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Zhang Y, Zhang J, Liu Y, Ren S, Tao N, Meng F, Cao Q, Liu R. High fat diet increases the severity of collagen-induced arthritis in mice by altering the gut microbial community. Adv Rheumatol 2024; 64:44. [PMID: 38816873 DOI: 10.1186/s42358-024-00382-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 05/06/2024] [Indexed: 06/01/2024] Open
Abstract
OBJECTIVES Research has demonstrated that obesity may be associated with rheumatoid arthritis (RA). In addition, gut microbiota and its metabolites contribute to the occurrence and development of RA and obesity. However, the mechanism by which obesity affects RA remains unclear. In this study, we aimed to investigate whether gut microbiota and their metabolites alter the effects of high fat diet (HFD) on the severity of collagen-induced arthritis (CIA) in mice. METHODS Briefly, mice were divided into normal group (N), CIA model group (C), HFD group (T), and HFD CIA group (CT). Hematoxylin and Eosin staining(HE) and Safranin O-fast green staining were conducted, and levels of blood lipid and inflammatory cytokines were measured. 16S rDNA sequencing technique and liquid chromatography-mass spectrometry (LC-MS)-based metabolomics were performed to explore changes in the microbiota structure to further reveal the pathomechanism of HFD on CIA. RESULTS HFD aggravated the severity of CIA in mice. The CT group had the highest proportion of microbial abundance of Blautia, Oscillibacter, Ruminiclostridium-9, and Lachnospiraceae UCG 006 at the genus level, but had a lower proportion of Alistipes. Additionally, the fecal metabolic phenotype of the combined CT group shows significant changes, with differential metabolites enriched in 9 metabolic pathways, including primary bile acid biosynthesis, arginine biosynthesis, sphingolipid metabolism, purine metabolism, linoleic acid metabolism, oxytocin signaling pathway, aminoacyl-tRNA biosynthesis, the pentose phosphate pathway, and sphingolipid signaling pathway. Correlation analysis revealed that some of the altered gut microbiota genera were strongly correlated with changes in fecal metabolites, total cholesterol (TC), triglyceride (TG), and inflammatory cytokine levels. CONCLUSIONS This study shows that HFD may aggravate inflammatory reaction in CIA mice by altering the gut microbiota and metabolic pathways.
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Affiliation(s)
- Yang Zhang
- The First Hospital of China Medical University, Shenyang, 110002, Liaoning, China
| | - Jie Zhang
- The First Hospital of China Medical University, Shenyang, 110002, Liaoning, China
| | - Yantong Liu
- The First Hospital of China Medical University, Shenyang, 110002, Liaoning, China
| | - Shuang Ren
- The First Hospital of China Medical University, Shenyang, 110002, Liaoning, China
| | - Ning Tao
- The First Hospital of China Medical University, Shenyang, 110002, Liaoning, China
| | - Fanyan Meng
- The First Hospital of China Medical University, Shenyang, 110002, Liaoning, China
| | - Qi Cao
- Liaoning University of Traditional Chinese Medicine, Shenyang, 110001, Liaoning, China
| | - Ruoshi Liu
- The First Hospital of China Medical University, Shenyang, 110002, Liaoning, China.
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2
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Curvino EJ, Roe EF, Freire Haddad H, Anderson AR, Woodruff ME, Votaw NL, Segura T, Hale LP, Collier JH. Engaging natural antibody responses for the treatment of inflammatory bowel disease via phosphorylcholine-presenting nanofibres. Nat Biomed Eng 2024; 8:628-649. [PMID: 38012308 PMCID: PMC11128482 DOI: 10.1038/s41551-023-01139-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/17/2023] [Indexed: 11/29/2023]
Abstract
Inflammatory bowel disease lacks a long-lasting and broadly effective therapy. Here, by taking advantage of the anti-infection and anti-inflammatory properties of natural antibodies against the small-molecule epitope phosphorylcholine (PC), we show in multiple mouse models of colitis that immunization of the animals with self-assembling supramolecular peptide nanofibres bearing PC epitopes induced sustained levels of anti-PC antibodies that were both protective and therapeutic. The strength and type of immune responses elicited by the nanofibres could be controlled through the relative valency of PC epitopes and exogenous T-cell epitopes on the nanofibres and via the addition of the adjuvant CpG. The nanomaterial-assisted induction of the production of therapeutic antibodies may represent a durable therapy for inflammatory bowel disease.
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Affiliation(s)
| | - Emily F Roe
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | | | - Alexa R Anderson
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Mia E Woodruff
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Nicole L Votaw
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Tatiana Segura
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Laura P Hale
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Joel H Collier
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.
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3
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Ahmad W, Din AU, Khan TM, Rehman MU, Hassan A, Aziz T, Alharbi M, Wu J. Lacticaseibacillusparacasei BNCC345679 revolutionizes DSS-induced colitis and modulates gut microbiota. Front Microbiol 2024; 15:1343891. [PMID: 38601942 PMCID: PMC11004379 DOI: 10.3389/fmicb.2024.1343891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/22/2024] [Indexed: 04/12/2024] Open
Abstract
The gut microbiota plays an important role in the disease progression of inflammatory bowel disease. Although probiotics are effective against IBD, not many studies have investigated their effects on gut microbiota composition and immunomodulation in mouse colitis models. Our study aimed at the therapeutic effects of Lacticaseibacillus paracasei BNCC345679 for the first time and explored its impact on gut microbiome dysbiosis, inflammatory cytokines, related miRNAs, VCAM-1, oxidative stress, intestinal integrity, and mucus barrier. We found that oral intervention of L. paracasei BNCC345679 affects recovering beneficial microbial taxa, including lactobacillus spp. and akkermansia spp., followed by improved body weight, DAI score, and inflammatory cytokines. L. paracasei BNCC345679 mitigated oxidative stress and increased the expression of intestinal integrity proteins MUC2 and ZO-1. These results suggested that L. paracasei BNCC345679 has the capacity to reduce DSS-induced colitis and has the potential as a supplement for the mitigation of IBD.
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Affiliation(s)
- Waqar Ahmad
- Basic Medicine Research Innovation Centre for Cardiometabolic Diseases, Ministry of Education, Southwest Medical University, Luzhou, China
| | - Ahmad Ud Din
- Basic Medicine Research Innovation Centre for Cardiometabolic Diseases, Ministry of Education, Southwest Medical University, Luzhou, China
- Plants for Human Health Institute, Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Kannapolis, NC, United States
| | - Taj Malook Khan
- Basic Medicine Research Innovation Centre for Cardiometabolic Diseases, Ministry of Education, Southwest Medical University, Luzhou, China
| | - Mujeeb Ur Rehman
- Department of Pharmacy, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Adil Hassan
- Laboratory of Nano/Micro Composite Materials and Devices, Chongqing University of Science and Technology, Chongqing, China
| | - Tariq Aziz
- Department of Agriculture, University of Ioannina, Ioannina, Greece
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Jianbo Wu
- Basic Medicine Research Innovation Centre for Cardiometabolic Diseases, Ministry of Education, Southwest Medical University, Luzhou, China
- Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research of Southwest Medical University, Luzhou, China
- Laboratory for Cardiovascular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
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Amara J, Itani T, Hajal J, Bakhos JJ, Saliba Y, Aboushanab SA, Kovaleva EG, Fares N, Mondragon AC, Miranda JM. Circadian Rhythm Perturbation Aggravates Gut Microbiota Dysbiosis in Dextran Sulfate Sodium-Induced Colitis in Mice. Nutrients 2024; 16:247. [PMID: 38257139 PMCID: PMC10819604 DOI: 10.3390/nu16020247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Circadian rhythm disruption is increasingly considered an environmental risk factor for the development and exacerbation of inflammatory bowel disease. We have reported in a previous study that nychthemeral dysregulation is associated with an increase in intestinal barrier permeability and inflammation in mice with dextran sulfate sodium (DSS)-induced colitis. To investigate the effect of circadian rhythm disruption on the composition and diversity of the gut microbiota (GM), sixty male C57BL/6J mice were initially divided to two groups, with the shifted group (n = 30) exposed to circadian shifts for three months and the non-shifted group (n = 30) kept under a normal light-dark cycle. The mice of the shifted group were cyclically housed for five days under the normal 12:12 h light-dark cycle, followed by another five days under a reversed light-dark cycle. At the end of the three months, a colitis was induced by 2% DSS given in the drinking water of 30 mice. Animals were then divided into four groups (n = 15 per group): sham group non-shifted (Sham-NS), sham group shifted (Sham-S), DSS non-shifted (DSS-NS) and DSS shifted (DSS-S). Fecal samples were collected from rectal content to investigate changes in GM composition via DNA extraction, followed by high-throughput sequencing of the bacterial 16S rRNA gene. The mouse GM was dominated by three phyla: Firmicutes, Bacteroidetes and Actinobacteria. The Firmicutes/Bacteroidetes ratio decreased in mice with induced colitis. The richness and diversity of the GM were reduced in the colitis group, especially in the group with inverted circadian rhythm. Moreover, the GM composition was modified in the inverted circadian rhythm group, with an increase in Alloprevotella, Turicibacter, Bacteroides and Streptococcus genera. Circadian rhythm inversion exacerbates GM dysbiosis to a less rich and diversified extent in a DSS-induced colitis model. These findings show possible interplay between circadian rhythm disruption, GM dynamics and colitis pathogenesis.
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Affiliation(s)
- Joseph Amara
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Tarek Itani
- Laboratoire de Microbiologie, Faculté de Pharmacie, Université Saint Joseph, Beirut 1104 2020, Lebanon;
| | - Joelle Hajal
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Jules-Joel Bakhos
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Youakim Saliba
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Saied A. Aboushanab
- Institute of Chemical Engineering, Ural Federal University Named after the First President of Russia B. N. Yeltsin, Mira 19, Yekaterinburg 620002, Russia; (S.A.A.); (E.G.K.)
| | - Elena G. Kovaleva
- Institute of Chemical Engineering, Ural Federal University Named after the First President of Russia B. N. Yeltsin, Mira 19, Yekaterinburg 620002, Russia; (S.A.A.); (E.G.K.)
| | - Nassim Fares
- Laboratoire de Recherche en Physiologie et Physiopathologie, Pôle Technologie Santé, Faculté de Médecine, Université Saint Joseph, Beirut 1104 2020, Lebanon; (J.A.); (J.H.); (Y.S.)
| | - Alicia C. Mondragon
- Laboratorio de Higiene, Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade da Santiago de Compostela, 27002 Lugo, Spain;
| | - Jose Manuel Miranda
- Laboratorio de Higiene, Inspección y Control de Alimentos, Departamento de Química Analítica, Nutrición y Bromatología, Campus Terra, Universidade da Santiago de Compostela, 27002 Lugo, Spain;
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Krause JL, Engelmann B, Schaepe SS, Rolle-Kampczyk U, Jehmlich N, Chang HD, Slanina U, Hoffman M, Lehmann J, Zenclussen AC, Herberth G, von Bergen M, Haange SB. DSS treatment does not affect murine colonic microbiota in absence of the host. Gut Microbes 2024; 16:2297831. [PMID: 38165179 PMCID: PMC10763643 DOI: 10.1080/19490976.2023.2297831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
The prevalence of inflammatory bowel disease (IBD) is rising globally; however, its etiology is still not fully understood. Patient genetics, immune system, and intestinal microbiota are considered critical factors contributing to IBD. Preclinical animal models are crucial to better understand the importance of individual contributing factors. Among these, the dextran sodium sulfate (DSS) colitis model is the most widely used. DSS treatment induces gut inflammation and dysbiosis. However, its exact mode of action remains unclear. To determine whether DSS treatment induces pathogenic changes in the microbiota, we investigated the microbiota-modulating effects of DSS on murine microbiota in vitro. For this purpose, we cultured murine microbiota from the colon in six replicate continuous bioreactors. Three bioreactors were supplemented with 1% DSS and compared with the remaining PBS-treated control bioreactors by means of microbiota taxonomy and functionality. Using metaproteomics, we did not identify significant changes in microbial taxonomy, either at the phylum or genus levels. No differences in the metabolic pathways were observed. Furthermore, the global metabolome and targeted short-chain fatty acid (SCFA) quantification did not reveal any DSS-related changes. DSS had negligible effects on microbial functionality and taxonomy in vitro in the absence of the host environment. Our results underline that the DSS colitis mouse model is a suitable model to study host-microbiota interactions, which may help to understand how intestinal inflammation modulates the microbiota at the taxonomic and functional levels.
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Affiliation(s)
- Jannike Lea Krause
- German Rheumatism Research Center Berlin, a Leibniz Institute – DRFZ, Schwiete laboratory for microbiota and inflammation, Berlin, Germany
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - Beatrice Engelmann
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Stephanie Serena Schaepe
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Ulrike Rolle-Kampczyk
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Hyun-Dong Chang
- German Rheumatism Research Center Berlin, a Leibniz Institute – DRFZ, Schwiete laboratory for microbiota and inflammation, Berlin, Germany
- Chair of Cytometry, Institute of Biotechnology, Technische Universität, Berlin, Germany
| | - Ulla Slanina
- Fraunhofer Cluster of Excellence Immune-mediated Diseases – CIMD, Leipzig, Germany
| | - Maximillian Hoffman
- Fraunhofer Cluster of Excellence Immune-mediated Diseases – CIMD, Leipzig, Germany
| | - Jörg Lehmann
- Fraunhofer Cluster of Excellence Immune-mediated Diseases – CIMD, Leipzig, Germany
- Department of Preclinical Development and Validation, Fraunhofer-Institute for Cell Therapy and Immunology – IZI, Leipzig, Germany
| | - Ana Claudia Zenclussen
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - Gunda Herberth
- Helmholtz-Centre for Environmental Research - UFZ, Department of Environmental Immunology, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany
| | - Sven-Bastiaan Haange
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ, Leipzig, Germany
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6
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Bu Y, Feng L, Xu D, Zhang S, Liang L, Si J, Lu Y, Liu Q, Yan G, Wang Y, Lan G, Liang J. Changes in Gut Microbiota Associated with Parity in Large White Sows. Animals (Basel) 2023; 14:112. [PMID: 38200843 PMCID: PMC10778104 DOI: 10.3390/ani14010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
As one of the most critical economic traits, the litter performance of sows is influenced by their parity. Some studies have indicated a connection between the gut microbiota and the litter performance of animals. In this study, we examined litter performance in 1363 records of different parities of Large White sows. We observed a marked decline in TNB (Total Number Born) and NBH (Number of Healthy Born) We observed a marked decline in TNB (Total Number Born) and NBH (Number of Healthy Born) among sows with parity 7 or higher. To gain a deeper understanding of the potential role of gut microbiota in this phenomenon, we conducted 16S rRNA amplicon sequencing of fecal DNA from 263 Large White sows at different parities and compared the changes in their gut microbiota with increasing parity. The results revealed that in comparison to sows with a parity from one to six, sows with a parity of seven or higher exhibited decreased alpha diversity in their gut microbiota. There was an increased proportion of pathogenic bacteria (such as Enterobacteriaceae, Streptococcus, and Escherichia-Shigella) and a reduced proportion of SCFA-producing families (such as Ruminococcaceae), indicating signs of inflammatory aging. The decline in sow function may be one of the primary reasons for the reduction in their litter performance.
