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Xu T, Lyu L, Zheng J, Li L. Advances in omics-based biomarker discovery for biliary tract malignancy Diagnosis:A narrative review. Mol Cell Probes 2024; 76:101970. [PMID: 38964426 DOI: 10.1016/j.mcp.2024.101970] [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: 01/30/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Biliary tract neoplasms, which originate from the intrahepatic or extrahepatic biliary epithelium, are relatively rare but diagnostically challenging types of tumours, and their morbidity and mortality have increased in recent years. Due to ineffective early diagnostic methods, once detected, patients are in an advanced stage with a poor prognosis and few treatment options. With the development of omics technologies, the associations between microorganisms, bile acid and salts, noncoding RNAs and biliary tract malignancies have been gradually revealed, providing new methods for the discovery of diagnostic biomarkers. Here, we review the research advances in microbiomics, transcriptomics, metabolomics, and proteomics in the discovery of diagnostic biomarkers for biliary tract malignancies.
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Affiliation(s)
- Tao Xu
- Department of Gastroenterology, Beijing Jishuitan Hospital, Capital Medical University, Beijing, 102200, China.
| | - Lingna Lyu
- Department of Hepatology and Gastroenterology, Beijing Youan Hospital, Capital Medical University, Beijing, 100069, China.
| | - Junfu Zheng
- Department of Gastroenterology, Beijing Jishuitan Hospital, Capital Medical University, Beijing, 102200, China.
| | - Lei Li
- Department of Gastroenterology, Beijing Jishuitan Hospital, Capital Medical University, Beijing, 102200, China.
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2
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Chen X, Zou T, Zeng Q, Chen Y, Zhang C, Jiang S, Ding G. Metagenomic analysis reveals ecological and functional signatures of oral phageome associated with severe early childhood caries. J Dent 2024; 146:105059. [PMID: 38801939 DOI: 10.1016/j.jdent.2024.105059] [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: 12/15/2023] [Revised: 05/05/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024] Open
Abstract
OBJECTIVES Severe early childhood caries (S-ECC) is highly prevalent, affecting children's oral health. S-ECC development is closely associated with the complex oral microbial microbiome and its microorganism interactions, such as the imbalance of bacteriophages and bacteria. Till now, little is known about oral phageome on S-ECC. Therefore, this study aimed to investigate the potential role of the oral phageome in the pathogenesis of S-ECC. METHODS Unstimulated saliva (2 mL) was collected from 20 children with and without S-ECC for metagenomics analysis. Metagenomics sequencing and bioinformatic analysis were performed to determine the two groups' phageome diversity, taxonomic and functional annotations. Statistical analysis and visualization were performed with R and SPSS Statistics software. RESULTS 85.7 % of the extracted viral sequences were predicted from phages, in which most phages were classified into Myoviridae, Siphoviridae, and Podoviridae. Alpha diversity decreased, and Beta diversity increased in the S-ECC phageome compared to the healthy group. The abundance of Podoviridae phages increased, and the abundance of Inoviridae, Herelleviridae, and Streptococcus phages decreased in the S-ECC group. Functional annotation revealed increased annotation on glycoside hydrolases and nucleotide metabolism, decreased glycosyl transferases, carbohydrate-binding modules, and biogenic metabolism in the S-ECC phageome. CONCLUSIONS Metagenomic analysis revealed reduced Streptococcus phages and significant changes in functional annotations within the S-ECC phageome. These findings suggest a potential weakening of the regulatory influence of oral bacteria, which may indicate the development of innovative prevention and treatment strategies for S-ECC. These implications deserve further investigation and hold promise for advancing our understanding and management of S-ECC. CLINICAL SIGNIFICANCE The findings of this study indicate that oral phageomes are associated with bacterial genomes and metabolic processes, affecting the development of S-ECC. The reduced modulatory effect of the oral phageome in counteracting S-ECC's cariogenic activity suggests a new avenue for the prevention and treatment of S-ECC.
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Affiliation(s)
- Xin Chen
- Shenzhen Children's Hospital of China Medical University (CMU), Shenzhen, PR China; Department of Stomatology, Shenzhen Children's Hospital, Shenzhen, PR China
| | - Ting Zou
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, Guangdong, PR China
| | - Qinglu Zeng
- The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China
| | - Yubing Chen
- The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, PR China
| | - Chengfei Zhang
- Endodontology, Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, PR China
| | - Shan Jiang
- Shenzhen Stomatology Hospital (Pingshan), Southern Medical University, Shenzhen, Guangdong, PR China.
| | - Guicong Ding
- Shenzhen Children's Hospital of China Medical University (CMU), Shenzhen, PR China; Department of Stomatology, Shenzhen Children's Hospital, Shenzhen, PR China.
