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Penarete-Acosta D, Stading R, Emerson L, Horn M, Chakraborty S, Han A, Jayaraman A. A microfluidic co-culture model for investigating colonocytes-microbiota interactions in colorectal cancer. LAB ON A CHIP 2024; 24:3690-3703. [PMID: 38973701 DOI: 10.1039/d4lc00013g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Changes in the abundance of certain bacterial species within the colorectal microbiota correlate with colorectal cancer (CRC) development. While carcinogenic mechanisms of single pathogenic bacteria have been characterized in vitro, limited tools are available to investigate interactions between pathogenic bacteria and both commensal microbiota and colonocytes in a physiologically relevant tumor microenvironment. To address this, we developed a microfluidic device that can be used to co-culture colonocyte spheroids and colorectal microbiota. The device was used to explore the effect of Fusobacterium nucleatum, an opportunistic pathogen associated with colorectal cancer development in humans, on colonocyte gene expression and microbiota composition. F. nucleatum altered the transcription of genes involved in cytokine production, epithelial-to-mesenchymal transition, and proliferation in colonocytes in a contact-independent manner; however, most of these effects were significantly diminished by the presence of commensal microbiota. Interestingly, F. nucleatum significantly altered the abundance of multiple bacterial clades associated with mucosal immune responses and cancer development in the colon. Our results highlight the importance of evaluating the potential carcinogenic activity of pathogens in the context of a commensal microbiota, and the potential to discover novel inter-species microbial interactions in the CRC microenvironment.
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Affiliation(s)
| | - Rachel Stading
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, USA
| | - Laura Emerson
- Department of Biomedical Engineering, Texas A&M University, USA.
| | - Mitchell Horn
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, USA
| | - Sanjukta Chakraborty
- Department of Medical Physiology, College of Medicine, Texas A&M University, USA
| | - Arum Han
- Department of Biomedical Engineering, Texas A&M University, USA.
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, USA
- Department of Electrical and Computer Engineering, Texas A&M University, USA
| | - Arul Jayaraman
- Department of Biomedical Engineering, Texas A&M University, USA.
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, USA
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2
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Gestation and lactation triphenyl phosphate exposure disturbs offspring gut microbiota in a sex-dependent pathway. Food Chem Toxicol 2023; 172:113579. [PMID: 36563926 DOI: 10.1016/j.fct.2022.113579] [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: 07/10/2022] [Revised: 10/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Triphenyl phosphate (TPhP) is an Organophosphate flame retardant (OPFR) that has been widely used in many commercial products. Following its widely usage, its health risk has been concerned. In this study, mice were exposed to TPhP (1 mg/kg) during pregnancy and lactation (E0-PND21), the effect of TPhP on gut microbiota and its role in TPhP mediated lipid metabolism disturbance of offspring was investigated. Our results showed that TPhP disturbed the gut microbiota in dam or offspring at different extent, with male offspring experiencing major effects. Both the composition, abundance or network of gut microbiome was affected in male offspring. In male offspring, expression of genes along gut-liver axis including FXR, CYP7A1, SREBP-1c and ChREBP was significantly up-regulated, and expression of SHP, FGF15 and ASBT was significantly down-regulated. Consistent with this, lipid accumulation in the liver, and increased level of triglyceride, total cholestrol and total bile acid in the serum was observed. The changed abundance of Ruminococcaceae, Clostridiaceae, and Bacteroidaceae shows strong correlation with disturbed lipid metabolism in male offspring. Our research showed that indirect TPhP exposure during early life stage could affect the gut microbiota and gene expression along gut-liver axis in offspring at sex-dependent pathways, with males experiencing more effects.