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Affiliation(s)
- Yage Bu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Lingli Feng
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Di Xu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Shuai Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Liang Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Jinglei Si
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
- Guangxi State Farms Yongxin Animal Husbandry Group Co., Ltd., Nanning 530022, China
| | - Yujie Lu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Qiaoling Liu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Gang Yan
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Yubin Wang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Ganqiu Lan
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China; (Y.B.); (L.F.); (D.X.); (S.Z.); (L.L.); (J.S.); (Y.L.); (Q.L.); (G.Y.); (Y.W.); (G.L.)
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Kong L, Yue Y, Li J, Yang B, Chen B, Liu J, Lu Z. Transcriptomics and metabolomics reveal improved performance of Hu sheep on hybridization with Southdown sheep. Food Res Int 2023; 173:113240. [PMID: 37803553 DOI: 10.1016/j.foodres.2023.113240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 10/08/2023]
Abstract
Consumers are increasingly demanding high-quality mutton. Cross breeding can improve meat quality and is widely used in sheep breeding. However, little is known about the molecular mechanism of cross breeding sheep meat quality. In this study, male Southdown and female Hu sheep were hybridized. The slaughter performance and longissimus dorsi quality of the 6-month-old hybrid offspring were measured, and the longissimus dorsi of the hybrid offspring was analyzed by transcriptomics and metabolomics to explore the effect of cross breeding on meat quality. The results showed that the production performance of Southdown × Hu F1 sheep was significantly improved, the carcass fat content was significantly decreased, and the eating quality of Southdown × Hu F1 sheep were better. Compared with the HS group (Hu × Hu), the NH group (Southdown × Hu) had 538 differentially expressed genes and 166 differentially expressed metabolites (P < 0.05), which were significantly enriched in amino acid metabolism and other related pathways. Up-regulated genes METTL21C, PPARGC1A and down-regulated gene WFIKKN2 are related to muscle growth and development. Among them, the METTL21C gene, which is related to muscle development, was highly correlated with carnosine, a metabolite related to meat quality (correlation > 0.6 and P < 0.05). Our results provide further understanding of the molecular mechanism of cross breeding for sheep muscle growth and meat quality optimization.
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Affiliation(s)
- Lingying Kong
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yaojing Yue
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianye Li
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Bohui Yang
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Bowen Chen
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China
| | - Jianbin Liu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
| | - Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on the Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; Sheep Breeding Engineering Technology Research Center of Chinese Academy of Agricultural Sciences, Lanzhou 730050, China.
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8
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Chang YT, Ko HT, Wu PL, Kumar R, Wang HC, Lu HP. Gut microbiota of Pacific white shrimp ( Litopenaeus vannamei) exhibits distinct responses to pathogenic and non-pathogenic Vibrio parahaemolyticus. Microbiol Spectr 2023; 11:e0118023. [PMID: 37750710 PMCID: PMC10580984 DOI: 10.1128/spectrum.01180-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 08/11/2023] [Indexed: 09/27/2023] Open
Abstract
Acute hepatopancreatic necrosis disease (AHPND), a high-mortality-rate shrimp disease, is caused by specific Vibrio parahaemolyticus (Vp) strains with a plasmid encoding the PirABVp toxins. As a bacterial pathogen, the invasion of AHPND-causing Vp might impose pressure on commensal microbiota in the shrimp gut, while the relationship between the pathogenesis of AHPND and the dysbiosis of gut bacterial communities remains unclear. Here we explored the temporal changes of shrimp gut microbiota in response to AHPND-causing and non-AHPND-causing Vp strains, with the non-infected controls as a baseline of the shrimp gut microbiota. The diversity and composition of bacterial communities from 168 gut samples (covering three treatments at seven time points with eight individuals per set) were investigated using 16S rRNA gene metabarcoding with high-throughput sequencing. The results showed that (i) species diversity of gut bacterial communities declined in Vp-infected shrimp, independent of the strain pathogenicity; (ii) taxonomic compositions of gut bacterial communities were significantly different between shrimp infected by AHPND-causing and non-AHPND-causing Vp strains; (iii) short-term (within 6 hours) compositional shifts in the gut microbiota were found only in AHPND-causing Vp-infected shrimp; (iv) the gut microbiota of AHPND-causing Vp-infected shrimp was enriched with genera Photobacterium and Vibrio, with a decline in Candidatus Bacilliplasma; and (v) functional predictions suggested the loss of normal metabolism due to compositional shifts in the gut microbiota. Our work reveals distinct features of community dynamics in shrimp gut microbiota, associated with pathogenic versus non-pathogenic Vibrio infections, providing a new perspective of the pathogenesis of AHPND. IMPORTANCE Shrimp production is continually threatened by newly emerging diseases, such as AHPND, which is caused by specific Vp strains. Previous studies on the pathogenesis of AHPND have mainly focused on the histopathology and immune responses of the host. However, more attention needs to be paid to the gut microbiota, which acts as the first barrier to pathogen colonization. In this study, we revealed that shrimp gut microbiota responded differently to pathogenic and non-pathogenic Vp strains, with bacterial genera Photobacterium and Vibrio enriched in pathogenic Vp-infected shrimp, and Candidatus Bacilliplasma enriched in non-pathogenic Vp-infected shrimp. Moreover, functional predictions suggested that changes in taxonomic compositions would further affect normal metabolic functions, emphasizing the importance of sustaining an equilibrium in the gut microbiota. Several biomarkers associated with specific microbial taxa and functional pathways were identified in our data sets, which help predict the incidence of disease outcomes.
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Affiliation(s)
- Yi-Ting Chang
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Hao-Ting Ko
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Lun Wu
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Ramya Kumar
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Han-Ching Wang
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- International Center for Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
| | - Hsiao-Pei Lu
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
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9
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Singh G, Brim H, Haileselassie Y, Varma S, Habtezion A, Rashid M, Sinha SR, Ashktorab H. Microbiomic and Metabolomic Analyses Unveil the Protective Effect of Saffron in a Mouse Colitis Model. Curr Issues Mol Biol 2023; 45:5558-5574. [PMID: 37504267 PMCID: PMC10378474 DOI: 10.3390/cimb45070351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 07/29/2023] Open
Abstract
Despite the existence of effective drugs used to treat inflammatory bowel disease (IBD), many patients fail to respond or lose response over time. Further, many drugs can carry serious adverse effects, including increased risk of infections and malignancies. Saffron (Crocus sativus) has been reported to have anti-inflammatory properties. Its protective role in IBD and how the microbiome and metabolome play a role has not been explored extensively. We aimed to establish whether saffron treatment modulates the host microbiome and metabolic profile in experimental colitis. Colitis was induced in C57BL/6 mice with 3% DSS and treated with either saffron in a dose of 20 mg/kg body weight or vehicle through daily gavage. On day 10, stool pellets from mice were collected and analyzed to assess saffron's effect on fecal microbiota and metabolites through 16S rRNA sequencing and untargeted primary metabolite analysis. Saffron treatment maintained gut microbiota homeostasis by counter-selecting pro-inflammatory bacteria and maintained Firmicutes/Bacteroides ratio, which was otherwise disturbed by DSS treatment. Several metabolites (uric acid, cholesterol, 2 hydroxyglutaric acid, allantoic acid, 2 hydroxyhexanoic acid) were altered significantly with saffron treatment in DSS-treated mice, and this might play a role in mediating saffron's colitis-mitigating effects. These data demonstrate saffron's therapeutic potential, and its protective role is modulated by gut microbiota, potentially acting through changes in metabolites.
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Affiliation(s)
- Gulshan Singh
- Division of Gastroenterology and Hepatology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Hassan Brim
- Department of Pathology, Howard University College of Medicine, Washington, DC 20059, USA
| | - Yeneneh Haileselassie
- Division of Gastroenterology and Hepatology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Sudhir Varma
- Hithru Analytics LLC, Silver Spring, MD 20877, USA
| | - Aida Habtezion
- Division of Gastroenterology and Hepatology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Mudasir Rashid
- Department of Pathology and Cancer Center, College of Medicine, Howard University College of Medicine, Washington, DC 20059, USA
| | - Sidhartha R Sinha
- Division of Gastroenterology and Hepatology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Hassan Ashktorab
- Department of Pathology and Cancer Center, College of Medicine, Howard University College of Medicine, Washington, DC 20059, USA
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10
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Van Pee T, Nawrot TS, van Leeuwen R, Hogervorst J. Ambient particulate air pollution and the intestinal microbiome; a systematic review of epidemiological, in vivo and, in vitro studies. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 878:162769. [PMID: 36907413 DOI: 10.1016/j.scitotenv.2023.162769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/13/2023] [Accepted: 03/06/2023] [Indexed: 05/13/2023]
Abstract
A healthy indigenous intestinal microbiome is indispensable for intra- and extra-intestinal human health. Since well-established factors such as diet and antibiotic use only explain 16 % of the inter-individual variation in gut microbiome composition, recent studies have focused on the association between ambient particulate air pollution and the intestinal microbiome. We systematically summarize and discuss all evidence concerning the effect of particulate air pollution on intestinal bacterial diversity indices, specific bacterial taxa, and potential underlying intestinal mechanisms. To this end, all possibly relevant publications published between February 1982 and January 2023 were screened, and eventually, 48 articles were included. The vast majority (n = 35) of these studies were animal studies. The exposure periods investigated in the human epidemiological studies (n = 12) ranged from infancy through elderly. This systematic review found that intestinal microbiome diversity indices were generally negatively associated with particulate air pollution in epidemiological studies, with an increase in taxa belonging to Bacteroidetes (two studies), Deferribacterota (one study), and Proteobacteria (four studies), a decrease in taxa belonging to Verrucomicrobiota (one study), and no consensus for taxa belonging to Actinobacteria (six studies) and Firmicutes (seven studies). There was no unequivocal effect of ambient particulate air pollution exposure on bacterial indices and taxa in animal studies. Only one study in humans examined a possible underlying mechanism; yet, the included in vitro and animal studies depicted higher gut damage, inflammation, oxidative stress, and permeability in exposed versus unexposed animals. Overall, the population-based studies showed a dose-related continuum of short- and long-term ambient particulate air pollution exposure on lower gut diversity and shifts in taxa over the entire life course.
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Affiliation(s)
- Thessa Van Pee
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium; Department of Public Health and Primary Care, Leuven University, Herestraat 49-box 706, 3000 Leuven, Belgium.
| | - Romy van Leeuwen
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| | - Janneke Hogervorst
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
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11
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Gierse LC, Meene A, Skorka S, Cuypers F, Surabhi S, Ferrero-Bordera B, Kreikemeyer B, Becher D, Hammerschmidt S, Siemens N, Urich T, Riedel K. Impact of Pneumococcal and Viral Pneumonia on the Respiratory and Intestinal Tract Microbiomes of Mice. Microbiol Spectr 2023; 11:e0344722. [PMID: 36988458 PMCID: PMC10269894 DOI: 10.1128/spectrum.03447-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
With 2.56 million deaths worldwide annually, pneumonia is one of the leading causes of death. The most frequent causative pathogens are Streptococcus pneumoniae and influenza A virus. Lately, the interaction between the pathogens, the host, and its microbiome have gained more attention. The microbiome is known to promote the immune response toward pathogens; however, our knowledge on how infections affect the microbiome is still scarce. Here, the impact of colonization and infection with S. pneumoniae and influenza A virus on the structure and function of the respiratory and gastrointestinal microbiomes of mice was investigated. Using a meta-omics approach, we identified specific differences between the bacterial and viral infection. Pneumococcal colonization had minor effects on the taxonomic composition of the respiratory microbiome, while acute infections caused decreased microbial complexity. In contrast, richness was unaffected following H1N1 infection. Within the gastrointestinal microbiome, we found exclusive changes in structure and function, depending on the pathogen. While pneumococcal colonization had no effects on taxonomic composition of the gastrointestinal microbiome, increased abundance of Akkermansiaceae and Spirochaetaceae as well as decreased amounts of Clostridiaceae were exclusively found during invasive S. pneumoniae infection. The presence of Staphylococcaceae was specific for viral pneumonia. Investigation of the intestinal microbiomés functional composition revealed reduced expression of flagellin and rubrerythrin and increased levels of ATPase during pneumococcal infection, while increased amounts of acetyl coenzyme A (acetyl-CoA) acetyltransferase and enoyl-CoA transferase were unique after H1N1 infection. In conclusion, identification of specific taxonomic and functional profiles of the respiratory and gastrointestinal microbiome allowed the discrimination between bacterial and viral pneumonia. IMPORTANCE Pneumonia is one of the leading causes of death worldwide. Here, we compared the impact of bacterial- and viral-induced pneumonia on the respiratory and gastrointestinal microbiome. Using a meta-omics approach, we identified specific profiles that allow discrimination between bacterial and viral causative.
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Affiliation(s)
| | - Alexander Meene
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Sebastian Skorka
- Department of Molecular Genetics and Infection Biology, Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Fabian Cuypers
- Department of Molecular Genetics and Infection Biology, Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Surabhi Surabhi
- Department of Molecular Genetics and Infection Biology, Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | | | - Bernd Kreikemeyer
- Institute for Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Sven Hammerschmidt
- Department of Molecular Genetics and Infection Biology, Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Nikolai Siemens
- Department of Molecular Genetics and Infection Biology, Institute for Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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12
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He S, Yang K, Wen J, Kuang T, Cao Z, Zhang L, Han S, Jian S, Chen X, Zhang L, Deng J, Deng B. Antimicrobial Peptides Relieve Transportation Stress in Ragdoll Cats by Regulating the Gut Microbiota. Metabolites 2023; 13:metabo13030326. [PMID: 36984766 PMCID: PMC10057407 DOI: 10.3390/metabo13030326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/25/2023] Open
Abstract
Transportation is common in cats and often causes stress and intestinal disorders. Antimicrobial peptides (AMPs) exhibit a broad spectrum of antibacterial activity, and they may have the capacity for antioxidant and immune regulation. The objective of this study was to investigate the effects of dietary supplementation with AMPs on stress response, gut microbiota and metabolites of cats that have undergone transport stress. A total of 14 Ragdoll cats were randomly allocated into 2 treatments: basal diet (CON) and a basal diet supplemented with 0.3% AMPs. After a 6-week feeding period, all cats were transported for 3 h and, then, fed for another week. The results show that the diarrhea rate of cats was markedly reduced by supplementation with AMPs throughout the trial period (p < 0.05). In addition, AMPs significantly reduced serum cortisol and serum amyloid A (p < 0.05) and increased apolipoprotein 1 after transportation (p < 0.05). Moreover, AMPs reduced the level of inflammatory factors in the serum caused by transportation stress, including tumor necrosis factor-alpha (TNF-α) and interleukin-1 beta (IL-1β) (p < 0.05). The AMPs enhanced the activities of glutathione peroxidase (p < 0.01) and superoxide dismutase (p < 0.05). Furthermore, cats fed AMPs had higher levels of branched chain fatty acids (BCFAs) and a relative abundance of Blautia and a lower relative abundance of Negativibacillus after transportation (p < 0.05). The serum metabolome analysis further revealed that AMPs markedly regulated lipid metabolism by upregulating cholic acid expression. In conclusion, AMP supplementation alleviated oxidative stress and inflammatory response in transportation by regulating the gut microbiota and metabolites, thereby relieving stress-induced diarrhea and supporting gut and host health in cats.