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Burgos-Molina AM, Téllez Santana T, Redondo M, Bravo Romero MJ. The Crucial Role of Inflammation and the Immune System in Colorectal Cancer Carcinogenesis: A Comprehensive Perspective. Int J Mol Sci 2024; 25:6188. [PMID: 38892375 PMCID: PMC11172443 DOI: 10.3390/ijms25116188] [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: 05/04/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Chronic inflammation drives the growth of colorectal cancer through the dysregulation of molecular pathways within the immune system. Infiltration of immune cells, such as macrophages, into tumoral regions results in the release of proinflammatory cytokines (IL-6; IL-17; TNF-α), fostering tumor proliferation, survival, and invasion. Tumors employ various mechanisms to evade immune surveillance, effectively 'cloaking' themselves from detection and subsequent attack. A comprehensive understanding of these intricate molecular interactions is paramount for advancing novel strategies aimed at modulating the immune response against cancer.
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Affiliation(s)
- Antonio Manuel Burgos-Molina
- Surgery, Biochemistry and Immunology Department, School of Medicine, University of Malaga, 29010 Málaga, Spain; (A.M.B.-M.); (T.T.S.); (M.J.B.R.)
| | - Teresa Téllez Santana
- Surgery, Biochemistry and Immunology Department, School of Medicine, University of Malaga, 29010 Málaga, Spain; (A.M.B.-M.); (T.T.S.); (M.J.B.R.)
- Research Network on Chronic Diseases, Primary Care, and Health Promotion (RICAPPS), Carlos III Health Institute (Instituto de Salud Carlos III), Av. de Monforte de Lemos, 5, 28029 Madrid, Spain
- Málaga Biomedical Research Institute (Instituto de Investigación Biomédica de Málaga, IBIMA), Calle Doctor Miguel Díaz Recio, 28, 29010 Málaga, Spain
| | - Maximino Redondo
- Surgery, Biochemistry and Immunology Department, School of Medicine, University of Malaga, 29010 Málaga, Spain; (A.M.B.-M.); (T.T.S.); (M.J.B.R.)
- Research Network on Chronic Diseases, Primary Care, and Health Promotion (RICAPPS), Carlos III Health Institute (Instituto de Salud Carlos III), Av. de Monforte de Lemos, 5, 28029 Madrid, Spain
- Málaga Biomedical Research Institute (Instituto de Investigación Biomédica de Málaga, IBIMA), Calle Doctor Miguel Díaz Recio, 28, 29010 Málaga, Spain
- Research Unit, Hospital Costa del Sol, Autovía A-7, km 187, 29603 Marbella, Spain
| | - María José Bravo Romero
- Surgery, Biochemistry and Immunology Department, School of Medicine, University of Malaga, 29010 Málaga, Spain; (A.M.B.-M.); (T.T.S.); (M.J.B.R.)
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Peres da Silva R, Suphavilai C, Nagarajan N. MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes. BMC Bioinformatics 2024; 25:153. [PMID: 38627615 PMCID: PMC11022314 DOI: 10.1186/s12859-024-05760-3] [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: 09/26/2022] [Accepted: 03/22/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND With the rapid increase in throughput of long-read sequencing technologies, recent studies have explored their potential for taxonomic classification by using alignment-based approaches to reduce the impact of higher sequencing error rates. While alignment-based methods are generally slower, k-mer-based taxonomic classifiers can overcome this limitation, potentially at the expense of lower sensitivity for strains and species that are not in the database. RESULTS We present MetageNN, a memory-efficient long-read taxonomic classifier that is robust to sequencing errors and missing genomes. MetageNN is a neural network model that uses short k-mer profiles of sequences to reduce the impact of distribution shifts on error-prone long reads. Benchmarking MetageNN against other machine learning approaches for taxonomic classification (GeNet) showed substantial improvements with long-read data (20% improvement in F1 score). By utilizing nanopore sequencing data, MetageNN exhibits improved sensitivity in situations where the reference database is incomplete. It surpasses the alignment-based MetaMaps and MEGAN-LR, as well as the k-mer-based Kraken2 tools, with improvements of 100%, 36%, and 23% respectively at the read-level analysis. Notably, at the community level, MetageNN consistently demonstrated higher sensitivities than the previously mentioned tools. Furthermore, MetageNN requires < 1/4th of the database storage used by Kraken2, MEGAN-LR and MMseqs2 and is > 7× faster than MetaMaps and GeNet and > 2× faster than MEGAN-LR and MMseqs2. CONCLUSION This proof of concept work demonstrates the utility of machine-learning-based methods for taxonomic classification using long reads. MetageNN can be used on sequences not classified by conventional methods and offers an alternative approach for memory-efficient classifiers that can be optimized further.
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Affiliation(s)
- Rafael Peres da Silva
- School of Computing, National University of Singapore, Singapore, 117417, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), Singapore, 138672, Republic of Singapore.
| | - Chayaporn Suphavilai
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), Singapore, 138672, Republic of Singapore
| | - Niranjan Nagarajan
- School of Computing, National University of Singapore, Singapore, 117417, Republic of Singapore.
