weight loss and anti-inflammatory response. However, no studies have been explored the effects of Sodium Alginate on colonic transcriptome, especially in obese individuals. Therefore, the current study was designed to detect whether Sodium Alginate could remit obesity and ease chronic metabolism disease through strengthening the bio-functionality of the lower intestine, particularly in colon. The data showed after Sodium Alginate gavaged for four weeks, the body weight, fat accumulation, triglyceride and total cholesterol were ameliorated in high fat diet induced obese mice. Sodium Alginate also improved the blood glucose level and lipopolysaccharides in serum. Furthermore, data from RNA sequence indicated that there were significantly changes in several genes, which involved in lipid metabolism and carbohydrate metabolism. In conclusion, these results suggested that Sodium Alginate could effectively suppress obesity and obesity related metabolic syndromes, due to the colonic transcriptome changes.
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Affiliation(s)
- Xiong Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, People's Republic of China
| | - Fang Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, People's Republic of China
| | - Yuan Gao
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, People's Republic of China
| | - Chang-Hu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, People's Republic of China
| | - Robert W Li
- USDA-ARS, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Qing-Juan Tang
- College of Food Science and Engineering, Ocean University of China, Qingdao, Shandong Province 266003, People's Republic of China.
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Chang PK, Scharfenstein LL, Li RW, Arroyo-Manzanares N, De Saeger S, Diana Di Mavungu J. Aspergillus flavus aswA, a gene homolog of Aspergillus nidulans oefC, regulates sclerotial development and biosynthesis of sclerotium-associated secondary metabolites. Fungal Genet Biol 2017; 104:29-37. [PMID: 28442441 DOI: 10.1016/j.fgb.2017.04.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/04/2017] [Accepted: 04/21/2017] [Indexed: 12/29/2022]
Abstract
Aspergillus flavus aswA (AFLA_085170) is a gene encoding a Zn(II)2Cys6 DNA-binding domain and a transcriptional activation domain, DUF3468. Disruption of aswA yielded strains that made a truncated gene transcript and generated a fungus that produced a greatly increased number of sclerotia. These sclerotia were odd-shaped and non-pigmented (white) and different from oval and pigmented (dark brown to black) mature sclerotia. Transcriptomic analysis of the ΔaswA strain grown on potato dextrose agar plates and Wickerham agar plates showed that expression of clustering genes involved in the biosynthesis of three sclerotium-associated secondary metabolites was down-regulated. These included gene clusters of asparasone, aflatrem, and aflavarin. In contrast, those of aflatoxin, cyclopiazonic acid and kojic acid were not affected. Metabolite analyses confirmed that the non-pigmented sclerotia contained aflatoxin and cyclopiazonic acid but not other aforementioned metabolites, three asparasone analogs and dihydroxyaflavinine commonly present in mature sclerotia. Impairment in aswA gene function stalls normal sclerotial development, which in turn prevents biosynthesis and accumulation of sclerotium-specific metabolites.
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Affiliation(s)
- Perng-Kuang Chang
- Southern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, United States.
| | - Leslie L Scharfenstein
- Southern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, 1100 Robert E. Lee Boulevard, New Orleans, LA 70124, United States
| | - Robert W Li
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, U.S. Department of Agriculture, 10300 Baltimore Avenue, Beltsville, MD 20705, United States
| | - Natalia Arroyo-Manzanares
- Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Sarah De Saeger
- Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - José Diana Di Mavungu
- Laboratory of Food Analysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
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Zhang N, Mao X, Li RW, Hou E, Wang Y, Xue C, Tang Q. Neoagarotetraose protects mice against intense exercise-induced fatigue damage by modulating gut microbial composition and function. Mol Nutr Food Res 2017; 61. [PMID: 28083922 DOI: 10.1002/mnfr.201600585] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 12/27/2016] [Accepted: 01/04/2017] [Indexed: 12/27/2022]
Abstract
SCOPE Exhaustive exercise stress has emerged as an important health issue, and gastrointestinal problems are a common concern during intense exercise. In this study, we investigated the potential antifatigue effects of neoagarotetraose (NAT) in mice under intense exercise stress. MATERIALS AND METHODS Exhaustive exercise stress significantly weakened several physiological and physical parameters of the mice, including decreased food intake, reduced body weight, and impaired integrity of the intestinal epithelial barrier. Our data showed that a 16-day NAT treatment resulted in a profound change in microbiome composition, which subsequently led to widespread shifts in the functional potential of the gut microbiome. Furthermore, NAT administration significantly increased the fecal concentration of total short-chain fatty acids (p < 0.01). CONCLUSION Together, our findings suggest that NAT may protect mice against intense exercise-induced fatigue and provide insights into the mechanisms of NAT as a potential prebiotic.