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Affiliation(s)
- Shansong He
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Kang Yang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiawei Wen
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Tao Kuang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhihao Cao
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Lingna Zhang
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Sufang Han
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Shiyan Jian
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xin Chen
- School of Medicine, Foshan University, Foshan 528000, China
- Correspondence: (X.C.); (B.D.)
| | - Limeng Zhang
- Research Center of Pet Nutrition, Guangzhou Qingke Biotechnology Co., Ltd., Guangzhou 510642, China
| | - Jinping Deng
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Baichuan Deng
- Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (X.C.); (B.D.)
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13
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Hill AA, Kim M, Zegarra-Ruiz DF, Chang LC, Norwood K, Assié A, Wu WJH, Renfroe MC, Song HW, Major AM, Samuel BS, Hyser JM, Longman RS, Diehl GE. Acute high-fat diet impairs macrophage-supported intestinal damage resolution. JCI Insight 2023; 8:e164489. [PMID: 36538527 PMCID: PMC9977439 DOI: 10.1172/jci.insight.164489] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Chronic exposure to high-fat diets (HFD) worsens intestinal disease pathology, but acute effects of HFD in tissue damage remain unclear. Here, we used short-term HFD feeding in a model of intestinal injury and found sustained damage with increased cecal dead neutrophil accumulation, along with dietary lipid accumulation. Neutrophil depletion rescued enhanced pathology. Macrophages from HFD-treated mice showed reduced capacity to engulf dead neutrophils. Macrophage clearance of dead neutrophils activates critical barrier repair and antiinflammatory pathways, including IL-10, which was lost after acute HFD feeding and intestinal injury. IL-10 overexpression restored intestinal repair after HFD feeding and intestinal injury. Macrophage exposure to lipids from the HFD prevented tethering and uptake of apoptotic cells and Il10 induction. Milk fat globule-EGF factor 8 (MFGE8) is a bridging molecule that facilitates macrophage uptake of dead cells. MFGE8 also facilitates lipid uptake, and we demonstrate that dietary lipids interfere with MFGE8-mediated macrophage apoptotic neutrophil uptake and subsequent Il10 production. Our findings demonstrate that HFD promotes intestinal pathology by interfering with macrophage clearance of dead neutrophils, leading to unresolved tissue damage.
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Affiliation(s)
| | - Myunghoo Kim
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel F. Zegarra-Ruiz
- Immunology Program of the Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Lin-Chun Chang
- Immunology Program of the Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Kendra Norwood
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Adrien Assié
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Wan-Jung H. Wu
- Immunology Program of the Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Michael C. Renfroe
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Hyo Wong Song
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Buck S. Samuel
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Joseph M. Hyser
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Randy S. Longman
- Jill Roberts Institute for Research in IBD and Jill Roberts Center for IBD, Weill Cornell Medicine, New York, New York, USA
| | - Gretchen E. Diehl
- Alkek Center for Metagenomics and Microbiome Research and the Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Immunology Program of the Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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14
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Oxymatrine ameliorated experimental colitis via mechanisms involving inflammatory DCs, gut microbiota and TLR/NF-κB pathway. Int Immunopharmacol 2023; 115:109612. [PMID: 36584572 DOI: 10.1016/j.intimp.2022.109612] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 12/29/2022]
Abstract
It is common knowledge that the crosstalk of gut microbiota (GM) and dendritic cells (DCs) are critical for the pathogenesis of inflammatory bowel disease (IBD). As a major bioactive constituent derived from the root of the Sophora flavescens, Oxymatrine (OMT) was used to treat IBD in China. However, it is still unknown whether OMT ameliorates IBD by regulating the crosstalk between DCs and GM. In the present study, after 10 days of OMT (100 mg/kg/day) treated mice with colitis induced by dextran sulfate sodium (DSS), the change rate of body weight, colon weight, colon weight index, colon length, DAI score and colonic pathological damage scores of colitis mice were significantly ameliorate, followed with fewer ulceration and inflammatory cell infiltration, the increased expression of IL-4 and IL-13, and the decreased expression of CCL-2, IL-33 and IFN-γ. The percents of inflammatory DCs (such as TNF-α+DCs, iNOS+DCs, CXCR5+DCs and E-cadherin+DCs) were markedly decreased, and the GM composition was regulated. Importantly, it is positive correlated between the efficacy of OMT on colitis, GM and inflammatory DCs. Meanwhile, Western blotting assay showed that OMT suppressed the activation of TLR4, Myd88, IRAK4, IRAK1, TRAF6, TAK1, TAB, MKK3, MKK6, P38, NF-κB in the TLR / NF-κB signaling pathway. In summary, OMT exhibits the protective effect against the DSS-induced experimental colitis, which was achieved by regulating the crosstalk of inflammatory DCs and GM, and inhibiting the TLR / NF-κB signaling pathway.
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15
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Peng Y, Wei J, Jia X, Luan F, Man M, Ma X, Luo Y, Li Y, Li N, Wang Q, Wang X, Zhou Y, Ji Y, Mu W, Wang J, Wang C, Zhang Q, Yu K, Zhao M, Wang C. Changes in the microbiota in different intestinal segments of mice with sepsis. Front Cell Infect Microbiol 2023; 12:954347. [PMID: 36704101 PMCID: PMC9871835 DOI: 10.3389/fcimb.2022.954347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 12/19/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction The small intestine, as the main digestion and absorption site of the gastrointestinal tract, is often overlooked in studies, and the overall microbiota does not reflect the makeup of the microbiota in different segments of the intestine. Therefore, we aimed to exclude the influence of routine ICU treatment measures on sepsis patients and observed changes in the diversity and abundance of gut microbiota in different intestinal segments of septic mice. Methods The mice were randomly divided into the CLP6h group and the sham group. The contents of the colon and small intestine of the experimental group and the control group were collected after 6 h. Results After CLP, the number and structure of the gut microbiota in the colon changed most obviously, among which Bacteroidetes had the most significant changes. Akkermansia, D.Firmicutes_bacterium_M10_2, Blautia, Bifidobacterium, Lactobacillus, Candidatus_Arthromitus, and Muribaculaceae were changed in the colon. Lactobacillus, Bifidobacterium, Akkermansia, Blautia, Candidatus_Arthromitus, and Lachnospiraceae_NK4A136_group were changed in the small intestine. Discussion Our experiment found that there were different numbers of unique and common gut microbiota in the small intestine and colon after sepsis, and the gut microbiota of the colon changed more drastically after sepsis than the small intestine. Thus, we should focus on protective gut microbiota and mucin-degrading microbes. We hope that these results will provide help for sepsis treatment in the future.
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Affiliation(s)
- Yahui Peng
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Jieling Wei
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Xiaonan Jia
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Feiyu Luan
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Mingyin Man
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Xiaohui Ma
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Yinghao Luo
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Yue Li
- Department of Critical Care Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Nana Li
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Qian Wang
- Department of Critical Care Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Xibo Wang
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Yang Zhou
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Yuanyuan Ji
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Wenjing Mu
- Department of Critical Care Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
| | - Jun Wang
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Chunying Wang
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Qianqian Zhang
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Kaijiang Yu
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Mingyan Zhao
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
| | - Changsong Wang
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin Medical University, Harbin, China
- Department of Critical Care Medicine, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China
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16
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Su S, Wang L, Fu S, Zhao J, He X, Chen Q, Belobrajdic DP, Yu C, Liu H, Wu H, Han P, Yang B, Huang Y, Liu Y, He J. Effects of oat ( Avena sativa L.) hay diet supplementation on the intestinal microbiome and metabolome of Small-tail Han sheep. Front Microbiol 2022; 13:1032622. [PMID: 36590432 PMCID: PMC9801518 DOI: 10.3389/fmicb.2022.1032622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Supplementation of the sheep diet with oats (Avena sativa L.) improves animal growth and meat quality, however effects on intestinal microbes and their metabolites was not clear. This study aimed to establish the effect of dietary oat supplementation on rumen and colonic microbial abundance and explore the relationship with subsequent changes in digesta metabolites. Twenty Small-tail Han sheep were randomly assigned to a diet containing 30 g/100 g of maize straw (Control) or oat hay (Oat). After 90-days on experimental diets, rumen and colon digesta were collected and microbial diversity was determined by 16S rRNA gene Illumina NovaSeq sequencing and metabolomics was conducted using Ultra-high performance liquid chromatography Q-Exactive mass spectrometry (UHPLC-QE-MS). Compared to Control group, oat hay increased the abundance of Bacteroidetes and Fibrobacteres as well as known short-chain fatty acid (SCFA) producers Prevotellaceae, Ruminococcaceae and Fibrobacteraceae in rumen (p < 0.05). In rumen digesta, the Oat group showed had higher levels of (3Z,6Z)-3,6-nonadienal, Limonene-1,2-epoxide, P-tolualdehyde, and Salicylaldehyde compared to Control (p < 0.05) and these metabolites were positively correlated with the abundance of cecal Prevotellaceae NK3B31. In conclusion, supplementation of the sheep diet with oat hay improved desirable microbes and metabolites in the rumen, providing insight into mechanisms whereby meat quality can be improved by oat hay supplementation.
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Affiliation(s)
- Shaofeng Su
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
| | - Liwei Wang
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China,State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China
| | - Shaoyin Fu
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
| | - Jie Zhao
- Center of Reproductive Medicine, The Affiliated Hospital of Inner Mongolia Medical Hospital, Hohhot, China
| | - Xiaolong He
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
| | - Qiuju Chen
- Bayannur Institute of Agriculture and Animal Husbandry Science, Bayannur, China
| | | | - Chuanzong Yu
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
| | - Hongkui Liu
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
| | - Haiqing Wu
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
| | - Pingan Han
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
| | - Bin Yang
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
| | - Yao Huang
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China
| | - Yongbin Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China,*Correspondence: Yongbin Liu,
| | - Jiangfeng He
- Inner Mongolia Academy of Agriculture and Husbandry Science, Hohhot, China,State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, China,Jiangfeng He,
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17
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Dietary Supplementation with Black Raspberries Altered the Gut Microbiome Composition in a Mouse Model of Colitis-Associated Colorectal Cancer, although with Differing Effects for a Healthy versus a Western Basal Diet. Nutrients 2022; 14:nu14245270. [PMID: 36558431 PMCID: PMC9786988 DOI: 10.3390/nu14245270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022] Open
Abstract
Black raspberries (BRB) are rich in anthocyanins with purported anti-inflammatory properties. However, it is not known whether dietary supplementation would ameliorate Western-diet enhanced gut inflammation and colon tumorigenesis. We employed a mouse model of colitis-associated colorectal cancer (CAC) to determine the effects of dietary supplementation with 5 to 10% (w/w) whole, freeze-dried BRB in male C57BL/6J mice fed either a standard healthy diet (AIN93G) or the total Western diet (TWD). In a pilot study, BRB suppressed colitis and colon tumorigenesis while also shifting the composition of the fecal microbiome in favor of taxa with purported health benefits, including Bifidobacterium pseudolongum. In a follow-up experiment using a 2 × 2 factorial design with AIN and TWD basal diets with and without 10% (w/w) BRB, supplementation with BRB reduced tumor multiplicity and increased colon length, irrespective of the basal diet, but it did not apparently affect colitis symptoms, colon inflammation or mucosal injury based on histopathological findings. However, BRB intake increased alpha diversity, altered beta diversity and changed the relative abundance of Erysipelotrichaceae, Bifidobacteriaceae, Streptococcaceae, Rikenellaceae, Ruminococcaceae and Akkermansiaceae, among others, of the fecal microbiome. Notably, changes in microbiome profiles were inconsistent with respect to the basal diet consumed. Overall, these studies provide equivocal evidence for in vivo anti-inflammatory effects of BRB on colitis and colon tumorigenesis; yet, BRB supplementation led to dynamic changes in the fecal microbiome composition over the course of disease development.
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18
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Deng Q, Yao Y, Yang J, Khoshaba R, Shen Y, Wang X, Cao D. AKR1B8 deficiency drives severe DSS-induced acute colitis through invasion of luminal bacteria and activation of innate immunity. Front Immunol 2022; 13:1042549. [PMID: 36518763 PMCID: PMC9742539 DOI: 10.3389/fimmu.2022.1042549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
Background Dysfunction of intestinal epithelial cells (IECs) promotes inflammatory bowel disease (IBD) and associated colorectal cancer (CRC). AKR1B8 deficiency impairs the IEC barrier function, leading to susceptibility to chronic colitis induced by dextran sulfate sodium (DSS), yet it remains unclear how acute colitic response is in AKR1B8 deficient mice. Methods AKR1B8 knockout (KO) and littermate wild type mice were exposed to oral 1.5% DSS in drinking water for 6 days. Disease activity index and histopathological inflammation scores by H&E staining were calculated for colitic severity; permeability was assessed by fluorescein isothiocyanate dextran (FITC-Dextran) probes and bacterial invasion and transmission were detected by in situ hybridization in mucosa or by culture in blood agar plates. Immunofluorescent staining and flow cytometry were applied for immune cell quantification. Toll-like receptor 4 (TLR4) and target gene expression was analyzed by Western blotting and qRT-PCR. Results AKR1B8 KO mice developed severe acute colitis at a low dose (1.5%) of DSS in drinking water compared to wild type controls. In AKR1B8 KO mice, FITC-dextran was penetrated easily and luminal bacteria invaded to the surface of IEC layer on day 3, and excessive bacteria translocated into the colonic mucosa, mesenteric lymph nodes (MLNs) and liver on day 6, which was much mild in wild type mice. Hyper-infiltration of neutrophils and basophils occurred in AKR1B8 KO mice, and monocytes in spleen and macrophages in colonic mucosa increased markedly compared to wild type mice. TLR4 signaling in colonic epithelial cells of AKR1B8 KO mice was activated to promote great IL-1β and IL-6 expression compared to wild type mice. Conclusions AKR1B8 deficiency in IECs drives severe acute colitis induced by DSS at a low dose through activation of the innate immunity, being a novel pathogenic factor of colitis.