- Agency for Science, Technology and Research (A*STAR), Genome Institute of Singapore (GIS), Singapore, 138672, Republic of Singapore.
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Republic of Singapore.
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Chen H, Huang S, Zhao Y, Sun R, Wang J, Yao S, Huang J, Yu Z. Metagenomic analysis of the intestinal microbiome reveals the potential mechanism involved in Bacillus amyloliquefaciens in treating schistosomiasis japonica in mice. Microbiol Spectr 2024; 12:e0373523. [PMID: 38441977 PMCID: PMC10986500 DOI: 10.1128/spectrum.03735-23] [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: 10/20/2023] [Accepted: 02/11/2024] [Indexed: 03/07/2024] Open
Abstract
Schistosomiasis japonica is one of the neglected tropical diseases characterized by chronic hepatic, intestinal granulomatous inflammation and fibrosis, as well as dysbiosis of intestinal microbiome. Previously, the probiotic Bacillus amyloliquefaciens has been shown to alleviate the pathological injuries in mice infected with Schistosoma japonicum by improving the disturbance of the intestinal microbiota. However, the underlying mechanisms involved in this process remain unclear. In this study, metagenomics sequencing and functional analysis were employed to investigate the differential changes in taxonomic composition and functional genes of the intestinal microbiome in S. japonicum-infected mice treated with B. amyloliquefaciens. The results revealed that intervention with B. amyloliquefaciens altered the taxonomic composition of the intestinal microbiota at the species level in infected mice and significantly increased the abundance of beneficial bacteria. Moreover, the abundance of predicted genes in the intestinal microbiome was also significantly changed, and the abundance of xfp/xpk and genes translated to urease was significantly restored. Further analysis showed that Limosilactobacillus reuteri was positively correlated with several KEGG Orthology (KO) genes and metabolic reactions, which might play important roles in alleviating the pathological symptoms caused by S. japonicum infection, indicating that it has the potential to function as another effective therapeutic agent for schistosomiasis. These data suggested that treatment of murine schistosomiasis japonica by B. amyloliquefaciens might be induced by alterations in the taxonomic composition and functional gene of the intestinal microbiome in mice. We hope this study will provide adjuvant strategies and methods for the early prevention and treatment of schistosomiasis japonica. IMPORTANCE Targeted interventions of probiotics on gut microbiome were used to explore the mechanism of alleviating schistosomiasis japonica. Through metagenomic analysis, there were significant changes in the composition of gut microbiota in mice infected with Schistosoma japonicum and significant increase in the abundance of beneficial bacteria after the intervention of Bacillus amyloliquefaciens. At the same time, the abundance of functional genes was found to change significantly. The abundance of genes related to urease metabolism and xfp/xpk related to D-erythrose 4-phosphate production was significantly restored, highlighting the importance of Limosilactobacillus reuteri in the recovery and abundance of predicted genes of the gut microbiome. These results indicated potential regulatory mechanism between the gene function of gut microbiome and host immune response. Our research lays the foundation for elucidating the regulatory mechanism of probiotic intervention in alleviating schistosomiasis japonica, and provides potential adjuvant treatment strategies for early prevention and treatment of schistosomiasis japonica.
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Affiliation(s)
- Hao Chen
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Shuaiqin Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Yiming Zhao
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Ruizheng Sun
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jingyan Wang
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Siqi Yao
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Zheng Yu
- Human Microbiome and Health Group, Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China
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Ankudavicius V, Nikitina D, Lukosevicius R, Tilinde D, Salteniene V, Poskiene L, Miliauskas S, Skieceviciene J, Zemaitis M, Kupcinskas J. Detailed Characterization of the Lung-Gut Microbiome Axis Reveals the Link between PD-L1 and the Microbiome in Non-Small-Cell Lung Cancer Patients. Int J Mol Sci 2024; 25:2323. [PMID: 38396998 PMCID: PMC10889071 DOI: 10.3390/ijms25042323] [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: 12/11/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Next-generation sequencing technologies have started a new era of respiratory tract research in recent years. Alterations in the respiratory microbiome between healthy and malignant conditions have been revealed. However, the composition of the microbiome varies among studies, even in similar medical conditions. Also, there is a lack of complete knowledge about lung-gut microbiome interactions in lung cancer patients. The aim of this study was to explore the lung-gut axis in non-small-cell lung cancer (NSCLC) patients and the associations between lung-gut axis microbiota and clinical parameters (CRP, NLR, LPS, CD8, and PD-L1). Lung tissue and fecal samples were used for bacterial 16S rRNA sequencing. The results revealed, for the first time, that the bacterial richness in lung tumor tissue gradually decreased with an increase in the level of PD-L1 expression (p < 0.05). An analysis of β-diversity indicated a significant positive correlation between the genera Romboutsia and Alistipes in both the lung tumor biopsies and stool samples from NSCLC patients (p < 0.05). Survival analysis showed that NSCLC patients with higher bacterial richness in their stool samples had prolonged overall survival (HR: 2.06, 95% CI: 1.025-4.17, p = 0.0426).