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3
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Yue B, Zong G, Tao R, Wei Z, Lu Y. Crosstalk between traditional Chinese medicine-derived polysaccharides and the gut microbiota: A new perspective to understand traditional Chinese medicine. Phytother Res 2022; 36:4125-4138. [PMID: 36100366 DOI: 10.1002/ptr.7607] [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: 04/07/2022] [Revised: 08/04/2022] [Accepted: 08/20/2022] [Indexed: 11/09/2022]
Abstract
Polysaccharide is a kind of macromolecule polymer composed of monosaccharides connected by glycosidic bonds. Traditional Chinese medicine (TCM), composed of various bioactive ingredients, is usually rich in polysaccharides. In recent years, extensive research on TCM polysaccharides has demonstrated their pharmacological effects. Polysaccharides can hardly be catabolized by enzymes encoded by the human genome but can be degraded to absorbable metabolites by bacteria inhabiting the colon. Hence, the gut microbiota plays a vital role in degrading TCM polysaccharides into short-chain fatty acids (SCFAs) which exert physiological functions locally and systemically. Besides, TCM polysaccharides can also modulate the composition and activities of the gut microbiota by promoting the growth of beneficial bacteria and inhibiting the colonization of pathogenic bacteria, ultimately restoring gut homeostasis and improving human health. In this review, we discuss the extraction and pharmacological effects of TCM polysaccharides, various functions of the gut microbiota, and the interactions between TCM polysaccharides and the gut microbiota, illuminating the mechanisms of TCM polysaccharides modulating host physiology via the gut microbiota. To firmly establish the clinical efficacy of TCM polysaccharides, further high-quality studies especially clinical trials are needed. Generally, discussion on the interplay between TCM polysaccharides and the gut microbiota is expected to elucidate their application prospects and inspire new thoughts in the development of TCM.
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Affiliation(s)
- Bingjie Yue
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Gangfan Zong
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ruizhi Tao
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhonghong Wei
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing, China
| | - Yin Lu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.,Jiangsu Joint International Research Laboratory of Chinese Medicine and Regenerative Medicine, Nanjing, China.,Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
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Abstract
Buffalo is an important livestock species. Here, we present a comprehensive metagenomic survey of the microbial communities along the buffalo digestive tract. We analysed 695 samples covering eight different sites in three compartments (four-chambered stomach, intestine, and rectum). We mapped ~85% of the raw sequence reads to 4,960 strain-level metagenome-assembled genomes (MAGs) and 3,255 species-level MAGs, 90% of which appear to correspond to new species. In addition, we annotated over 5.8 million nonredundant proteins from the MAGs. In comparison with the rumen microbiome of cattle, the buffalo microbiota seems to present greater potential for fibre degradation and less potential for methane production. Our catalogue of microbial genomes and the encoded proteins provides insights into microbial functions and interactions at distinct sites along the buffalo digestive tract.
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5
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Singh R, Dutta A, Bose T, Mande SS. A compendium of predicted growths and derived symbiotic relationships between 803 gut microbes in 13 different diets. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100127. [PMID: 35909605 PMCID: PMC9325735 DOI: 10.1016/j.crmicr.2022.100127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 03/11/2022] [Accepted: 03/20/2022] [Indexed: 11/30/2022] Open
Abstract
Simulated growth of 803 gut microbes in mono- and co-cultures in 13 distinct diets. Inferred symbiotic relationships and metabolic co-operation among gut microbes. Diet-based variations in metabolic co-operation among gut microbes. Validation of in silico findings against existing literature evidence.
Gut health is intimately linked to dietary habits and the microbial community (microbiota) that flourishes within. The delicate dependency of the latter on nutritional availability is also strongly influenced by interactions (such as, parasitic or mutualistic) between the resident microbes, often affecting their growth rate and ability to produce key metabolites. Since, cultivating the entire repertoire of gut microbes is a challenging task, metabolic models (genome-based metabolic reconstructions) could be employed to predict their growth patterns and interactions. Here, we have used 803 gut microbial metabolic models from the Virtual Metabolic Human repository, and subsequently optimized and simulated them to grow on 13 dietary compositions. The presented pairwise interaction data (https://osf.io/ay8bq/) and the associated bacterial growth rates are expected to be useful for (a) deducing microbial association patterns, (b) diet-based inference of personalised gut profiles, and (c) as a steppingstone for studying multi-species metabolic interactions.