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Affiliation(s)
- Qiulin Deng
- Department of Proctology, The Affiliated Nanhua Hospital, University of South China Hengyang Medical School, Hengyang, Hunan, China
| | - Yichen Yao
- Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-sen University and Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, China
| | - Jing Yang
- Department of Gastroenterology, The First Affiliated Hospital, University of South China Hengyang Medical School, Hengyang, Hunan, China
| | - Ramina Khoshaba
- Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University, School of Medicine, Springfield, IL, United States,Department of Biotechnology, College of Science, University of Baghdad, Baghdad, Iraq
| | - Yi Shen
- Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University, School of Medicine, Springfield, IL, United States
| | - Xin Wang
- Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University, School of Medicine, Springfield, IL, United States,Department of Medicine, Harvard Medical School, Boston, MA, United States,Jeff and Penny Vinik Center for Translational Immunology Research, Division of Allergy and Clinical Immunology, Brigham and Women’s Hospital, Boston, MA, United States,*Correspondence: Xin Wang, ; Deliang Cao,
| | - Deliang Cao
- Department of Gastroenterology, The First Affiliated Hospital, University of South China Hengyang Medical School, Hengyang, Hunan, China,Department of Medical Microbiology, Immunology, and Cell Biology, Southern Illinois University, School of Medicine, Springfield, IL, United States,*Correspondence: Xin Wang, ; Deliang Cao,
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19
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Liu W, Yang J, Meng Y, Wu D, Cui L, Li T, Sun B, Liu P. The divergent effects of moderate climate warming on the gut microbiota and energetic state of cold-climate lizards from open and semi-closed microhabitats. Front Microbiol 2022; 13:1050750. [PMID: 36483215 PMCID: PMC9722725 DOI: 10.3389/fmicb.2022.1050750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/07/2022] [Indexed: 10/29/2023] Open
Abstract
INTRODUCTION Understanding the physiological responses to warming temperatures is critical for evaluating the vulnerabilities of animals to climate warming. The physiological responses are increasingly affected by gut microbiota. However, the interactions between physiological responses and the gut microbiota of sympatric animals from various microhabitats in the face of climate change remain largely unknown. METHODS To evaluate the effects of warming temperatures on animals from different microhabitats, we compared locomotor performance, metabolic rate, growth, survival, and gut microbiota of two sympatric ectothermic species (Eremias argus and Takydromus amurensis) from open and semi-closed microhabitats under present and moderate warming climate conditions, respectively. RESULTS AND DISCUSSION We found that locomotor performance and growth rates of snout-vent length (SVL) were enhanced in both lizard species by warming climate. Interestingly, warming temperatures enhanced resting metabolic rates (RMR) in the open-habitat lizard, E. argus, but depressed them in the semi-closed habitat lizard, T. amurensis. Reversely, the metabolism-related gut microbiota was not affected by warming in E. argus, whereas it was significantly enhanced by warming in T. amurensis, indicating a plausible compensatory effect of the gut microbiota on the metabolic regulation of T. amurensis. Furthermore, warming likely improved immunity in both lizard species by significantly reducing pathogenic bacteria while increasing probiotics. This study found that high-latitude sympatric lizards from both open and semi-closed habitats were beneficial to warming temperatures by physiological modification and regulation of the gut microbiota and highlighted the importance of integrating the physiology and gut microbiota in evaluating the vulnerability of animals to climate warming.
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Affiliation(s)
- Wanli Liu
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, China
| | - Jing Yang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yu Meng
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, China
| | - Danyang Wu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Luoxin Cui
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, China
| | - Teng Li
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Baojun Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Peng Liu
- College of Life Science and Technology, Harbin Normal University, Harbin, Heilongjiang, China
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20
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Zhang K, Xu Y, Yang Y, Guo M, Zhang T, Zong B, Huang S, Suo L, Ma B, Wang X, Wu Y, Brugger D, Chen Y. Gut microbiota-derived metabolites contribute negatively to hindgut barrier function development at the early weaning goat model. ANIMAL NUTRITION 2022; 10:111-123. [PMID: 35663372 PMCID: PMC9136126 DOI: 10.1016/j.aninu.2022.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/27/2021] [Accepted: 04/11/2022] [Indexed: 11/24/2022]
Abstract
Early weaning induces intestinal injury, leading to a series of long-term symptoms such as inflammation, malabsorption and diarrhea. In this study, we hypothesized that microbes and their metabolites modulate the host's inflammatory response to early weaning stress in a goat model. A total of 18 female Tibetan goat kids (n = 9) were weaned from their mothers at 28 d (D28) and 60 d (D60) postpartum. D60 and D28 groups were fed the same solid diet ad libitum from weaning to 75 d of age. The colonic epithelium was subject to RNA-sequencing, the caecal digesta metabolomics were assessed by liquid chromatography–tandem mass spectrometry (LC-MS/MS), and the caecal microbiota composition was analysed by 16S ribosomal RNA gene sequencing. We found that early weaning substantially increased the colonic pro-apoptotic gene expression of B-cell lymphoma associated X (Bax), caspase-9, and caspase-3, and decreased the expression of zonula occludens-1 (ZO-1) and claudin-1 (P < 0.01). In addition, a significant Bacteroides acidifaciens enrichment was observed in the hindgut of early-weaned goats (P < 0.01), which negatively correlated with lysophosphatidylcholine products. Similarly, the chemokine signaling, IL-17 signaling, and peroxisome proliferators-activated receptor (PPAR) signaling pathways were upregulated in the colonic mucosa of the early-weaned goats. By applying caecal microbiota transplantation from goats to defaunated C57/6J mice, we confirmed that caecal microbiota of D28 goat kids increased the relative abundance of B. acidifaciens and significantly up-regulated the genes of Bax, G protein–coupled receptor (GPR) 109A, GPR 43, fatty acid binding protein 6, nuclear receptor subfamily 1 group H member 3, angiotensin converting enzyme 2, and IL-6 expression (P < 0.05), and decreased ZO-1, and claudin-1 protein expression in the mice jejunum and colon (P < 0.001). These results proposed that the hindgut microbiota and metabolites mediate the barrier function weakening during early weaning, and the relative abundance of B. acidifaciens was negatively correlated with the hindgut barrier gene expression. This study demonstrates how weaning stress can affect key host–microbe interaction regulators in the hindgut, in a lysophosphatidylcholine dependent and independent manner. Furthermore, based on our mice data, these results are transferable to other mammal species.
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21
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Xia X, Gong R, Zhang C. Integrative analysis of transcriptome and metabolome reveals flavonoid biosynthesis regulation in Rhododendron pulchrum petals. BMC PLANT BIOLOGY 2022; 22:401. [PMID: 35974307 PMCID: PMC9380304 DOI: 10.1186/s12870-022-03762-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/15/2022] [Indexed: 06/02/2023]
Abstract
BACKGROUND Color is the major ornamental feature of the Rhododendron genus, and it is related to the contents of flavonoid in petals. However, the regulatory mechanism of flavonoid biosynthesis in Rhododendron pulchrum remains unknown. The transcriptome and metabolome analysis of Rhododendron pulchrum with white, pink and purple color in this study aimed to reveal the mechanism of flavonoid biosynthesis and to provide insight for improving the petal color. RESULTS Flavonoids and flavonols are the major components of flavonoid metabolites in R.pulchrum, such as laricitrin, apigenin, tricin, luteolin, isoorientin, isoscutellarein, diosmetin and their glycosides derivatives. With transcriptome and metabolome analysis, we found CHS, FLS, F3'H, F3'5'H, DFR, ANS, GT, FNS, IFR and FAOMT genes showed significantly differential expression in cultivar 'Zihe'. FNS and IFR were discovered to be associated with coloration in R.pulchrum for the first time. The FNS gene existed in the form of FNSI. The IFR gene and its related metabolites of medicarpin derivatives were highly expressed in purple petal. In cultivar 'Fenhe', up-regulation of F3'H and F3'5'H and down-regulation of 4CL, DFR, ANS, and GT were associated with pink coloration. With the transcription factor analysis, a subfamily of DREBs was found to be specifically enriched in pink petals. This suggested that the DREB family play an important role in pink coloration. In cultivars 'Baihe', flavonoid biosynthesis was inhibited by low expression of CHS, while pigment accumulation was inhibited by low expression of F3'5'H, DFR, and GT, which led to a white coloration. CONCLUSIONS By analyzing the transcriptome and metabolome of R.pulchrum, principal differential expression genes and metabolites of flavonoid biosynthesis pathway were identified. Many novel metabolites, genes, and transcription factors associated with coloration have been discovered. To reveal the mechanism of the coloration of different petals, a model of the flavonoid biosynthesis pathway of R.pulchrum was constructed. These results provide in depth information regarding the coloration of the petals and the flavonoid metabolism of R.pulcherum. The study of transcriptome and metabolome profiling gains insight for further genetic improvement in Rhododendron.
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Affiliation(s)
- Xi Xia
- Shanghai Urban Plant Resources Development and Application Engineering Research Center, Shanghai Botanical Garden, Shanghai, China
| | - Rui Gong
- Shanghai Urban Plant Resources Development and Application Engineering Research Center, Shanghai Botanical Garden, Shanghai, China
| | - Chunying Zhang
- Shanghai Urban Plant Resources Development and Application Engineering Research Center, Shanghai Botanical Garden, Shanghai, China.
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22
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Herfindal AM, Rocha SDC, Papoutsis D, Bøhn SK, Carlsen H. The ROS-generating enzyme NADPH oxidase 1 modulates the colonic microbiota but offers minor protection against dextran sulfate sodium-induced low-grade colon inflammation in mice. Free Radic Biol Med 2022; 188:298-311. [PMID: 35752373 DOI: 10.1016/j.freeradbiomed.2022.06.234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/13/2022] [Accepted: 06/19/2022] [Indexed: 10/17/2022]
Abstract
The enzyme NADPH oxidase 1 (NOX1) is a major producer of superoxide which together with other reactive oxygen and nitrogen species (ROS/RNS) are implicated in maintaining a healthy epithelial barrier in the gut. While previous studies have indicated NOX1's involvement in microbial modulation in the small intestine, less is known about the effects of NOX1-dependent ROS/RNS formation in the colon. We investigated the role of NOX1 in the colon of NOX1 knockout (KO) and wild type (WT) mice, under mild and subclinical low-grade colon inflammation induced by 1% dextran sulfate sodium (DSS). Ex vivo imaging of ROS/RNS in the colon revealed that absence of NOX1 strongly decreased ROS/RNS production, particularly during DSS treatment. Furthermore, while absence of NOX1 did not affect disease activity, some markers of inflammation (mRNA: Tnfa, Il6, Ptgs2; protein: lipocalin 2) in the colonic mucosa tended to be higher in NOX1 KO than in WT mice following DSS treatment. Lack of NOX1 also extensively modulated the bacterial community in the colon (16S rRNA gene sequencing), where NOX1 KO mice were characterized mainly by lower α-diversity (richness and evenness), higher abundance of Firmicutes, Akkermansia, and Oscillibacter, and lower abundance of Bacteroidetes and Alistipes. Together, our data suggest that NOX1 is pivotal for colonic ROS/RNS production in mice both during steady-state (i.e., no DSS treatment) and during 1% DSS-induced low-grade inflammation and for modulation of the colonic microbiota, with potential beneficial consequences for intestinal health.
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Affiliation(s)
- Anne Mari Herfindal
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432, Ås, Norway.
| | - Sérgio Domingos Cardoso Rocha
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432, Ås, Norway; Faculty of Biosciences, Norwegian University of Life Sciences, P. O. Box 5003, N-1432, Ås, Norway.
| | - Dimitrios Papoutsis
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432, Ås, Norway.
| | - Siv Kjølsrud Bøhn
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432, Ås, Norway.
| | - Harald Carlsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P. O. Box 5003, N-1432, Ås, Norway.
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23
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Sugihara K, Kitamoto S, Saraithong P, Nagao-Kitamoto H, Hoostal M, McCarthy C, Rosevelt A, Muraleedharan CK, Gillilland MG, Imai J, Omi M, Bishu S, Kao JY, Alteri CJ, Barnich N, Schmidt TM, Nusrat A, Inohara N, Golob JL, Kamada N. Mucolytic bacteria license pathobionts to acquire host-derived nutrients during dietary nutrient restriction. Cell Rep 2022; 40:111093. [PMID: 35858565 PMCID: PMC10903618 DOI: 10.1016/j.celrep.2022.111093] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 04/26/2022] [Accepted: 06/21/2022] [Indexed: 12/26/2022] Open
Abstract
Pathobionts employ unique metabolic adaptation mechanisms to maximize their growth in disease conditions. Adherent-invasive Escherichia coli (AIEC), a pathobiont enriched in the gut mucosa of patients with inflammatory bowel disease (IBD), utilizes diet-derived L-serine to adapt to the inflamed gut. Therefore, the restriction of dietary L-serine starves AIEC and limits its fitness advantage. Here, we find that AIEC can overcome this nutrient limitation by switching the nutrient source from the diet to the host cells in the presence of mucolytic bacteria. During diet-derived L-serine restriction, the mucolytic symbiont Akkermansia muciniphila promotes the encroachment of AIEC to the epithelial niche by degrading the mucus layer. In the epithelial niche, AIEC acquires L-serine from the colonic epithelium and thus proliferates. Our work suggests that the indirect metabolic network between pathobionts and commensal symbionts enables pathobionts to overcome nutritional restriction and thrive in the gut.
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Affiliation(s)
- Kohei Sugihara
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Sho Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Prakaimuk Saraithong
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Hiroko Nagao-Kitamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Matthew Hoostal
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Caroline McCarthy
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Alexandra Rosevelt
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Merritt G Gillilland
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Jin Imai
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Maiko Omi
- Department of Biologic and Materials Sciences and Prosthodontics, University of Michigan School of Dentistry, Ann Arbor, MI, USA
| | - Shrinivas Bishu
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - John Y Kao
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Nicolas Barnich
- M2iSH, UMR1071 Inserm/University Clermont Auvergne, Clermont-Ferrand, France
| | - Thomas M Schmidt
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Asma Nusrat
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Naohiro Inohara
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan L Golob
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Nobuhiko Kamada
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan.