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Affiliation(s)
- Vytautas Ankudavicius
- Department of Pulmonology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Darja Nikitina
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Rokas Lukosevicius
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Deimante Tilinde
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Violeta Salteniene
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Lina Poskiene
- Department of Pathology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Skaidrius Miliauskas
- Department of Pulmonology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Marius Zemaitis
- Department of Pulmonology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
- Department of Gastroenterology, Lithuanian University of Health Sciences, LT-44307 Kaunas, Lithuania
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Mohamed AA, al-Ramadi BK, Fernandez-Cabezudo MJ. Interplay between Microbiota and γδ T Cells: Insights into Immune Homeostasis and Neuro-Immune Interactions. Int J Mol Sci 2024; 25:1747. [PMID: 38339023 PMCID: PMC10855551 DOI: 10.3390/ijms25031747] [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: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 02/12/2024] Open
Abstract
The gastrointestinal (GI) tract of multicellular organisms, especially mammals, harbors a symbiotic commensal microbiota with diverse microorganisms including bacteria, fungi, viruses, and other microbial and eukaryotic species. This microbiota exerts an important role on intestinal function and contributes to host health. The microbiota, while benefiting from a nourishing environment, is involved in the development, metabolism and immunity of the host, contributing to the maintenance of homeostasis in the GI tract. The immune system orchestrates the maintenance of key features of host-microbe symbiosis via a unique immunological network that populates the intestinal wall with different immune cell populations. Intestinal epithelium contains lymphocytes in the intraepithelial (IEL) space between the tight junctions and the basal membrane of the gut epithelium. IELs are mostly CD8+ T cells, with the great majority of them expressing the CD8αα homodimer, and the γδ T cell receptor (TCR) instead of the αβ TCR expressed on conventional T cells. γδ T cells play a significant role in immune surveillance and tissue maintenance. This review provides an overview of how the microbiota regulates γδ T cells and the influence of microbiota-derived metabolites on γδ T cell responses, highlighting their impact on immune homeostasis. It also discusses intestinal neuro-immune regulation and how γδ T cells possess the ability to interact with both the microbiota and brain.
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Affiliation(s)
- Alaa A. Mohamed
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
| | - Basel K. al-Ramadi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Maria J. Fernandez-Cabezudo
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain P.O. Box 15551, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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Peng W, He CX, Li RL, Qian D, Wang LY, Chen WW, Zhang Q, Wu CJ. Zanthoxylum bungeanum amides ameliorates nonalcoholic fatty liver via regulating gut microbiota and activating AMPK/Nrf2 signaling. JOURNAL OF ETHNOPHARMACOLOGY 2024; 318:116848. [PMID: 37423515 DOI: 10.1016/j.jep.2023.116848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/24/2023] [Accepted: 06/24/2023] [Indexed: 07/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Zanthoxylum bungeanum Maxim. (Rutaceae) is a known herbal medicine with various bioactivities, including anti-obesity, lipid-lowering, learning & memory improving and anti-diabetes, and amides in Z. bungeanum (AZB) are considered as the major active agents for its bioactivities. AIM OF THE STUDY This research was carried out to uncover the anti-NAFL effect of AZB and its corresponding molecular mechanisms. METHODS The central composite design-response surface methodology (CCD-RSM) was utilized to optimize the AZB extraction process, and the anti-NAFL effect of AZB was investigated on high fat diet (HFD) fed mice (HFD mice). The levels of ROS in liver tissues were determined using laser confocal microscopy with DCFH-DA probe staining, and anti-enzymes (such as HO-1, SOD, CAT & GSH-PX) and MDA in liver tissues were measured using commercial detecting kits. GC-MS was used to determine the short-chain fatty acids (SCFAs) contents in feces and blood of mice. 16S high-throughput sequencing, western blotting (WB) assay and immunofluorescence (IF) were used to explore the intestinal flora changes in mice and the potential mechanisms of AZB for treatment of NAFL. RESULTS Our results showed AZB reduced body weight, alleviated liver pathological changes, reduced fat accumulation, and improved oxidative stress in HFD mice. In addition, we also found AZB improved OGTT and ITT, reduced TG, TC, LDL-C, whereas increased HDL-C in HFD mice. AZB increased total number of the species and interspecies kinship of gut microbiota and reduced the richness and diversity of gut microbiota in HFD mice. Moreover, AZB decreased the ratio of Firmicutes/Bacteroidota, whereas increased the abundance of Allobaculum, Bacteroides and Dubosiella in feces of HFD-fed mice. Furthermore, AZB increased the production of SCFAs, and up-regulated the phosphorylation of AMPK and increased the nuclear transcription of Nrf2 in liver of HFD mice. CONCLUSION Collectively, our results suggested AZB can improve NAFL, which could reduce body weight, reverse liver lesions and fat accumulation, improve oxidative stress in liver tissues of HFD mice. Furthermore, the mechanisms are related to increase of the abundance of high-producing bacteria for SCFAs (e.g. Allobaculum, Bacteroides and Dubosiella) to activate AMPK/Nrf2 signaling.