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Affiliation(s)
- Na Zhang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Robert W Li
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agriculture Research Service (USDA-ARS), Beltsville, MD, USA
| | - Enling Hou
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Yuming Wang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Changhu Xue
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Qingjuan Tang
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
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Li W, Richter RA, Jung Y, Zhu Q, Li RW. Web-based bioinformatics workflows for end-to-end RNA-seq data computation and analysis in agricultural animal species. BMC Genomics 2016; 17:761. [PMID: 27678198 PMCID: PMC5039875 DOI: 10.1186/s12864-016-3118-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/23/2016] [Indexed: 11/18/2022] Open
Abstract
Background Remarkable advances in Next Generation Sequencing (NGS) technologies, bioinformatics algorithms and computational technologies have significantly accelerated genomic research. However, complicated NGS data analysis still remains as a major bottleneck. RNA-seq, as one of the major area in the NGS field, also confronts great challenges in data analysis. Results To address the challenges in RNA-seq data analysis, we developed a web portal that offers three integrated workflows that can perform end-to-end compute and analysis, including sequence quality control, read-mapping, transcriptome assembly, reconstruction and quantification, and differential analysis. The first workflow utilizes Tuxedo (Tophat, Cufflink, Cuffmerge and Cuffdiff suite of tools). The second workflow deploys Trinity for de novo assembly and uses RSEM for transcript quantification and EdgeR for differential analysis. The third combines STAR, RSEM, and EdgeR for data analysis. All these workflows support multiple samples and multiple groups of samples and perform differential analysis between groups in a single workflow job submission. The calculated results are available for download and post-analysis. The supported animal species include chicken, cow, duck, goat, pig, horse, rabbit, sheep, turkey, as well as several other model organisms including yeast, C. elegans, Drosophila, and human, with genomic sequences and annotations obtained from ENSEMBL. The RNA-seq portal is freely available from http://weizhongli-lab.org/RNA-seq. Conclusions The web portal offers not only bioinformatics software, workflows, computation and reference data, but also an integrated environment for complex RNA-seq data analysis for agricultural animal species. In this project, our aim is not to develop new RNA-seq tools, but to build web workflows for using popular existing RNA-seq methods and make these tools more accessible to the communities.
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Affiliation(s)
- Weizhong Li
- J. Craig Venter Institute, La Jolla, CA, 92037, USA.
| | | | - Yunsup Jung
- J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Qiyun Zhu
- J. Craig Venter Institute, La Jolla, CA, 92037, USA
| | - Robert W Li
- United States Department of Agriculture, Agriculture Research Service (USDA-ARS), Animal Genomics and Improvement Laboratory, Beltsville, MD, 20705, USA
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Li CJ, Li RW, Baldwin RL, Blomberg LA, Wu S, Li W. Transcriptomic Sequencing Reveals a Set of Unique Genes Activated by Butyrate-Induced Histone Modification. Gene Regul Syst Bio 2016; 10:1-8. [PMID: 26819550 PMCID: PMC4723047 DOI: 10.4137/grsb.s35607] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/18/2015] [Accepted: 11/18/2015] [Indexed: 01/19/2023]
Abstract
Butyrate is a nutritional element with strong epigenetic regulatory activity as a histone deacetylase inhibitor. Based on the analysis of differentially expressed genes in the bovine epithelial cells using RNA sequencing technology, a set of unique genes that are activated only after butyrate treatment were revealed. A complementary bioinformatics analysis of the functional category, pathway, and integrated network, using Ingenuity Pathways Analysis, indicated that these genes activated by butyrate treatment are related to major cellular functions, including cell morphological changes, cell cycle arrest, and apoptosis. Our results offered insight into the butyrate-induced transcriptomic changes and will accelerate our discerning of the molecular fundamentals of epigenomic regulation.