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24
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Abstract
Despite a short history since its first isolation, Akkermansia muciniphila has been extensively studied in relation to its effects on human metabolism. A recent human intervention study also demonstrated that the bacterium is safe to use for therapeutic purposes. The best-known effects of A. muciniphila in human health and disease relate to its ability to strengthen gut integrity, modulate insulin resistance, and protect the host from metabolic inflammation. A further molecular mechanism, induction of GLP-1 secretion through ICAM-2 receptor, was recently discovered with the identification of a new bacterial protein produced by A. muciniphila. However, other studies have suggested a detrimental role for A. muciniphila in specific host immune settings. Here, we evaluate the molecular, mechanistic effects of A. muciniphila in host health and suggest some of the missing links to be connected before the organism should be considered as a next-generation biotherapeutic agent.
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Affiliation(s)
- Jiyeon Si
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea
| | - Hyena Kang
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea
| | - Hyun Ju You
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea,Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea,CONTACT Hyun Ju You Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - GwangPyo Ko
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Korea,Center for Human and Environmental Microbiome, Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea,KoBioLabs, Inc, Seoul, Republic of Korea,Bio, Seoul National UniversityBio-MAX/N-, Seoul, Republic of Korea,GwangPyo Ko Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul08826, Republic of Korea
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25
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Yan J, Chen Q, Tian L, Li K, Lai W, Bian L, Han J, Jia R, Liu X, Xi Z. Intestinal toxicity of micro- and nano-particles of foodborne titanium dioxide in juvenile mice: Disorders of gut microbiota-host co-metabolites and intestinal barrier damage. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 821:153279. [PMID: 35074372 DOI: 10.1016/j.scitotenv.2022.153279] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/09/2022] [Accepted: 01/16/2022] [Indexed: 05/28/2023]
Abstract
The wide use of TiO2 particles in food and the high exposure risk to children have prompted research into the health risks of TiO2. We used the microbiome and targeted metabolomics to explore the potential mechanism of intestinal toxicity of foodborne TiO2 micro-/nanoparticles after oral exposure for 28 days in juvenile mice. Results showed that the gut microbiota-including the abundance of Bacteroides, Bifidobacterium, Lactobacillus, and Prevotella-changed dynamically during exposure. The organic inflammatory response was activated, and lipopolysaccharide levels increased. Intestinal toxicity manifested as increased mucosal permeability, impaired intestinal barrier, immune damage, and pathological changes. The expression of antimicrobial peptides, occludin, and ZO-1 significantly reduced, while that of JNK2 and Src/pSrc increased. Compared with micro-TiO2 particles, the nano-TiO2 particles had strong toxicity. Fecal microbiota transplant confirmed the key role of gut microbiota in intestinal toxicity. The levels of gut microbiota-host co-metabolites, including pyroglutamic acid, L-glutamic acid, phenylacetic acid, and 3-hydroxyphenylacetic acid, changed significantly. Significant changes were observed in the glutathione and propanoate metabolic pathways. There was a significant correlation between the changes in gut microbiota, metabolites, and intestinal cytokine levels. These, together with the intestinal barrier damage signaling pathway, constitute the network mechanism of the intestinal toxicity of TiO2 particles.
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Affiliation(s)
- Jun Yan
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Qi Chen
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Lei Tian
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Kang Li
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Wenqing Lai
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Liping Bian
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Jie Han
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Rui Jia
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China
| | - Xiaohua Liu
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China.
| | - Zhuge Xi
- Tianjin Institute of Environmental & Operational Medicine, No. 1, Dali Road, Heping District, Tianjin 300050, China.
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Gomes MJC, da Silva JS, Alves NEG, de Assis A, de Mejía EG, Mantovani HC, Martino HSD. Cooked common bean flour, but not its protein hydrolysate, has the potential to improve gut microbiota composition and function in BALB/c mice fed a high-fat diet added with 6-propyl-2-thiouracil. J Nutr Biochem 2022; 106:109022. [DOI: 10.1016/j.jnutbio.2022.109022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 10/29/2021] [Accepted: 03/18/2022] [Indexed: 12/28/2022]
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Fecal miR-142a-3p from dextran sulfate sodium-challenge recovered mice prevents colitis by promoting the growth of Lactobacillus reuteri. Mol Ther 2022; 30:388-399. [PMID: 34450255 PMCID: PMC8753372 DOI: 10.1016/j.ymthe.2021.08.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 07/07/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
Feces are enriched with microRNAs (miRNAs) that shape the gut microbiota. These miRNAs are differentially expressed in the feces of healthy and diseased subjects. However, whether fecal miRNAs in subjects with inflammatory bowel diseases are involved in regulating microbiota composition and whether they have any beneficial effects remains unknown. Here, we studied the fecal microbiome composition and miRNA abundance in mice with dextran sulfate sodium (DSS)-induced colitis and mice at the recovery phase to explore different miRNAs expressed, their relations with microbial abundance, and their effects on colitis. We found that miR-142a-3p expression was significantly increased in the feces of mice recovered from colitis and that it could alleviate disease symptoms in mice treated with DSS in a microbiome-dependent manner. Specifically, miR-142a-3p promoted the growth of Lactobacillus reuteri, which had a high abundance in the feces of mice recovered from colitis, by regulating transcripts of polA and locus tag LREU_RS03575. Moreover, L. reuteri, as well as its metabolite reuterin, could alleviate DSS-induced disease symptoms. These results highlight the role of fecal miR-142a-3p in the prevention of colitis. We propose that the feces of subjects who have recovered from diseases might be enriched with miRNAs with preventive effects against those diseases.
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HE Y, LUO Y, HUANG Q, ZHOU H, QIAN M, GUAN Z, LIU Q, ZHAO Q. Effect of Xiaoning liquid on gut microbiota in asthmatic mice by 16S rDNA high-throughput sequencing. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.40721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Yuanyuan HE
- Hospital of Chengdu University of Traditional Chinese Medicine, P. R. China
| | - Yating LUO
- Xinjiang Yili Maternal and Child Health Care Hospital, China
| | - Qinwan HUANG
- Hospital of Chengdu University of Traditional Chinese Medicine, P. R. China
| | - Hongyun ZHOU
- Hospital of Chengdu University of Traditional Chinese Medicine, P. R. China
| | - Ming QIAN
- Xiangyang Hospital of Traditional Chinese Medicine, China
| | - Zhiwei GUAN
- Hospital of Chengdu University of Traditional Chinese Medicine, P. R. China
| | - Qianwei LIU
- Beijing University of Traditional Chinese Medicine, China
| | - Qiong ZHAO
- Hospital of Chengdu University of Traditional Chinese Medicine, P. R. China
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Taguer M, Darbinian E, Wark K, Ter-Cheam A, Stephens DA, Maurice CF. Changes in Gut Bacterial Translation Occur before Symptom Onset and Dysbiosis in Dextran Sodium Sulfate-Induced Murine Colitis. mSystems 2021; 6:e0050721. [PMID: 34874778 PMCID: PMC8651081 DOI: 10.1128/msystems.00507-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/20/2021] [Indexed: 11/30/2022] Open
Abstract
Longitudinal studies on the gut microbiome that follow the effect of a perturbation are critical in understanding the microbiome's response and succession to disease. Here, we use a dextran sodium sulfate (DSS) mouse model of colitis as a tractable perturbation to study how gut bacteria change their physiology over the course of a perturbation. Using single-cell methods such as flow cytometry, bioorthogonal noncanonical amino acid tagging (BONCAT), and population-based cell sorting combined with 16S rRNA sequencing, we determine the diversity of physiologically distinct fractions of the gut microbiota and how they respond to a controlled perturbation. The physiological markers of bacterial activity studied here include relative nucleic acid content, membrane damage, and protein production. There is a distinct and reproducible succession in bacterial physiology, with an increase in bacteria with membrane damage and diversity changes in the translationally active fraction, both, critically, occurring before symptom onset. Large increases in the relative abundance of Akkermansia were seen in all physiological fractions, most notably in the translationally active bacteria. Performing these analyses within a detailed, longitudinal framework determines which bacteria change their physiology early on, focusing therapeutic efforts in the future to predict or even mitigate relapse in diseases like inflammatory bowel diseases. IMPORTANCE Most studies on the gut microbiome focus on the composition of this community and how it changes in disease. However, how the community transitions from a healthy state to one associated with disease is currently unknown. Additionally, common diversity metrics do not provide functional information on bacterial activity. We begin to address these two unknowns by following bacterial activity over the course of disease progression, using a tractable mouse model of colitis. We find reproducible changes in gut bacterial physiology that occur before symptom onset, with increases in the proportion of bacteria with membrane damage, and changes in community composition of the translationally active bacteria. Our data provide a framework to identify possible windows of intervention and which bacteria to target in microbiome-based therapeutics.
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Affiliation(s)
- M. Taguer
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - E. Darbinian
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - K. Wark
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
| | - A. Ter-Cheam
- Department of Mathematics and Statistics, Faculty of Science, McGill University, Montreal, Quebec, Canada
| | - D. A. Stephens
- Department of Mathematics and Statistics, Faculty of Science, McGill University, Montreal, Quebec, Canada
| | - C. F. Maurice
- Department of Microbiology & Immunology, Faculty of Medicine and Health Sciences, McGill University, Montreal, Quebec, Canada
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Mehrotra I, Serena G, Cetinbas M, Kenyon V, Martin VM, Harshman SG, Zomorrodi AR, Sadreyev RI, Fasano A, Leonard MM. Characterization of the blood microbiota in children with Celiac disease. CURRENT RESEARCH IN MICROBIAL SCIENCES 2021; 2:100069. [PMID: 34841359 PMCID: PMC8610358 DOI: 10.1016/j.crmicr.2021.100069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/27/2021] [Accepted: 08/28/2021] [Indexed: 11/11/2022] Open
Abstract
Celiac Disease (CD) is an autoimmune disorder triggered by gluten ingestion that can develop in genetically predisposed individuals. Alterations in the gut microbiota have been suggested to contribute to development of autoimmune conditions including CD. Recent work suggests the existence of a blood microbiota. Evidence that alterations in the blood microbiota potentially influence the development of chronic immune based diseases is increasing. However, there is no published literature regarding the blood microbiota in children, including those with CD. This study aimed to characterize the diversity and taxonomic composition of the blood microbiota of children with CD compared to controls. Whole blood samples were collected from children with active CD, CD in remission, and control subjects and 16S rRNA sequencing was utilized to analyze the blood microbiota. We found 16s rRNA present throughout all pediatric blood samples, providing evidence for the presence of a pediatric blood microbiota. We found significant differences in beta diversity and in abundance of certain taxa (Campylobacterales order, Odoribacteraceae and Helicobacteraceae families, Odoribacter genus and species, and Bacteroides acidifaciens species) between subjects with active CD and controls. These taxa have been previously reported to be associated with immune response and gut-inflammatory diseases. We did not find significant differences between subjects with active and remission CD or between remission CD and controls. Conclusions: We provide evidence for a pediatric blood microbiota and identified higher beta diversity and alterations in the composition of blood microbiota in subjects with active CD compared to controls.
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Affiliation(s)
- Isha Mehrotra
- Center for Celiac Research and Treatment, MassGeneral Hospital for Children, Yawkey Center for Outpatient Care, Suite 6B, 32 Fruit Street, Boston, MA 02114, USA
| | - Gloria Serena
- Center for Celiac Research and Treatment, MassGeneral Hospital for Children, Yawkey Center for Outpatient Care, Suite 6B, 32 Fruit Street, Boston, MA 02114, USA
- Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Jackson, 55 Fruit Street, Boston, MA 02114, USA
- Celiac Research Program, Harvard Medical School, Boston, MA, USA
| | - Murat Cetinbas
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
- Department of Molecular Biology, Massachusetts General Hospital, Simches Research Center, 185 Cambridge Street, CPZN7250 Boston, MA 02114, USA
| | - Victoria Kenyon
- Center for Celiac Research and Treatment, MassGeneral Hospital for Children, Yawkey Center for Outpatient Care, Suite 6B, 32 Fruit Street, Boston, MA 02114, USA
- Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Jackson, 55 Fruit Street, Boston, MA 02114, USA
- Celiac Research Program, Harvard Medical School, Boston, MA, USA
| | - Victoria M. Martin
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
- Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Yawkey Center for Outpatient Care, Yawkey 6B-6800 Suite, 55 Fruit Street Boston, MA 02114, USA
- Food Allergy Center, Massachusetts General Hospital, MGH Professional Office Building, Suite 530, 275 Cambridge Street Boston, MA 02114, USA
| | - Stephanie G. Harshman
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
- Eating Disorders Clinical and Research Program, Massachusetts General Hospital: West End Apartments 2 Longfellow Place, Suite 200 Boston, MA 02114, USA
- Neuroendocrine Unit, Massachusetts General Hospital, 100 Blossom St, Boston, MA 02114, USA
| | - Ali R. Zomorrodi
- Center for Celiac Research and Treatment, MassGeneral Hospital for Children, Yawkey Center for Outpatient Care, Suite 6B, 32 Fruit Street, Boston, MA 02114, USA
- Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Jackson, 55 Fruit Street, Boston, MA 02114, USA
- Celiac Research Program, Harvard Medical School, Boston, MA, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
| | - Ruslan I. Sadreyev
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
- Department of Molecular Biology, Massachusetts General Hospital, Simches Research Center, 185 Cambridge Street, CPZN7250 Boston, MA 02114, USA
| | - Alessio Fasano
- Center for Celiac Research and Treatment, MassGeneral Hospital for Children, Yawkey Center for Outpatient Care, Suite 6B, 32 Fruit Street, Boston, MA 02114, USA
- Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Jackson, 55 Fruit Street, Boston, MA 02114, USA
- Celiac Research Program, Harvard Medical School, Boston, MA, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
- Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Yawkey Center for Outpatient Care, Yawkey 6B-6800 Suite, 55 Fruit Street Boston, MA 02114, USA
| | - Maureen M. Leonard
- Center for Celiac Research and Treatment, MassGeneral Hospital for Children, Yawkey Center for Outpatient Care, Suite 6B, 32 Fruit Street, Boston, MA 02114, USA
- Mucosal Immunology and Biology Research Center, MassGeneral Hospital for Children, Jackson, 55 Fruit Street, Boston, MA 02114, USA
- Celiac Research Program, Harvard Medical School, Boston, MA, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
- Division of Pediatric Gastroenterology and Nutrition, MassGeneral Hospital for Children, Yawkey Center for Outpatient Care, Yawkey 6B-6800 Suite, 55 Fruit Street Boston, MA 02114, USA
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Gierse LC, Meene A, Schultz D, Schwaiger T, Schröder C, Mücke P, Zühlke D, Hinzke T, Wang H, Methling K, Kreikemeyer B, Bernhardt J, Becher D, Mettenleiter TC, Lalk M, Urich T, Riedel K. Influenza A H1N1 Induced Disturbance of the Respiratory and Fecal Microbiome of German Landrace Pigs - a Multi-Omics Characterization. Microbiol Spectr 2021; 9:e0018221. [PMID: 34612695 PMCID: PMC8510242 DOI: 10.1128/spectrum.00182-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/20/2021] [Indexed: 12/13/2022] Open
Abstract
Seasonal influenza outbreaks represent a large burden for the health care system as well as the economy. While the role of the microbiome has been elucidated in the context of various diseases, the impact of respiratory viral infections on the human microbiome is largely unknown. In this study, swine was used as an animal model to characterize the temporal dynamics of the respiratory and gastrointestinal microbiome in response to an influenza A virus (IAV) infection. A multi-omics approach was applied on fecal samples to identify alterations in microbiome composition and function during IAV infection. We observed significantly altered microbial richness and diversity in the gastrointestinal microbiome after IAV infection. In particular, increased abundances of Prevotellaceae were detected, while Clostridiaceae and Lachnospiraceae decreased. Moreover, our metaproteomics data indicated that the functional composition of the microbiome was heavily affected by the influenza infection. For instance, we identified decreased amounts of flagellin, correlating with reduced abundances of Lachnospiraceae and Clostridiaceae, possibly indicating involvement of a direct immune response toward flagellated Clostridia during IAV infection. Furthermore, enzymes involved in short-chain fatty acid (SCFA) synthesis were identified in higher abundances, while metabolome analyses revealed rather stable concentrations of SCFAs. In addition, 16S rRNA gene sequencing was used to characterize effects on the composition and natural development of the upper respiratory tract microbiome. Our results showed that IAV infection resulted in significant changes in the abundance of Moraxellaceae and Pasteurellaceae in the upper respiratory tract. Surprisingly, temporal development of the respiratory microbiome structure was not affected. IMPORTANCE Here, we used swine as a biomedical model to elucidate the impact of influenza A H1N1 infection on structure and function of the respiratory and gastrointestinal tract microbiome by employing a multi-omics analytical approach. To our knowledge, this is the first study to investigate the temporal development of the porcine microbiome and to provide insights into the functional capacity of the gastrointestinal microbiome during influenza A virus infection.