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Affiliation(s)
- Wei Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Cheng-Xun He
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Ruo-Lan Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Die Qian
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Ling-Yu Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wen-Wen Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Qing Zhang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| | - Chun-Jie Wu
- Innovative Institute of Chinese Medicine and Pharmacy/Academy for Interdiscipline, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
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Cerk K, Ugalde‐Salas P, Nedjad CG, Lecomte M, Muller C, Sherman DJ, Hildebrand F, Labarthe S, Frioux C. Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing. Microb Biotechnol 2024; 17:e14396. [PMID: 38243750 PMCID: PMC10832553 DOI: 10.1111/1751-7915.14396] [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: 01/09/2023] [Revised: 11/27/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024] Open
Abstract
Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome-scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta-)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third-generation sequencing, and we discuss the opportunities of long-read sequencing, strain-level characterisation and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.
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Affiliation(s)
- Klara Cerk
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | | | - Chabname Ghassemi Nedjad
- Inria, University of Bordeaux, INRAETalenceFrance
- University of Bordeaux, CNRS, Bordeaux INP, LaBRI, UMR 5800TalenceFrance
| | - Maxime Lecomte
- Inria, University of Bordeaux, INRAETalenceFrance
- INRAE STLO¸University of RennesRennesFrance
| | | | | | - Falk Hildebrand
- Quadram Institute BioscienceNorwichUK
- Earlham InstituteNorwichUK
| | - Simon Labarthe
- Inria, University of Bordeaux, INRAETalenceFrance
- INRAE, University of Bordeaux, BIOGECO, UMR 1202CestasFrance
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10
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Yi X, Lu H, Liu X, He J, Li B, Wang Z, Zhao Y, Zhang X, Yu X. Unravelling the enigma of the human microbiome: Evolution and selection of sequencing technologies. Microb Biotechnol 2024; 17:e14364. [PMID: 37929823 PMCID: PMC10832515 DOI: 10.1111/1751-7915.14364] [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: 07/22/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023] Open
Abstract
The human microbiome plays a crucial role in maintaining health, with advances in high-throughput sequencing technology and reduced sequencing costs triggering a surge in microbiome research. Microbiome studies generally incorporate five key phases: design, sampling, sequencing, analysis, and reporting, with sequencing strategy being a crucial step offering numerous options. Present mainstream sequencing strategies include Amplicon sequencing, Metagenomic Next-Generation Sequencing (mNGS), and Targeted Next-Generation Sequencing (tNGS). Two innovative technologies recently emerged, namely MobiMicrobe high-throughput microbial single-cell genome sequencing technology and 2bRAD-M simplified metagenomic sequencing technology, compensate for the limitations of mainstream technologies, each boasting unique core strengths. This paper reviews the basic principles and processes of these three mainstream and two novel microbiological technologies, aiding readers in understanding the benefits and drawbacks of different technologies, thereby guiding the selection of the most suitable method for their research endeavours.
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Affiliation(s)
- Xin Yi
- Department of PharmacyShanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Hong Lu
- Department of Clinical laboratoryThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xiang Liu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Junyi He
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Bing Li
- Department of Public HealthShanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Zhelong Wang
- Department of PharmacyGuangdong Pharmaceutical UniversityGuangzhouPeople's Republic of China
| | - Yujing Zhao
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xinri Zhang
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
| | - Xiao Yu
- NHC Key Laboratory of Pneumoconiosis, Shanxi Key Laboratory of Respiratory Diseases, Department of Pulmonary and Critical Care MedicineThe First Hospital of Shanxi Medical UniversityTaiyuanPeople's Republic of China
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11
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Duffy EP, Bachtell RK, Ehringer MA. Opioid trail: Tracking contributions to opioid use disorder from host genetics to the gut microbiome. Neurosci Biobehav Rev 2024; 156:105487. [PMID: 38040073 PMCID: PMC10836641 DOI: 10.1016/j.neubiorev.2023.105487] [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: 08/29/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023]
Abstract
Opioid use disorder (OUD) is a worldwide public health crisis with few effective treatment options. Traditional genetics and neuroscience approaches have provided knowledge about biological mechanisms that contribute to OUD-related phenotypes, but the complexity and magnitude of effects in the brain and body remain poorly understood. The gut-brain axis has emerged as a promising target for future therapeutics for several psychiatric conditions, so characterizing the relationship between host genetics and the gut microbiome in the context of OUD will be essential for development of novel treatments. In this review, we describe evidence that interactions between host genetics, the gut microbiome, and immune signaling likely play a key role in mediating opioid-related phenotypes. Studies in humans and model organisms consistently demonstrated that genetic background is a major determinant of gut microbiome composition. Furthermore, the gut microbiome is susceptible to environmental influences such as opioid exposure. Additional work focused on gene by microbiome interactions will be necessary to gain improved understanding of their effects on OUD-related behaviors.