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Chen F, Luo Y, Li C, Wang J, Chen L, Zhong X, Zhang B, Zhu Q, Zou R, Guo X, Zhou Y, Guo L. Sub-chronic low-dose arsenic in rice exposure induces gut microbiome perturbations in mice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 227:112934. [PMID: 34755630 DOI: 10.1016/j.ecoenv.2021.112934] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 10/14/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
Long-term consumption of arsenic-contaminated rice has become a public health issue that urgently needs to be addressed. In this study, mice were exposed to arsenic in rice (low dose, 0.91 mg/kg; medium dose, 9.1 mg/kg) for 30 days and 60 days, respectively, and the effects on pathological structures of spleen and skin, as well as the structure of the fecal microbiome were examined. The findings revealed dose/time cumulative effects on pathological changes, with even a low dose exposure for 30 days causing destruction of splenic follicular structure and thickening of dermal keratinized and epidermal layers. The Firmicutes/Bacteroidetes ratio in the community and the positive/negative ratio in network links were higher in arsenic groups, suggesting that arsenic resulted in a less healthy and unstable microbiome for the host. Thus lifetime consumption of arsenic in rice may have potential health effects on humans and must be carefully assessed to safeguard human health. Furthermore, in arsenic groups, arsenic-resistant bacteria or arsenic hazards remediation bacteria changed to be the dominant bacteria and acted as the core bacteria in the network modules. Some microbial arsenic transforming genes (arsC, arsR, arsA, ACR3, and aoxB) differed, indicating that the gut microbiome changed to withstand arsenic stress. Furthermore, Faecalibaculum, Lachnospiraceae_NK4A136_group, Angelakisella, Ruminiclostridium, and Desulfovibrionaceae are positively associated with arsenic dosage and may be useful in the early detection of arsenicals.
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Affiliation(s)
- Fubin Chen
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Yu Luo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Chengji Li
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Jiating Wang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China; Guangdong Provincial Key Laboratory of Food, Nutrition and Health; Department of Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China..
| | - Linkang Chen
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Xiaoting Zhong
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Bin Zhang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Qijiong Zhu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Rong Zou
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Xuming Guo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
| | - Yubin Zhou
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China; Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, and School of Pharmacy, Guangdong Medical University, Dongguan 523808, PR China.
| | - Lianxian Guo
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Guangdong 523808, China.
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Jayanama K, Theou O. Effects of Probiotics and Prebiotics on Frailty and Ageing: A Narrative Review. ACTA ACUST UNITED AC 2020; 15:183-192. [PMID: 31750806 DOI: 10.2174/1574884714666191120124548] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 02/08/2023]
Abstract
Globally, the population over the age of 60 is growing fast, but people age in different ways. Frailty, shown by the accumulation of age-related deficits, is a state of increased vulnerability to adverse outcomes among people of the same chronological age. Ageing results in a decline in diversity and homeostasis of microbiomes, and gut flora changes are related to health deficit accumulation and adverse health outcomes. In older people, health deficits including inappropriate intake, sarcopenia, physical inactivity, polypharmacy, and social vulnerability are factors associated with gut dysbiosis. The use of probiotics and prebiotics is a cost-effective and widely available intervention. Intake of probiotics and prebiotics may improve the homeostasis of gut microflora and prevent frailty and unhealthy aging. However, health effects vary among probiotics and prebiotics and among individual populations. This narrative review summarizes recent evidence about the relationship between prebiotic and probiotic consumption with health outcomes in older people.