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Affiliation(s)
| | - Alexander Meene
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Daniel Schultz
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Theresa Schwaiger
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Charlotte Schröder
- Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Greifswald, Germany
| | - Pierre Mücke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Daniela Zühlke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Tjorven Hinzke
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
- Institute of Marine Biotechnology e.V., Greifswald, Germany
| | - Haitao Wang
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Karen Methling
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Bernd Kreikemeyer
- Institute for Medical Microbiology, Virology and Hygiene, Rostock University Medical Centre, Rostock, Germany
| | - Jörg Bernhardt
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | | | - Michael Lalk
- Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany
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Huangfu LX, Cai XT, Yang JN, Wang HC, Li YX, Dai ZF, Yang RL, Lin XH. Irisin attenuates inflammation in a mouse model of ulcerative colitis by altering the intestinal microbiota. Exp Ther Med 2021; 22:1433. [PMID: 34707714 PMCID: PMC8543469 DOI: 10.3892/etm.2021.10868] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 05/13/2020] [Indexed: 12/16/2022] Open
Abstract
Evidence has demonstrated that the gut microbiota, which consists of probiotics and pathogenic microorganisms, is involved in the initiation of ulcerative colitis (UC) via the dysregulation of intestinal microflora and normal immune interactions, which ultimately leads to intestinal mucosal dysfunction. Irisin is released from muscle cells and displays anti-inflammatory effects; however, the mechanisms underlying irisin-mediated anti-inflammatory effects in UC have not been previously reported. In the present study, mice were divided into the following four groups: i) Control; ii) irisin; iii) dextran sulfate sodium (DSS) salt; and iv) DSS + irisin. Subsequently, the effects of irisin were investigated by observing alterations in intestinal microbes. Irisin significantly reduced the degree of inflammation in UC by reversing alterations to the macroscopic score, histological score, number of CD64+ cells and inflammatory cytokine alterations (P<0.05). Analysis of the microbial diversity in the stools of mice with active UC indicated that the five bacteria that displayed the greatest alterations in relative abundance were Alloprevotella, Bacteroides, Lachnospiraceae-UCG-001, Prebotellaceae-UCG-001 and Rikenellaceae-RCB-gut-group. Furthermore, Bactoroides were positively correlated with the histopathological score (P=0.001; R=0.977) and interleukin (IL)-23 levels (P=0.008; R=0.924). Alloprevotella (P=0.001; R=-0.943), Lachnospiraceae-UCG-001 (P=0.000; R=-0.973) and Rikenollaceae-RC8-gut-group (P=0.001; R=-0.971) were negatively correlated with the histopathological score. Furthermore, Lachnospiraceae-UCG-001 (P=0.01; R=-0.873) and Rikenollaceae-RC8-gut-group (P=0.049; R=-0.814) were negatively correlated with IL-23 levels. In summary, the results of the present study suggested that irisin improved inflammation in a UC mouse model potentially via altering the gut microbiota.
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Affiliation(s)
- Lu Xin Huangfu
- Department of Gastroenterology, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China.,Department of Geriatrics, Henan Provincial People's Hospital, Zhengzhou, Henan 450000, P.R. China
| | - Xin Tong Cai
- Department of Pathology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450000, P.R. China
| | - Jing Nan Yang
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Hui Chao Wang
- Department of Nephrology, The First Affiliated Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Yu Xia Li
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Zhi Feng Dai
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Rui Lin Yang
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
| | - Xu Hong Lin
- Department of Clinical Laboratory, Translational Medicine Center, Huaihe Hospital of Henan University, Kaifeng, Henan 475000, P.R. China
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The soil microbial food web revisited: Predatory myxobacteria as keystone taxa? THE ISME JOURNAL 2021; 15:2665-2675. [PMID: 33746204 PMCID: PMC8397742 DOI: 10.1038/s41396-021-00958-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 02/24/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023]
Abstract
Trophic interactions are crucial for carbon cycling in food webs. Traditionally, eukaryotic micropredators are considered the major micropredators of bacteria in soils, although bacteria like myxobacteria and Bdellovibrio are also known bacterivores. Until recently, it was impossible to assess the abundance of prokaryotes and eukaryotes in soil food webs simultaneously. Using metatranscriptomic three-domain community profiling we identified pro- and eukaryotic micropredators in 11 European mineral and organic soils from different climes. Myxobacteria comprised 1.5-9.7% of all obtained SSU rRNA transcripts and more than 60% of all identified potential bacterivores in most soils. The name-giving and well-characterized predatory bacteria affiliated with the Myxococcaceae were barely present, while Haliangiaceae and Polyangiaceae dominated. In predation assays, representatives of the latter showed prey spectra as broad as the Myxococcaceae. 18S rRNA transcripts from eukaryotic micropredators, like amoeba and nematodes, were generally less abundant than myxobacterial 16S rRNA transcripts, especially in mineral soils. Although SSU rRNA does not directly reflect organismic abundance, our findings indicate that myxobacteria could be keystone taxa in the soil microbial food web, with potential impact on prokaryotic community composition. Further, they suggest an overlooked, yet ecologically relevant food web module, independent of eukaryotic micropredators and subject to separate environmental and evolutionary pressures.
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Sauvaitre T, Etienne-Mesmin L, Sivignon A, Mosoni P, Courtin CM, Van de Wiele T, Blanquet-Diot S. Tripartite relationship between gut microbiota, intestinal mucus and dietary fibers: towards preventive strategies against enteric infections. FEMS Microbiol Rev 2021; 45:5918835. [PMID: 33026073 DOI: 10.1093/femsre/fuaa052] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023] Open
Abstract
The human gut is inhabited by a large variety of microorganims involved in many physiological processes and collectively referred as to gut microbiota. Disrupted microbiome has been associated with negative health outcomes and especially could promote the onset of enteric infections. To sustain their growth and persistence within the human digestive tract, gut microbes and enteric pathogens rely on two main polysaccharide compartments, namely dietary fibers and mucus carbohydrates. Several evidences suggest that the three-way relationship between gut microbiota, dietary fibers and mucus layer could unravel the capacity of enteric pathogens to colonise the human digestive tract and ultimately lead to infection. The review starts by shedding light on similarities and differences between dietary fibers and mucus carbohydrates structures and functions. Next, we provide an overview of the interactions of these two components with the third partner, namely, the gut microbiota, under health and disease situations. The review will then provide insights into the relevance of using dietary fibers interventions to prevent enteric infections with a focus on gut microbial imbalance and impaired-mucus integrity. Facing the numerous challenges in studying microbiota-pathogen-dietary fiber-mucus interactions, we lastly describe the characteristics and potentialities of currently available in vitro models of the human gut.
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Affiliation(s)
- Thomas Sauvaitre
- Université Clermont Auvergne, UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Clermont-Ferrand, France.,Ghent University, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent, Belgium
| | - Lucie Etienne-Mesmin
- Université Clermont Auvergne, UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Clermont-Ferrand, France
| | - Adeline Sivignon
- Université Clermont Auvergne, UMR 1071 Inserm, USC-INRAe 2018, Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte (M2iSH), Clermont-Ferrand, France
| | - Pascale Mosoni
- Université Clermont Auvergne, UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Clermont-Ferrand, France
| | - Christophe M Courtin
- KU Leuven, Faculty of Bioscience Engineering, Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), Leuven, Belgium
| | - Tom Van de Wiele
- Ghent University, Faculty of Bioscience Engineering, Center for Microbial Ecology and Technology (CMET), Ghent, Belgium
| | - Stéphanie Blanquet-Diot
- Université Clermont Auvergne, UMR 454 INRAe, Microbiology, Digestive Environment and Health (MEDIS), Clermont-Ferrand, France
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Ecological Adaptation and Succession of Human Fecal Microbial Communities in an Automated In Vitro Fermentation System. mSystems 2021; 6:e0023221. [PMID: 34313459 PMCID: PMC8409738 DOI: 10.1128/msystems.00232-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Longitudinal studies of gut microbiota following specific interventions are vital for understanding how they influence host health. However, robust longitudinal sampling of gut microbiota is a major challenge, which can be addressed using in vitro fermentors hosting complex microbial communities. Here, by employing 16S rRNA gene amplicon sequencing, we investigated the adaptation and succession of human fecal microbial communities in an automated multistage fermentor. We performed two independent experiments using different human donor fecal samples, one configured with two units of three colon compartments each studied for 22 days and another with one unit of two colon compartments studied for 31 days. The fermentor maintained a trend of increasing microbial alpha diversity along colon compartments. Within each experiment, microbial compositions followed compartment-specific trajectories and reached independent stable configurations. While compositions were highly similar between replicate units, they were clearly separated between different experiments, showing that they maintained the individuality of fecal inoculum rather than converging on a fermentor-specific composition. While some fecal amplicon sequence variants (ASVs) were undetected in the fermentor, many ASVs undetected in the fecal samples flourished in vitro. These bloomer ASVs accounted for significant proportions of the population and included prominent health-associated microbes such as Bacteroides fragilis and Akkermansia muciniphila. Turnover in community compositions is likely explained by feed composition and pH, suggesting that these communities can be easily modulated. Our results suggest that in vitro fermentors are promising tools to study complex microbial communities harboring important members of human gut microbiota. IMPORTANCE In vitro fermentors that can host complex gut microbial communities are promising tools to investigate the dynamics of human gut microbiota. In this work, using an automated in vitro gut fermentor consisting of different colon compartments, we investigated the adaptation dynamics of two different human fecal microbial communities over 22 and 31 days. By observing the temporal trends of different community members, we found that many dominant members of the fecal microbiota failed to maintain their dominance in vitro, and some of the low-abundance microbes undetected in the fecal microbiota successfully grew in the in vitro communities. Microbiome compositional changes and blooming could largely be explained by feed composition and pH, suggesting that these communities can be modulated to desired compositions via optimizing culture conditions. Thus, our results open up the possibility of modulating in vitro microbial communities to predefined compositions by optimizing feed composition and culture conditions.
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Zhang Y, Thompson KN, Branck T, Yan Yan, Nguyen LH, Franzosa EA, Huttenhower C. Metatranscriptomics for the Human Microbiome and Microbial Community Functional Profiling. Annu Rev Biomed Data Sci 2021; 4:279-311. [PMID: 34465175 DOI: 10.1146/annurev-biodatasci-031121-103035] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial community gene function and regulation at scale. This review begins by summarizing the motivations for community transcriptomics and the history of the field. We then explore the principles, best practices, and challenges of contemporary MTX workflows: beginning with laboratory methods for isolation and sequencing of community RNA, followed by informatics methods for quantifying RNA features, and finally statistical methods for detecting differential expression in a community context. In thesecond half of the review, we survey important biological findings from the MTX literature, drawing examples from the human microbiome, other (nonhuman) host-associated microbiomes, and the environment. Across these examples, MTX methods prove invaluable for probing microbe-microbe and host-microbe interactions, the dynamics of energy harvest and chemical cycling, and responses to environmental stresses. We conclude with a review of open challenges in the MTX field, including making assays and analyses more robust, accessible, and adaptable to new technologies; deciphering roles for millions of uncharacterized microbial transcripts; and solving applied problems such as biomarker discovery and development of microbial therapeutics.
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Affiliation(s)
- Yancong Zhang
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kelsey N Thompson
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Tobyn Branck
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Systems, Synthetic, and Quantitative Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Yan Yan
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Long H Nguyen
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.,Clinical and Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02108, USA
| | - Eric A Franzosa
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center and Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA; , .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, USA
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Shang L, Yu H, Liu H, Chen M, Zeng X, Qiao S. Recombinant antimicrobial peptide microcin J25 alleviates DSS-induced colitis via regulating intestinal barrier function and modifying gut microbiota. Biomed Pharmacother 2021; 139:111127. [PMID: 33819810 DOI: 10.1016/j.biopha.2020.111127] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is rising constantly all over the world. However, current medical treatments are not universally practical. Microcin J25 (MccJ25), a member of the lasso peptides class, has excellent antimicrobial activity both in vitro and in vivo. Here, we assessed the anti-inflammatory effects of MccJ25 through DSS-induced UC mouse model. MccJ25 significantly ameliorated the UC-associated parameters such as decreased body weight, increased disease activity index (DAI) and shortened colon length. MccJ25 also provides barrier protection by preserving structural integrity and reducing inflammatory infiltrates of colon epithelium. The underlying mechanism may be associated with gut microbiota. To test this uncertainty, co-housing experiment was performed, and results indicate homogenized microbiota could relief the inflammatory. Meanwhile, we also proved the prominent role of the possible targets of MccJ25, namely genus Lactobacillus, Bacteroides and Akkermansia (as well as the possible strains related to the important OTUs) in inflammation status through comprehensive analysis. In conclusion, MccJ25 effectively attenuates inflammation and improves disrupted barrier function, and the MccJ25-modified gut microbiota plays a central role in this process.