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Affiliation(s)
- Eamonn P Duffy
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA; Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA.
| | - Ryan K Bachtell
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA; Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Marissa A Ehringer
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA; Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
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12
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Li D, Zhong C, Yang M, He L, Chang H, Zhu N, Celniker SE, Threadgill DW, Snijders AM, Mao JH, Yuan Y. Genetic and microbial determinants of azoxymethane-induced colorectal tumor susceptibility in Collaborative Cross mice and their implication in human cancer. Gut Microbes 2024; 16:2341647. [PMID: 38659246 PMCID: PMC11057575 DOI: 10.1080/19490976.2024.2341647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
The insights into interactions between host genetics and gut microbiome (GM) in colorectal tumor susceptibility (CTS) remains lacking. We used Collaborative Cross mouse population model to identify genetic and microbial determinants of Azoxymethane-induced CTS. We identified 4417 CTS-associated single nucleotide polymorphisms (SNPs) containing 334 genes that were transcriptionally altered in human colorectal cancers (CRCs) and consistently clustered independent human CRC cohorts into two subgroups with different prognosis. We discovered a set of genera in early-life associated with CTS and defined a 16-genus signature that accurately predicted CTS, the majority of which were correlated with human CRCs. We identified 547 SNPs associated with abundances of these genera. Mediation analysis revealed GM as mediators partially exerting the effect of SNP UNC3869242 within Duox2 on CTS. Intestine cell-specific depletion of Duox2 altered GM composition and contribution of Duox2 depletion to CTS was significantly influenced by GM. Our findings provide potential novel targets for personalized CRC prevention and treatment.
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Affiliation(s)
- Dan Li
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, ZJ, China
| | - Chenhan Zhong
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mengyuan Yang
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
| | - Li He
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan, China
| | - Hang Chang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ning Zhu
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
| | - Susan E Celniker
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David W Threadgill
- Texas A&M Institute for Genome Sciences and Society, Texas A&M University, College Station, TX, USA
- Department of Molecular and Cellular Medicine and Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX, USA
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Berkeley Biomedical Data Science Center, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ying Yuan
- Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou, ZJ, China
- Zhejiang Provincial Clinical Research Center for CANCER, Hangzhou, ZJ, China
- Cancer Center, Zhejiang University, Hangzhou, ZJ, China
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13
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Hou T, Wang Q, Dai H, Hou Y, Zheng J, Wang T, Lin H, Wang S, Li M, Zhao Z, Chen Y, Xu Y, Lu J, Liu R, Ning G, Wang W, Xu M, Bi Y. Interactive Association Between Gut Microbiota and Thyroid Cancer. Endocrinology 2023; 165:bqad184. [PMID: 38051644 DOI: 10.1210/endocr/bqad184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 11/17/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023]
Abstract
CONTEXT The association between the gut microbiota and thyroid cancer remains controversial. OBJECTIVE We aimed to systematically investigate the interactive causal relationships between the abundance and metabolism pathways of gut microbiota and thyroid cancer. METHODS We leveraged genome-wide association studies for the abundance of 211 microbiota taxa from the MiBioGen study (N = 18 340), 205 microbiota metabolism pathways from the Dutch Microbiome Project (N = 7738), and thyroid cancer from the Global Biobank Meta-analysis Initiative (N cases = 6699 and N participants = 1 620 354). We performed a bidirectional Mendelian randomization (MR) to investigate the causality from microbiota taxa and metabolism pathways to thyroid cancer and vice versa. We performed a systematic review of previous observational studies and compared MR results with observational findings. RESULTS Eight taxa and 12 metabolism pathways had causal effects on thyroid cancer, where RuminococcaceaeUCG004 genus (P = .001), Streptococcaceae family (P = .016), Olsenella genus (P = .029), ketogluconate metabolism pathway (P = .003), pentose phosphate pathway (P = .016), and L-arginine degradation II in the AST pathway (P = .0007) were supported by sensitivity analyses. Conversely, thyroid cancer had causal effects on 3 taxa and 2 metabolism pathways, where the Holdemanella genus (P = .015) was supported by sensitivity analyses. The Proteobacteria phylum, Streptococcaceae family, Ruminococcus2 genus, and Holdemanella genus were significantly associated with thyroid cancer in both the systematic review and MR, whereas the other 121 significant taxa in observational results were not supported by MR. DISCUSSIONS These findings implicated the potential role of host-microbiota crosstalk in thyroid cancer, while the discrepancy among observational studies calls for further investigations.