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Affiliation(s)
- Cong-Jun Li
- United States Department of Agriculture, Agriculture Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA
| | - Robert W Li
- United States Department of Agriculture, Agriculture Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA
| | - Ransom L Baldwin
- United States Department of Agriculture, Agriculture Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD, USA
| | - Le Ann Blomberg
- United States Department of Agriculture, Agriculture Research Service, Animal Biosciences and Biotechnology Laboratory, Beltsville, MD, USA
| | - Sitao Wu
- Informatics Group, J. Craig Venter Institute, La Jolla, CA. USA
| | - Weizhong Li
- Informatics Group, J. Craig Venter Institute, La Jolla, CA. USA
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Chang PK, Hua SST, Sarreal SBL, Li RW. Suppression of Aflatoxin Biosynthesis in Aspergillus flavus by 2-Phenylethanol Is Associated with Stimulated Growth and Decreased Degradation of Branched-Chain Amino Acids. Toxins (Basel) 2015; 7:3887-902. [PMID: 26404375 PMCID: PMC4626709 DOI: 10.3390/toxins7103887] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/02/2015] [Accepted: 09/17/2015] [Indexed: 11/30/2022] Open
Abstract
The saprophytic soil fungus Aspergillus flavus infects crops and produces aflatoxin. Pichia anomala, which is a biocontrol yeast and produces the major volatile 2-phenylethanol (2-PE), is able to reduce growth of A. flavus and aflatoxin production when applied onto pistachio trees. High levels of 2-PE are lethal to A. flavus and other fungi. However, at low levels, the underlying mechanism of 2-PE to inhibit aflatoxin production remains unclear. In this study, we characterized the temporal transcriptome response of A. flavus to 2-PE at a subinhibitory level (1 µL/mL) using RNA-Seq technology and bioinformatics tools. The treatment during the entire 72 h experimental period resulted in 131 of the total A. flavus 13,485 genes to be significantly impacted, of which 82 genes exhibited decreased expression. They included those encoding conidiation proteins and involved in cyclopiazonic acid biosynthesis. All genes in the aflatoxin gene cluster were also significantly decreased during the first 48 h treatment. Gene Ontology (GO) analyses showed that biological processes with GO terms related to catabolism of propionate and branched-chain amino acids (valine, leucine and isoleucine) were significantly enriched in the down-regulated gene group, while those associated with ribosome biogenesis, translation, and biosynthesis of α-amino acids were over-represented among the up-regulated genes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that metabolic pathways negatively impacted among the down-regulated genes parallel to those active at 30 °C, a condition conducive to aflatoxin biosynthesis. In contrast, metabolic pathways positively related to the up-regulated gene group resembled those at 37 °C, which favors rapid fungal growth and is inhibitory to aflatoxin biosynthesis. The results showed that 2-PE at a low level stimulated active growth of A. flavus but concomitantly rendered decreased activities in branched-chain amino acid degradation. Since secondary metabolism occurs after active growth has ceased, this growth stimulation resulted in suppression of expression of aflatoxin biosynthesis genes. On the other hand, increased activities in degradation pathways for branched-chain amino acids probably are required for the activation of the aflatoxin pathway by providing building blocks and energy regeneration. Metabolic flux in primary metabolism apparently has an important role in the expression of genes of secondary metabolism.