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Affiliation(s)
- Lijun Shang
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China.
| | - Haitao Yu
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China
| | - Hongbin Liu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen 518000, PR China
| | - Meixia Chen
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China.
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Huang H, Li M, Wang Y, Wu X, Shen J, Xiao Z, Zhao Y, Du F, Chen Y, Wu Z, Ji H, Zhang C, Li J, Wen Q, Kaboli PJ, Cho CH, Wang S, Wang Y, He Y, Wu X. Excessive Intake of Longan Arillus Alters gut Homeostasis and Aggravates Colitis in Mice. Front Pharmacol 2021; 12:640417. [PMID: 33841158 PMCID: PMC8033040 DOI: 10.3389/fphar.2021.640417] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/18/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Longan is the fruit of Dimocarpus longan Lour. and the longan arillus has long been used in traditional Chinese medicine possessing various health benefits. However, the excessive intake of longan is found in daily life to cause “shanghuo” syndrome. “Shanghuo” has been linked to increased disease susceptibility. The present study thus aimed to investigate the toxicological outcomes after excessive longan treatment. Methods: Longan extract at a normal dosage of 4 g/kg and two excess dosages of 8 and 16 g/kg was orally administered to normal C57BL/6J mice for two weeks or to C57BL/6J mice with DSS-induced colitis. Mouse gut microbiome were analyzed by 16S rRNA sequencing. Short chain fatty acid (SCFA) contents in colonic contents were measured by GC-MS. Colon tissue was used for histopathological observation after H and E staining, detection of protein expression by western blot, analysis of gene expression by qPCR, and detection of apoptotic cells by TUNEL assay. ELISA was used for biochemical analysis in serum. Results: In normal mice, repeated longan intake at excess doses, but not the normal dose, increased infiltration of inflammatory cells, elevated serum levels of TNF-α and IL-6 and reduced production of SCFAs. In DSS-induced colitic mice, longan intake at 4 g/kg did not promote colitis in mice, while excessive longan (8 or 16 g/kg) aggravated colitis in mice, showing increased inflammation, more serious histological abnormalities, increased gut permeability, and increased epithelia injury when compared to DSS alone. Excessive longan induced a significant reduction of microbial diversity in colitic mice, accompanied with aggravated alterations of DSS-associated bacteria including the increase of Proteobacteria phylum and genera of Bacteroides, Akkermansia, Turicibacter and Escherchia-Shigella, and the decrease of norank_f__Muribaculaceae. The changed microbial compositions were accompanied with decreased SCFAs when longan was supplemented with DSS. The aggravated colon injury by excessive intake of longan in colitic mice was tightly correlated with the altered microbial communities and decreased SCFAs production. Conclusion: Excessive longan intake disturbs gut homeostasis and aggravates colitis via promoting inflammation and altering gut microbe compositions and associated metabolism in mice. Our findings warrant rational longan arillus consumption as a dietary supplement or herbal medicine.
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Affiliation(s)
- Huimin Huang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yi Wang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Xiaoxiao Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yu Chen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Zhigui Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Huijiao Ji
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Chunyuan Zhang
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Jing Li
- Department of Oncology and Hematology, Hospital (T.C.M) Affiliated to Southwest Medical University, Luzhou, China
| | - Qinglian Wen
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, China
| | - Parham Jabbarzadeh Kaboli
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Chi Hin Cho
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Shengpeng Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Yisheng He
- Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
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Becattini S, Sorbara MT, Kim SG, Littmann EL, Dong Q, Walsh G, Wright R, Amoretti L, Fontana E, Hohl TM, Pamer EG. Rapid transcriptional and metabolic adaptation of intestinal microbes to host immune activation. Cell Host Microbe 2021; 29:378-393.e5. [PMID: 33539766 PMCID: PMC7954923 DOI: 10.1016/j.chom.2021.01.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/08/2020] [Accepted: 01/07/2021] [Indexed: 12/17/2022]
Abstract
The gut microbiota produces metabolites that regulate host immunity, thereby impacting disease resistance and susceptibility. The extent to which commensal bacteria reciprocally respond to immune activation, however, remains largely unexplored. Herein, we colonized mice with four anaerobic symbionts and show that acute immune responses result in dramatic transcriptional reprogramming of these commensals with minimal changes in their relative abundance. Transcriptomic changes include induction of stress-response mediators and downregulation of carbohydrate-degrading factors such as polysaccharide utilization loci (PULs). Flagellin and anti-CD3 antibody, two distinct immune stimuli, induced similar transcriptional profiles, suggesting that commensal bacteria detect common effectors or activate shared pathways when facing different host responses. Immune activation altered the intestinal metabolome within 6 hours, decreasing luminal short-chain fatty acid and increasing aromatic metabolite concentrations. Thus, intestinal bacteria, prior to detectable shifts in community composition, respond to acute host immune activation by rapidly changing gene transcription and immunomodulatory metabolite production.
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Affiliation(s)
- Simone Becattini
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology and Immunology, School of Medicine, University of Geneva, 1206 Geneva, Switzerland.
| | - Matthew T Sorbara
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Sohn G Kim
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Eric L Littmann
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Qiwen Dong
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Gavin Walsh
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Roberta Wright
- Center for Microbes Inflammation and Cancer, Molecular Microbiology Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Luigi Amoretti
- Center for Microbes Inflammation and Cancer, Molecular Microbiology Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Emily Fontana
- Center for Microbes Inflammation and Cancer, Molecular Microbiology Core Facility, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Tobias M Hohl
- Immunology Program, Sloan Kettering Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA; Infectious Diseases Service, Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Eric G Pamer
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA.
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40
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Liu W, Feng H, Zheng S, Xu S, Massey IY, Zhang C, Wang X, Yang F. Pb Toxicity on Gut Physiology and Microbiota. Front Physiol 2021; 12:574913. [PMID: 33746764 PMCID: PMC7970193 DOI: 10.3389/fphys.2021.574913] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 01/27/2021] [Indexed: 12/19/2022] Open
Abstract
Lead (Pb) is a toxic heavy metal, having profound threats to the global population. Multiple organs such as kidney, and liver, as well as nervous, hematologic, and reproductive systems, are commonly considered the targets of Pb toxicity. Increasing researches reported that the effects of Pb on gastrointestinal tracts are equally intensive, especially on intestinal microbiota. This review summarized Pb toxicity on gut physiology and microbiota in different animal models and in humans, of which the alterations may further have effects on other organs in host. To be more specific, Pb can impair gut barrier and increase gut permeability, which make inflammatory cytokines, immunologic factors, as well as microbial metabolites such as bile acids (BA) and short-chain fatty acids (SCFAs) enter the enterohepatic circulation easily, and finally induce multiple systematic lesion. In addition, we emphasized that probiotic treatment may be one of the feasible and effective strategies for preventing Pb toxicity.
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Affiliation(s)
- Wenya Liu
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Hai Feng
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Shuilin Zheng
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Shuaishuai Xu
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Isaac Yaw Massey
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Chengcheng Zhang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Xiaoyan Wang
- Department of Gastroenterology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Fei Yang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, China
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41
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Huang Y, Yang Q, Mi X, Qiu L, Tao X, Zhang Z, Xia J, Wu Q, Wei H. Ripened Pu-erh Tea Extract Promotes Gut Microbiota Resilience against Dextran Sulfate Sodium Induced Colitis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2190-2203. [PMID: 33570405 DOI: 10.1021/acs.jafc.0c07537] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Ripened Pu-erh tea (RPT) has been shown to be an effective natural ingredient to defend against experimentally induced colitis. We hypothesized that RPT would alleviate dextran sulfate sodium (DSS) induced colitis via modulating intestinal microbiota. The effect of RPT on mice gut microbiota was evaluated using 16S rRNA gene amplicon sequencing, broad-spectrum antibiotic (ABX) treatment, and fecal microbiota transplantation (FMT). Pretreatment with RPT enhanced intestinal barrier function, reduced colonic and serum proinflammatory cytokine and macrophage infiltration, and preserved the resilience of gut microbiota in mice during a DSS challenge. Administration of either RPT-regulated or healthy control-derived gut microbiota showed similar protection against colitis, and such protection could not be recapitulated with fecal microbiota from ABX-treated mice, suggesting a key role of protective consortium in the disease protection. Mechanistically, cecal contents of short-chain fatty acids (SCFAs) and colonic peroxisome proliferator activated receptor-γ (PPAR-γ) expression in colitis mice increased significantly by RPT intervention. Collectively, RPT treatment improved DSS-induced colitis by partially reversing the dysbiosis state of gut microbiota, which might be associated with an increase in SCFA level and PPAR-γ expression.
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Affiliation(s)
- Yina Huang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330031, People's Republic of China
| | - Qin Yang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330031, People's Republic of China
| | - Xuan Mi
- Wanlongshan Tea Plantation, Pingxiang, Jiangxi 337000, People's Republic of China
| | - Liang Qiu
- Jiangxi University of Traditional Chinese Medicine, Nanchang, Jiangxi 330006, People's Republic of China
| | - Xueying Tao
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330031, People's Republic of China
| | - Zhihong Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330031, People's Republic of China
| | - Jun Xia
- Veterinary Medicine and Feed Supervision Institute, Nanchang, Jiangxi 330096, People's Republic of China
| | - Qinglong Wu
- Wanlongshan Tea Plantation, Pingxiang, Jiangxi 337000, People's Republic of China
- Texas Children's Microbiome Center, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Hua Wei
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, Jiangxi 330031, People's Republic of China
- Wanlongshan Tea Plantation, Pingxiang, Jiangxi 337000, People's Republic of China
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42
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Yang Y, Wang X, Xie K, Zhu C, Chen N, Chen T. kLDM: Inferring Multiple Metagenomic Association Networks based on the Variation of Environmental Factors. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:834-847. [PMID: 33607296 PMCID: PMC9170748 DOI: 10.1016/j.gpb.2020.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/16/2020] [Accepted: 08/15/2020] [Indexed: 11/05/2022]
Abstract
Identification of significant biological relationships or patterns is central to many metagenomic studies. Methods that estimate association networks have been proposed for this purpose; however, they assume that associations are static, neglecting the fact that relationships in a microbial ecosystem may vary with changes in environmental factors (EFs), which can result in inaccurate estimations. Therefore, in this study, we propose a computational model, called the k-Lognormal-Dirichlet-Multinomial (kLDM) model, which estimates multiple association networks that correspond to specific environmental conditions, and simultaneously infers microbe–microbe and EF–microbe associations for each network. The effectiveness of the kLDM model was demonstrated on synthetic data, a colorectal cancer (CRC) dataset, the Tara Oceans dataset, and the American Gut Project dataset. The results revealed that the widely-used Spearman’s rank correlation coefficient method performed much worse than the other methods, indicating the importance of separating samples by environmental conditions. Cancer fecal samples were then compared with cancer-free samples, and the estimation achieved by kLDM exhibited fewer associations among microbes but stronger associations between specific bacteria, especially five CRC-associated operational taxonomic units, indicating gut microbe translocation in cancer patients. Some EF-dependent associations were then found within a marine eukaryotic community. Finally, the gut microbial heterogeneity of inflammatory bowel disease patients was detected. These results demonstrate that kLDM can elucidate the complex associations within microbial ecosystems. The kLDM program, R, and Python scripts, together with all experimental datasets, are accessible at https://github.com/tinglab/kLDM.git.
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Affiliation(s)
- Yuqing Yang
- Department of Computer Science and Technology and Institute of Artificial Intelligence, Tsinghua University, Beijing 100084, China; Sogou Inc., Beijing 100084, China
| | - Xin Wang
- Peking Union Medical College, Chinese Academy of Medical Science, Beijing, 100005, China; Department of Ultrasound, Peking Union Medical College Hospital, Beijing 100005, China
| | - Kaikun Xie
- Department of Computer Science and Technology and Institute of Artificial Intelligence, Tsinghua University, Beijing 100084, China
| | - Congmin Zhu
- Department of Computer Science and Technology and Institute of Artificial Intelligence, Tsinghua University, Beijing 100084, China; Beijing National Research Center for Information Science and Technology, Beijing 100084, China
| | - Ning Chen
- Department of Computer Science and Technology and Institute of Artificial Intelligence, Tsinghua University, Beijing 100084, China.
| | - Ting Chen
- Department of Computer Science and Technology and Institute of Artificial Intelligence, Tsinghua University, Beijing 100084, China; Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou 350122, China; Beijing National Research Center for Information Science and Technology, Beijing 100084, China.
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43
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Park H, Yeo S, Kang S, Huh CS. Longitudinal Microbiome Analysis in a Dextran Sulfate Sodium-Induced Colitis Mouse Model. Microorganisms 2021; 9:370. [PMID: 33673349 PMCID: PMC7917662 DOI: 10.3390/microorganisms9020370] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 02/09/2021] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
The role of the gut microbiota in the pathogenesis of inflammatory bowel disease (IBD) has been in focus for decades. Although metagenomic observations in patients/animal colitis models have been attempted, the microbiome results were still indefinite and broad taxonomic presumptions were made due to the cross-sectional studies. Herein, we conducted a longitudinal microbiome analysis in a dextran sulfate sodium (DSS)-induced colitis mouse model with a two-factor design based on serial DSS dose (0, 1, 2, and 3%) and duration for 12 days, and four mice from each group were sacrificed at two-day intervals. During the colitis development, a transition of the cecal microbial diversity from the normal state to dysbiosis and dynamic changes of the populations were observed. We identified genera that significantly induced or depleted depending on DSS exposure, and confirmed the correlations of the individual taxa to the colitis severity indicated by inflammatory biomarkers (intestinal bleeding and neutrophil-derived indicators). Of note, each taxonomic population showed its own susceptibility to the changing colitis status. Our findings suggest that an understanding of the individual susceptibility to colitis conditions may contribute to identifying the role of the gut microbes in the pathogenesis of IBD.