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Affiliation(s)
- Tianzhichao Hou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Qi Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Huajie Dai
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yanan Hou
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jie Zheng
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Tiange Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Hong Lin
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Shuangyuan Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mian Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhiyun Zhao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yuhong Chen
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jieli Lu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ruixin Liu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Weiqing Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Min Xu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yufang Bi
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
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14
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Xiong Q, Yang J, Ni S. Microbiome-Mediated Protection against Pathogens in Woody Plants. Int J Mol Sci 2023; 24:16118. [PMID: 38003306 PMCID: PMC10671361 DOI: 10.3390/ijms242216118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.
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Affiliation(s)
- Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (J.Y.); (S.N.)
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15
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Huttenhower C, Finn RD, McHardy AC. Challenges and opportunities in sharing microbiome data and analyses. Nat Microbiol 2023; 8:1960-1970. [PMID: 37783751 DOI: 10.1038/s41564-023-01484-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 08/28/2023] [Indexed: 10/04/2023]
Abstract
Microbiome data, metadata and analytical workflows have become 'big' in terms of volume and complexity. Although the infrastructure and technologies to share data have been established, the interdisciplinary and multi-omic nature of the field can make resources difficult to identify and use. Following best practices for data deposition requires substantial effort, with sometimes little obvious reward. Gaps remain where microbiome-specific resources for data sharing or reproducibility do not yet exist. We outline available best practices, challenges to their adoption and opportunities in data sharing in microbiome research. We showcase examples of best practices and advocate for their enforcement and incentivization for data sharing. This includes recognition of data curation and sharing endeavours by individuals, institutions, journals and funders. Opportunities for progress include enabling microbiome-specific databases to incorporate future methods for data analysis, integration and reuse.
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Affiliation(s)
- Curtis Huttenhower
- Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Departments of Biostatistics and Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alice Carolyn McHardy
- Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany.
- Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.
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16
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Yang P, Yang J, Long H, Huang K, Ji L, Lin H, Jiang X, Wang AK, Tian G, Ning K. MicroEXPERT: Microbiome profiling platform with cross-study metagenome-wide association analysis functionality. IMETA 2023; 2:e131. [PMID: 38868224 PMCID: PMC10989818 DOI: 10.1002/imt2.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/06/2023] [Accepted: 07/10/2023] [Indexed: 06/14/2024]
Abstract
The framework of the MicroEXPERT platform. Our Platform was composed of five modules. Data management module: Users upload raw data and metadata to the system using a guided workflow. Data processing module: Uploaded data is processed to generate taxonomical distribution and functional composition results. Metagenome-wide association studies module (MWAS): Various methods, including biomarker analysis, PCA, co-occurrence networks, and sample classification, are employed using metadata. Data search module: Users can query nucleotide sequences to retrieve information in the MicroEXPERT database. Data visualization module: Visualization tools are used to illustrate the metagenome analysis results.
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Affiliation(s)
- Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center of AI Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanHubeiChina
- Institute of Medical GenomicsBiomedical Sciences College, Shandong First Medical UniversityJinanShandongChina
| | - Jialiang Yang
- Department of SciencesGeneis Beijing Co., Ltd.BeijingChina
- Department of SciencesQingdao Geneis Institute of Big Data Mining and Precision MedicineQingdaoChina
- Department of SciencesAcademician Workstation, Changsha Medical UniversityChangshaChina
| | - Haixia Long
- Department of Information Science TechnologyHainan Normal UniversityHaikouChina
| | - Kaimei Huang
- Department of MathematicsZhejiang Normal UniversityJinhuaChina
| | - Lei Ji
- Department of SciencesGeneis Beijing Co., Ltd.BeijingChina
- Department of SciencesQingdao Geneis Institute of Big Data Mining and Precision MedicineQingdaoChina
| | - Hanyang Lin
- Department of SciencesSequenxe Biological Technology Co., Ltd.XiamenChina
| | - Xiuli Jiang
- Department of SciencesSequenxe Biological Technology Co., Ltd.XiamenChina
| | | | - Geng Tian
- Department of SciencesGeneis Beijing Co., Ltd.BeijingChina
- Department of SciencesQingdao Geneis Institute of Big Data Mining and Precision MedicineQingdaoChina
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular‐imaging, Center of AI Biology, Department of Bioinformatics and Systems BiologyCollege of Life Science and Technology, Huazhong University of Science and TechnologyWuhanHubeiChina
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17
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Zahavi L, Lavon A, Reicher L, Shoer S, Godneva A, Leviatan S, Rein M, Weissbrod O, Weinberger A, Segal E. Bacterial SNPs in the human gut microbiome associate with host BMI. Nat Med 2023; 29:2785-2792. [PMID: 37919437 PMCID: PMC10999242 DOI: 10.1038/s41591-023-02599-8] [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: 06/26/2022] [Accepted: 09/19/2023] [Indexed: 11/04/2023]
Abstract
Genome-wide association studies (GWASs) have provided numerous associations between human single-nucleotide polymorphisms (SNPs) and health traits. Likewise, metagenome-wide association studies (MWASs) between bacterial SNPs and human traits can suggest mechanistic links, but very few such studies have been done thus far. In this study, we devised an MWAS framework to detect SNPs and associate them with host phenotypes systematically. We recruited and obtained gut metagenomic samples from a cohort of 7,190 healthy individuals and discovered 1,358 statistically significant associations between a bacterial SNP and host body mass index (BMI), from which we distilled 40 independent associations. Most of these associations were unexplained by diet, medications or physical exercise, and 17 replicated in a geographically independent cohort. We uncovered BMI-associated SNPs in 27 bacterial species, and 12 of them showed no association by standard relative abundance analysis. We revealed a BMI association of an SNP in a potentially inflammatory pathway of Bilophila wadsworthia as well as of a group of SNPs in a region coding for energy metabolism functions in a Faecalibacterium prausnitzii genome. Our results demonstrate the importance of considering nucleotide-level diversity in microbiome studies and pave the way toward improved understanding of interpersonal microbiome differences and their potential health implications.