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Affiliation(s)
- Kulapong Jayanama
- Physiotherapy and Medicine, Dalhousie University & Nova Scotia Health Authority, Halifax, Nova Scotia, Canada
| | - Olga Theou
- Physiotherapy and Medicine, Dalhousie University & Nova Scotia Health Authority, Halifax, Nova Scotia, Canada
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8
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Rodríguez C, Romero E, Garrido-Sanchez L, Alcaín-Martínez G, Andrade RJ, Taminiau B, Daube G, García-Fuentes E. MICROBIOTA INSIGHTS IN CLOSTRIDIUM DIFFICILE INFECTION AND INFLAMMATORY BOWEL DISEASE. Gut Microbes 2020; 12:1725220. [PMID: 32129694 PMCID: PMC7524151 DOI: 10.1080/19490976.2020.1725220] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) is characterized by chronic intestinal inflammation that includes Crohn´s disease (CD) and ulcerative colitis (UC). Although the etiology is still unknown, some specific factors have been directly related to IBD, including genetic factors, abnormal intestinal immunity, and/or gut microbiota modifications. Recent findings highlight the primary role of the gut microbiota closely associated with a persistent inappropriate inflammatory response. This gut environment of dysbiosis in a susceptible IBD host can increasingly worsen and lead to colonization and infection with some opportunistic pathogens, especially Clostridium difficile. C. difficile is an intestinal pathogen considered the main cause of antibiotic-associated diarrhea and colitis and an important complication of IBD, which can trigger or worsen an IBD flare. Recent findings have highlighted the loss of bacterial cooperation in the gut ecosystem, as well as the pronounced intestinal dysbiosis, in patients suffering from IBD and concomitant C. difficile infection (CDI). The results of intestinal microbiota studies are still limited and often difficult to compare because of the variety of disease conditions. However, these data provide important clues regarding the main modifications and interrelations in the complicated gut ecosystem to better understand both diseases and to take advantage of the development of new therapeutic strategies. In this review, we analyze in depth the gut microbiota changes associated with both forms of IBD and CDI and their similarity with the dysbiosis that occurs in CDI. We also discuss the metabolic pathways that favor the proliferation or decrease in several important taxa directly related to the disease.
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Affiliation(s)
- C. Rodríguez
- Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain,Unidad de Gestión Clínica de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, Málaga, Spain,CONTACT C. Rodríguez Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, SpainUnidad de Gestión Clínica de Aparato Digestivo, Hospital Universitario Virgen de la Vitoria, Málaga, Spain
| | - E. Romero
- Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain
| | - L. Garrido-Sanchez
- Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain,Unidad de Gestión Clínica de Endocrinología y Nutrición, Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - G. Alcaín-Martínez
- Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain,Unidad de Gestión Clínica de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, Málaga, Spain
| | - RJ. Andrade
- Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain,Unidad de Gestión Clínica de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, Málaga, Spain,Department of Medicine and Dermatology, Universidad de Málaga, Málaga, Spain,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Málaga, Spain
| | - B. Taminiau
- Fundamental and Applied Research for Animals & Health (FARAH), Department of Food Microbiology, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - G. Daube
- Fundamental and Applied Research for Animals & Health (FARAH), Department of Food Microbiology, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - E. García-Fuentes
- Instituto de Investigación Biomédica de Málaga-IBIMA, Málaga, Spain,Unidad de Gestión Clínica de Aparato Digestivo, Hospital Universitario Virgen de la Victoria, Málaga, Spain
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9
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Jing W, Liu Q, Wang W. Bifidobacterium bifidum
TMC3115 ameliorates milk protein allergy in by affecting gut microbiota: A randomized double‐blind control trial. J Food Biochem 2020; 44:e13489. [PMID: 32996156 DOI: 10.1111/jfbc.13489] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/06/2020] [Accepted: 08/30/2020] [Indexed: 12/11/2022]
Affiliation(s)
- Wei Jing
- Department of Pediatric Affiliated Hospital of Changchun University of Traditional Chinese Medicine Changchun China
| | - Qingbin Liu
- Department of Pediatric Affiliated Hospital of Changchun University of Traditional Chinese Medicine Changchun China
| | - Wei Wang
- Department of Pediatric Affiliated Hospital of Changchun University of Traditional Chinese Medicine Changchun China
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10
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The Potential Effects of Probiotics and ω-3 Fatty Acids on Chronic Low-Grade Inflammation. Nutrients 2020; 12:nu12082402. [PMID: 32796608 PMCID: PMC7468753 DOI: 10.3390/nu12082402] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/03/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic low-grade inflammation negatively impacts health and is associated with aging and obesity, among other health outcomes. A large number of immune mediators are present in the digestive tract and interact with gut bacteria to impact immune function. The gut microbiota itself is also an important initiator of inflammation, for example by releasing compounds such as lipopolysaccharides (LPS) that may influence cytokine production and immune cell function. Certain nutrients (e.g., probiotics, ω-3 fatty acids [FA]) may increase gut microbiota diversity and reduce inflammation. Lactobacilli and Bifidobacteria, among others, prevent gut hyperpermeability and lower LPS-dependent chronic low-grade inflammation. Furthermore, ω-3 FA generate positive effects on inflammation-related conditions (e.g., hypertriglyceridemia, diabetes) by interacting with immune, metabolic, and inflammatory pathways. Ω-3 FA also increase LPS-suppressing bacteria (i.e., Bifidobacteria) and decrease LPS-producing bacteria (i.e., Enterobacteria). Additionally, ω-3 FA appear to promote short-chain FA production. Therefore, combining probiotics with ω-3 FA presents a promising strategy to promote beneficial immune regulation via the gut microbiota, with potential beneficial effects on conditions of inflammatory origin, as commonly experienced by aged and obese individuals, as well as improvements in gut-brain-axis communication.