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Affiliation(s)
- Hyunjoon Park
- Research Institute of Eco-Friendly Livestock Science, Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon 25354, Korea;
- Advanced Green Energy and Environment Institute, Handong Global University, Pohang 37554, Korea
| | - Soyoung Yeo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea;
| | - Seokwon Kang
- Department of Life Sciences, Handong Global University, Pohang 37554, Korea;
| | - Chul Sung Huh
- Research Institute of Eco-Friendly Livestock Science, Institute of Green-Bio Science and Technology, Seoul National University, Pyeongchang, Gangwon 25354, Korea;
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang, Gangwon 25354, Korea
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Ding Y, Li X, Liu Y, Wang S, Cheng D. Protection Mechanisms Underlying Oral Administration of Chlorogenic Acid against Cadmium-Induced Hepatorenal Injury Related to Regulating Intestinal Flora Balance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:1675-1683. [PMID: 33494608 DOI: 10.1021/acs.jafc.0c06698] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Cadmium (Cd) is a heavy metal, which is widely used in the industry and daily life. It has a long half-life, so large amounts of Cd can accumulate in humans and become toxic. Chlorogenic acid (CGA) can eliminate free radicals and inhibit lipid peroxidation and is mainly used to prevent metal toxicity. In the present study, mice are given CGA by intraperitoneal injection or gavage, respectively, to explore the mechanism of preventing Cd toxicity. In acute Cd-exposed mice, CGA treatment (ip) alleviated Cd-induced oxidative damage and reduced the production of NO and MPO in the liver and kidney tissues, while TLR4 expression levels did not change significantly. After 8 weeks of Cd exposure, CGA administration (gavage) significantly alleviated gut dysbiosis by decreasing the Firmicutes to Bacteroidetes ratio, enhancing the relative abundances of bacteria, including Ruminiclostridium_9, Alloprevotella, and Rikenella, and inhibiting the activation of the TLR4/MyD88/NF-κB signaling pathway. These findings suggested that protection mechanisms underlying the oral administration of CGA against the Cd-induced hepatorenal injury was related to the regulation of the intestinal flora balance. CGA can be used as an effective component in daily diet to prevent Cd toxicity.
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Affiliation(s)
- Yixin Ding
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Xiang Li
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Yutong Liu
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Shuo Wang
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Dai Cheng
- State Key Laboratory of Food Nutrition and Safety, Tianjin University of Science & Technology, Tianjin 300457, China
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
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45
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Dacquay LC, Tsang D, Chan D, Parkinson J, Philpott DJ, McMillen DR. E.coli Nissle increases transcription of flagella assembly and formate hydrogenlyase genes in response to colitis. Gut Microbes 2021; 13:1994832. [PMID: 34751631 PMCID: PMC8583297 DOI: 10.1080/19490976.2021.1994832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/31/2021] [Accepted: 10/11/2021] [Indexed: 02/04/2023] Open
Abstract
Escherichia coli Nissle (EcN), a probiotic bacterium, has been employed in treating inflammatory bowel disease, but the nature of its therapeutic effect is not fully understood. Intestinal inflammation alters the environment, exposing the microbial population to new stresses and eliciting transcriptional responses. We administered EcN to germ-free mice and then compared its transcriptional response between DSS-treated and untreated conditions using RNA-seq analysis to identify 187 differentially expressed genes (119 upregulated, 68 downregulated) and verifying a subset with qRT-PCR. The upregulated genes included many involved in flagella biosynthesis and motility, as well as several members of the formate hydrogenlyase complex. Despite prior evidence that these pathways are both transcriptionally regulated by nitric oxide, in vitro tests did not establish that nitric oxide exposure alone elicited the transcriptional response. The results provide new information on the transcriptional response of EcN to inflammation and establish a basis for further investigation of its anti-inflammatory activity.
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Affiliation(s)
- Louis C Dacquay
- Departments of Chemical and Physical Sciences, Cell and Systems Biology, Chemistry, and Physics, University of Toronto, Toronto, Canada
| | - Derek Tsang
- Departments of Chemical and Physical Sciences, Cell and Systems Biology, Chemistry, and Physics, University of Toronto, Toronto, Canada
| | - Donny Chan
- Departments of Chemical and Physical Sciences, Cell and Systems Biology, Chemistry, and Physics, University of Toronto, Toronto, Canada
| | - John Parkinson
- Departments of Chemical and Physical Sciences, Cell and Systems Biology, Chemistry, and Physics, University of Toronto, Toronto, Canada
| | - Dana J Philpott
- Departments of Chemical and Physical Sciences, Cell and Systems Biology, Chemistry, and Physics, University of Toronto, Toronto, Canada
| | - David R McMillen
- Departments of Chemical and Physical Sciences, Cell and Systems Biology, Chemistry, and Physics, University of Toronto, Toronto, Canada
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Crosstalk Between Lung and Extrapulmonary Organs in Infection and Inflammation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1303:333-350. [PMID: 33788201 DOI: 10.1007/978-3-030-63046-1_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Acute and chronic lung inflammation is a risk factor for various diseases involving lungs and extrapulmonary organs. Intercellular and interorgan networks, including crosstalk between lung and brain, intestine, heart, liver, and kidney, coordinate host immunity against infection, protect tissue, and maintain homeostasis. However, this interaction may be counterproductive and cause acute or chronic comorbidities due to dysregulated inflammation in the lung. In this chapter, we review the relationship of the lung with other key organs during normal cell processes and disease development. We focus on how pneumonia may lead to a systemic pathophysiological response to acute lung injury and chronic lung disease through organ interactions, which can facilitate the development of undesirable and even deleterious extrapulmonary sequelae.
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Kim S, Lee JY, Shin SG, Kim JK, Silwal P, Kim YJ, Shin NR, Kim PS, Won M, Lee SH, Kim SY, Sasai M, Yamamoto M, Kim JM, Bae JW, Jo EK. ESRRA (estrogen related receptor alpha) is a critical regulator of intestinal homeostasis through activation of autophagic flux via gut microbiota. Autophagy 2020; 17:2856-2875. [PMID: 33172329 DOI: 10.1080/15548627.2020.1847460] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The orphan nuclear receptor ESRRA (estrogen related receptor alpha) is critical in mitochondrial biogenesis and macroautophagy/autophagy function; however, the roles of ESRRA in intestinal function remain uncharacterized. Herein we identified that ESRRA acts as a key regulator of intestinal homeostasis by amelioration of colonic inflammation through activation of autophagic flux and control of host gut microbiota. Esrra-deficient mice presented with increased susceptibility to dextran sodium sulfate (DSS)-induced colitis with upregulation of intestinal inflammation. In addition, esrra-null mice had depressed AMP-activated protein kinase phosphorylation (AMPK), lower levels of TFEB (transcription factor EB), and accumulation of SQSTM1/p62 (sequestosome 1) with defective mitochondria in intestinal tissues. Esrra-deficient mice showed distinct gut microbiota composition and significantly higher microbial diversity than wild-type (WT) mice. Cohousing or fecal microbiota transplantation from WT mice to Esrra-deficient mice ameliorated DSS-induced colitis severity. Importantly, patients with ulcerative colitis (UC) had significantly decreased ESRRA expression in intestinal mucosal tissues that correlated with disease activity, suggesting clinical relevance of ESRRA in UC. Taken together, our results show that ESRRA contributes to intestinal homeostasis through autophagy activation and gut microbiota control to protect the host from detrimental inflammation and dysfunctional mitochondria.
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Affiliation(s)
- Sup Kim
- Department of Radiation Oncology, Chungnam National University Hospital, Daejeon, Korea
| | - June-Young Lee
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Dongdaemun-gu, Seoul, Korea
| | - Seul Gi Shin
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon Korea.,Infection Control Convergence Research Center, Chungnam National University School of Medicine Daejeon, Korea
| | - Jin Kyung Kim
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon Korea.,Infection Control Convergence Research Center, Chungnam National University School of Medicine Daejeon, Korea
| | - Prashanta Silwal
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon Korea.,Infection Control Convergence Research Center, Chungnam National University School of Medicine Daejeon, Korea
| | - Young Jae Kim
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon Korea.,Infection Control Convergence Research Center, Chungnam National University School of Medicine Daejeon, Korea
| | - Na-Ri Shin
- Korean Collection for Type Cultures, Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Dongdaemun-gu, Seoul, Korea
| | - Minho Won
- Biotechnology Process Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Chungcheongbuk-do Korea
| | - Sang-Hee Lee
- Center for Research Equipment, Korea Basic Science Institute, Chungbuk, Korea
| | - Soo Yeon Kim
- Future Medicine Division, Korea Institute of Oriental Medicine, Daejeon Korea
| | - Miwa Sasai
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka, Japan.,Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka Japan
| | - Masahiro Yamamoto
- Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka, Japan.,Laboratory of Immunoparasitology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka Japan
| | - Jin-Man Kim
- Infection Control Convergence Research Center, Chungnam National University School of Medicine Daejeon, Korea.,Pathology and.,Department of Medical Science, Chungnam National University School of Medicine, Daejeon Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Dongdaemun-gu, Seoul, Korea
| | - Eun-Kyeong Jo
- Department of Microbiology, Chungnam National University School of Medicine, Daejeon Korea.,Infection Control Convergence Research Center, Chungnam National University School of Medicine Daejeon, Korea
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Choi EY, Choi JO, Park CY, Kim SH, Kim D. Water Extract of Artemisia annua L. Exhibits Hepatoprotective Effects Through Improvement of Lipid Accumulation and Oxidative Stress-Induced Cytotoxicity. J Med Food 2020; 23:1312-1322. [PMID: 33202166 DOI: 10.1089/jmf.2020.4696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a metabolic liver disease with a complex underlying mechanism that has not been completely understood. Thus, effective and safe drugs for this disease are not yet available. Artemisia annua L. is a medicinal plant with potent antimicrobial and antioxidant activities. In this study, we prepared a water extract of A. annua (WEAA) and examined its potential for NAFLD treatment. First, we pretreated HepG2 cells (human hepatocarcinoma cell line) with WEAA and then treated the cells with oleic acid or tert-butylhydroperoxide to examine the effect of WEAA on the lipid accumulation and the cytotoxicity, respectively. WEAA not only inhibited lipid accumulation within HepG2 cells but also protected cells from oxidative stress-mediated damage through the activation of antioxidant enzymes (such as activation of superoxide dismutase and production of glutathione) and its own scavenging activity. Next, to confirm protective effect of the WEAA in in vivo, mice were intragastrically administered with WEAA, extract of Silybum marianum or water once a day, and simultaneously provided with high-fat diet to induce fatty liver and hepatic steatosis. Oral administration of WEAA ameliorated weight gain and hepatic lipid accumulation in high-fat diet-fed mice. Moreover, the plasma levels of triglyceride, aspartate aminotransferase, and alanine aminotransferase were reduced in the WEAA-treated group. Our findings indicated that WEAA may be a potential intervention for preventing or treating hepatic lipid accumulation and liver damage.
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Affiliation(s)
| | - Jin Ouk Choi
- Department of Biomedical Sciences and Seoul National University College of Medicine, Seoul, Korea.,Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Korea
| | | | | | - Donghyun Kim
- Department of Biomedical Sciences and Seoul National University College of Medicine, Seoul, Korea.,Department of Microbiology and Immunology, Seoul National University College of Medicine, Seoul, Korea
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Li Q, Guo L, Wang L, Miao J, Cui H, Li L, Geng K, Zhao L, Sun X, Jia J, Bian Y. Composition of "gold juice" using an ancient method based on intestinal microecology. J Int Med Res 2020; 48:300060520931288. [PMID: 32993381 PMCID: PMC7545780 DOI: 10.1177/0300060520931288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Objective To identify potentially effective bacterial components of gold juice, a traditional Chinese medicine treatment used for fecal microbiota transplantation. Methods Fecal samples were collected from five healthy children (two boys and three girls; mean age, 7.52 ± 2.31 years). The children had no history of antibiotic use or intestinal microecological preparation in the preceding 3 months. Fresh fecal samples were collected from children to prepare gold juice in mid-to-late November, in accordance with traditional Chinese medicine methods, then used within 7 days. Finally, 16S rDNA sequence analysis was used to identify potentially effective bacterial components of gold juice. QIIME software was used for comparisons of microbial species among gold juice, diluent, filtrate, and loess samples. Results Microflora of gold juice exhibited considerable changes following “ancient method” processing. Microbial components significantly differed between gold juice and filtrate samples. The gold juice analyzed in our study consisted of microbes that synthesize carbohydrates and amino acids by degrading substances, whereas the filtrate contained probiotic flora, Bacteroides, and Prevotella 9. Conclusions This study of microbial components in gold juice and filtrate provided evidence regarding effective bacterial components in gold juice, which may aid in clinical decisions concerning fecal microbiota transplantation.
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Affiliation(s)
- Qiuwei Li
- Tianjin Second People's Hospital, Tianjin, China
| | - Liying Guo
- Tianjin Second People's Hospital, Tianjin, China
| | - Li Wang
- Tianjin Second People's Hospital, Tianjin, China
| | - Jing Miao
- Tianjin Second People's Hospital, Tianjin, China
| | - Huantian Cui
- Integrative Medicine Institute, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Li Li
- Integrative Medicine Institute, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Kan Geng
- Shanghai Ooyi Biomedical Technology Co. Ltd., Shanghai, China
| | - Licong Zhao
- Integrative Medicine Institute, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xiaoxue Sun
- Integrative Medicine Institute, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jianwei Jia
- Tianjin Second People's Hospital, Tianjin, China
| | - Yuhong Bian
- Integrative Medicine Institute, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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50
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Xu N, Wang L, Li C, Ding C, Li C, Fan W, Cheng C, Gu B. Microbiota dysbiosis in lung cancer: evidence of association and potential mechanisms. Transl Lung Cancer Res 2020; 9:1554-1568. [PMID: 32953527 PMCID: PMC7481604 DOI: 10.21037/tlcr-20-156] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Over the past decade, revolution in microbial research has provided valuable insights into the function of microbes that inhabit human body. This complex community of microbes, collectively named as microbiota, displays tremendous interaction with a host to maintain homeostasis of the local environment. Lungs were even previously regarded as sterile for a long time. With the development of high-throughput next-generation sequencing technology, a low-density, diversified microbial ecosystem is found in bronchoalveolar lavage fluid, sputum, and lung tissues. Current research confirms that, compared with healthy people, patients with lung cancer show changes in the relative abundance of multiple genera. Emerging evidence has suggested that dysbiosis of the lung microbiota may play a critical role in lung carcinogenesis by affecting metabolic, inflammatory pathways and immune response. We briefly summarize the relationship between lung microbiome and lung cancer and discuss the potential mechanisms mediating lung microbiota and lung cancer. Thus, we provide innovative strategies for early prevention and personalized treatment of lung cancer.
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Affiliation(s)
- Nana Xu
- Laboratory of Morphology, Xuzhou Medical University, Xuzhou, China
| | - Lei Wang
- Department of Histology and Embryology, Xuzhou Medical University, Xuzhou, China
| | - Chenxi Li
- Medical Technology Institute of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou, China
| | - Chao Ding
- Department of General Surgery, Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Cong Li
- Emergency Intensive Care Unit, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Wenting Fan
- Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Chen Cheng
- Medical Technology Institute of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou, China
| | - Bing Gu
- Medical Technology Institute of Xuzhou Medical University, Xuzhou Key Laboratory of Laboratory Diagnostics, Xuzhou, China.,Department of Laboratory Medicine, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
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