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Affiliation(s)
- Perng-Kuang Chang
- Southern Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, New Orleans, LA 70124, USA.
| | - Sui Sheng T Hua
- Western Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, Albany, CA 94710, USA.
| | - Siov Bouy L Sarreal
- Western Regional Research Center, Agricultural Research Service, U. S. Department of Agriculture, Albany, CA 94710, USA.
| | - Robert W Li
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, U. S. Department of Agriculture, Beltsville, MD 20705, USA.
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Li CZ, Zhang P, Li RW, Wu CT, Zhang XP, Zhu HC. Axillary lymph node dissection versus sentinel lymph node biopsy alone for early breast cancer with sentinel node metastasis: A meta-analysis. Eur J Surg Oncol 2015; 41:958-66. [PMID: 26054706 DOI: 10.1016/j.ejso.2015.05.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/21/2015] [Accepted: 05/06/2015] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In early breast cancer patients with sentinel node metastasis, the effect of axillary lymph node dissection (ALND) is controversial. The purpose of this study is to compare the safety and efficacy of sentinel lymph node biopsy (SLNB) alone versus ALND in patients with early breast cancer and sentinel node metastasis. METHODS We searched PubMed, Embase, Web of Science, and Cochrane Library databases from 1965 to February 2014. All data were analyzed using Review Manager Software 5.2. RESULTS 12 studies, which included 130,575 patients from five randomized controlled trials and seven observational studies, met our inclusion criteria. 26,870 early breast cancer patients underwent SLNB alone and 103,705 underwent ALND. Patients underwent ALND had more paresthesia (risk ratio [RR] 0.26, 95% confidence interval [CI] 0.20-0.33; p < 0.01) and lymphedema (RR 0.28, 95% CI 0.20-0.41; p < 0.01) than those had SLNB alone. There were no significant differences in overall survival (hazard ratio [HR] 0.95, 95% CI 0.85-1.06; p = 0.35), disease-free survival (HR 1.00, 95% CI 0.98-1.02, p = 0.96), and locoregional recurrence (RR 0.92, 95% CI 0.59-1.44; p = 0.73). CONCLUSION Current evidence indicates that axillary dissection may be omitted in early breast cancer patients with sentinel lymph metastasis.
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Affiliation(s)
- C Z Li
- Oncological Surgery, Affiliate Hospital of Hebei United University, Tangshan 063000, Hebei, China
| | - P Zhang
- Nursing and Rehabilitation College, Hebei United University, Tangshan 063000, Hebei, China
| | - R W Li
- Oncological Surgery, Affiliate Hospital of Hebei United University, Tangshan 063000, Hebei, China
| | - C T Wu
- Oncological Surgery, Affiliate Hospital of Hebei United University, Tangshan 063000, Hebei, China
| | - X P Zhang
- Oncological Surgery, Affiliate Hospital of Hebei United University, Tangshan 063000, Hebei, China
| | - H C Zhu
- Oncological Surgery, Affiliate Hospital of Hebei United University, Tangshan 063000, Hebei, China.