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11
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Wu S, Sun C, Li Y, Wang T, Jia L, Lai S, Yang Y, Luo P, Dai D, Yang YQ, Luo Q, Gao NL, Ning K, He LJ, Zhao XM, Chen WH. GMrepo: a database of curated and consistently annotated human gut metagenomes. Nucleic Acids Res 2020; 48:D545-D553. [PMID: 31504765 PMCID: PMC6943048 DOI: 10.1093/nar/gkz764] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/20/2019] [Accepted: 08/30/2019] [Indexed: 12/29/2022] Open
Abstract
GMrepo (data repository for Gut Microbiota) is a database of curated and consistently annotated human gut metagenomes. Its main purpose is to facilitate the reusability and accessibility of the rapidly growing human metagenomic data. This is achieved by consistently annotating the microbial contents of collected samples using state-of-art toolsets and by manual curation of the meta-data of the corresponding human hosts. GMrepo organizes the collected samples according to their associated phenotypes and includes all possible related meta-data such as age, sex, country, body-mass-index (BMI) and recent antibiotics usage. To make relevant information easier to access, GMrepo is equipped with a graphical query builder, enabling users to make customized, complex and biologically relevant queries. For example, to find (1) samples from healthy individuals of 18 to 25 years old with BMIs between 18.5 and 24.9, or (2) projects that are related to colorectal neoplasms, with each containing >100 samples and both patients and healthy controls. Precomputed species/genus relative abundances, prevalence within and across phenotypes, and pairwise co-occurrence information are all available at the website and accessible through programmable interfaces. So far, GMrepo contains 58 903 human gut samples/runs (including 17 618 metagenomes and 41 285 amplicons) from 253 projects concerning 92 phenotypes. GMrepo is freely available at: https://gmrepo.humangut.info.
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Affiliation(s)
- Sicheng Wu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China
| | - Yanze Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China
| | - Teng Wang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China
| | - Longhao Jia
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China
| | - Senying Lai
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China
| | - Yaling Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China.,Shenzhen Digital Life Institute, 518053 Shenzhen, Guangdong, China
| | - Pengyu Luo
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China
| | - Die Dai
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China
| | - Yong-Qing Yang
- Huazhong University of Science and Technology School of Physics, 430070 Wuhan, Hubei, China
| | - Qibin Luo
- Department of Genome Oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
| | - Na L Gao
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China.,Institute for Computer Science and Dept. of Biology, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China.,Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, 436044 Ezhou, Hubei, China
| | - Li-Jie He
- Department of Medical Oncology, People's Hospital of Liaoning Province, 110016 Shenyang, China
| | - Xing-Ming Zhao
- Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University, 200433 Shanghai, China.,Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, Ministry of Education, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 430074 Wuhan, Hubei, China.,Huazhong University of Science and Technology Ezhou Industrial Technology Research Institute, 436044 Ezhou, Hubei, China.,College of Life Science, HeNan Normal University, 453007 Xinxiang, Henan, China
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