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Van Meulder F, Ratman D, Van Coppernolle S, Borloo J, Li RW, Chiers K, Van den Broeck W, De Bosscher K, Claerebout E, Geldhof P. Analysis of the protective immune response following intramuscular vaccination of calves against the intestinal parasite Cooperia oncophora. Int J Parasitol 2015; 45:637-46. [PMID: 25937360 DOI: 10.1016/j.ijpara.2015.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 03/23/2015] [Accepted: 03/24/2015] [Indexed: 12/16/2022]
Abstract
Recently we reported the successful vaccination of calves against Cooperia oncophora with a double domain activation-associated secreted protein, purified from the excretory-secretory material of adult stage parasites. In an attempt to elucidate the immune mechanisms involved in protection, the humoral and cell-mediated immune responses following vaccination and infection were compared with non-vaccinated control animals. Antigen-specific IgG1, IgG2 and IgA levels were significantly increased in sera of vaccinated animals post vaccination, whereas no effect was observed for IgM. Antigen-specific intestinal IgG1 levels were significantly increased in the vaccinated animals, whereas no differences were observed for antigen-specific IgA, IgM and IgG2 levels. Upon re-stimulation in vitro with the vaccine antigen, a significant proliferation of both αβ- and γδ-T cells, and B cells, collected from mesenteric lymph nodes, was only observed in vaccinated animals. RNA-seq analysis of intestinal tissue yielded a list of 67 genes that were differentially expressed in vaccinated animals following challenge infection, amongst which were several cell adhesion molecules, lectins and glycosyl transferases. A correlation analysis between all immunological and parasitological parameters indicated that intestinal anti-double domain activation-associated secreted protein IgG1 levels correlated negatively with cumulative faecal egg counts and positively with the proportion of L4s and L5s. The proportion of immature stages was also positively correlated with the proliferation of αβ T cells. Worm length was negatively correlated with the transcript levels of several lectins and cell adhesion molecules. Overall, the results indicate that intramuscular administration of the vaccine resulted in an immune memory response particularly characterised by increased antigen-specific IgG1 levels in the intestinal mucosa.
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Affiliation(s)
- F Van Meulder
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - D Ratman
- Receptor Research Laboratories, Nuclear Receptor Lab, VIB-Department of Medical Protein Research, VIB, Ghent University, Ghent, Belgium
| | - S Van Coppernolle
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - J Borloo
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - R W Li
- Bovine Functional Genomics Laboratory, Animal and Natural Resources Institute, USDA-ARS, Beltsville, USA
| | - K Chiers
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - W Van den Broeck
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - K De Bosscher
- Receptor Research Laboratories, Nuclear Receptor Lab, VIB-Department of Medical Protein Research, VIB, Ghent University, Ghent, Belgium
| | - E Claerebout
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - P Geldhof
- Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
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Shin JH, Xu L, Li RW, Gao Y, Bickhart D, Liu GE, Baldwin R, Li CJ. A high-resolution whole-genome map of the distinctive epigenomic landscape induced by butyrate in bovine cells. Anim Genet 2014; 45 Suppl 1:40-50. [PMID: 24990294 DOI: 10.1111/age.12147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2014] [Indexed: 12/11/2022]
Abstract
This report presents a study utilizing next-generation sequencing technology, combined with chromatin immunoprecipitation (ChIP-seq) technology to analyze histone modification induced by butyrate and to construct a high-definition map of the epigenomic landscape with normal histone H3 and H4 and their variants in bovine cells at the whole-genome scale. A total of 10 variants of histone H3 and H4 modifications were mapped at the whole-genome scale (acetyl-H3K18-ChIP-seq, trimethy-H3K9, histone H4 ChIP-seq, acetyl-H4K5 ChIP-seq, acetyl-H4K12 ChIP-seq, acetyl-H4K16 ChIP-seq, histone H3 ChIP-seq, acetyl H3H9 ChIP-seq, acetyl H3K27 ChIP-seq and tetra-acetyl H4 ChIP-seq). Integrated experiential data and an analysis of histone and histone modification at a single base resolution across the entire genome are presented. We analyzed the enriched binding regions in the proximal promoter (within 5 kb upstream or at the 5'-untranslated region from the transcriptional start site (TSS)), and the exon, intron and intergenic regions (defined by regions 25 kb upstream and 10 kb downstream from the TSS). A de novo search for the binding motif of the 10 ChIP-seq datasets discovered numerous motifs from each of the ChIP-seq datasets. These consensus sequences indicated that histone modification at different locations changes the histone H3 and H4 binding preferences. Nevertheless, a high degree of conservation in histone binding also was presented in these motifs. This first extensive epigenomic landscape mapping in bovine cells offers a new framework and a great resource for testing the role of epigenomes in cell function and transcriptomic regulation.
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Affiliation(s)
- J H Shin
- Lieber Institute for Brain Development, Johns Hopkins University, 855 North Wolfe Street, Suite 102, Baltimore, MD, 21205, USA
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