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Affiliation(s)
- Liron Zahavi
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Amit Lavon
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Lee Reicher
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Lis Maternity and Women's Hospital, Tel Aviv Sourasky Medical Center, Tel Aviv University (affiliated with Sackler Faculty of Medicine), Tel Aviv, Israel
| | - Saar Shoer
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Anastasia Godneva
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Sigal Leviatan
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Michal Rein
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Adina Weinberger
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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18
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Meng D, Ai S, Spanos M, Shi X, Li G, Cretoiu D, Zhou Q, Xiao J. Exercise and microbiome: From big data to therapy. Comput Struct Biotechnol J 2023; 21:5434-5445. [PMID: 38022690 PMCID: PMC10665598 DOI: 10.1016/j.csbj.2023.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Exercise is a vital component in maintaining optimal health and serves as a prospective therapeutic intervention for various diseases. The human microbiome, comprised of trillions of microorganisms, plays a crucial role in overall health. Given the advancements in microbiome research, substantial databases have been created to decipher the functionality and mechanisms of the microbiome in health and disease contexts. This review presents an initial overview of microbiomics development and related databases, followed by an in-depth description of the multi-omics technologies for microbiome. It subsequently synthesizes the research pertaining to exercise-induced modifications of the microbiome and diseases that impact the microbiome. Finally, it highlights the potential therapeutic implications of an exercise-modulated microbiome in intestinal disease, obesity and diabetes, cardiovascular disease, and immune/inflammation-related diseases.
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Affiliation(s)
- Danni Meng
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Songwei Ai
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Michail Spanos
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Xiaohui Shi
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Guoping Li
- Cardiovascular Division of the Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Dragos Cretoiu
- Department of Medical Genetics, Carol Davila University of Medicine and Pharmacy, Bucharest 020031, Romania
- Materno-Fetal Assistance Excellence Unit, Alessandrescu-Rusescu National Institute for Mother and Child Health, Bucharest 011062, Romania
| | - Qiulian Zhou
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
| | - Junjie Xiao
- Institute of Geriatrics (Shanghai University), Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), School of Medicine, Shanghai University, Nantong 226011, China
- Cardiac Regeneration and Ageing Lab, Institute of Cardiovascular Sciences, Shanghai Engineering Research Center of Organ Repair, School of Life Science, Shanghai University, Shanghai 200444, China
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19
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Nguyen PN, Rehan SM. Environmental Effects on Bee Microbiota. MICROBIAL ECOLOGY 2023; 86:1487-1498. [PMID: 37099156 DOI: 10.1007/s00248-023-02226-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/19/2023] [Indexed: 06/19/2023]
Abstract
Anthropogenic activities and increased land use, which include industrialization, agriculture and urbanization, directly affect pollinators by changing habitats and floral availability, and indirectly by influencing their microbial composition and diversity. Bees form vital symbioses with their microbiota, relying on microorganisms to perform physiological functions and aid in immunity. As altered environments and climate threaten bees and their microbiota, characterizing the microbiome and its complex relationships with its host offers insights into understanding bee health. This review summarizes the role of sociality in microbiota establishment, as well as examines if such factors result in increased susceptibility to altered microbiota due to environmental changes. We characterize the role of geographic distribution, temperature, precipitation, floral resources, agriculture, and urbanization on bee microbiota. Bee microbiota are affected by altered surroundings regardless of sociality. Solitary bees that predominantly acquire their microbiota through the environment are particularly sensitive to such effects. However, the microbiota of obligately eusocial bees are also impacted by environmental changes despite typically well conserved and socially inherited microbiota. We provide an overview of the role of microbiota in plant-pollinator relationships and how bee microbiota play a larger role in urban ecology, offering microbial connections between animals, humans, and the environment. Understanding bee microbiota presents opportunities for sustainable land use restoration and aiding in wildlife conservation.
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Affiliation(s)
| | - Sandra M Rehan
- Department of Biology, York University, Toronto, Canada.
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20
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He G, Chen T, Huang L, Zhang Y, Feng Y, Liu Q, Yin X, Qu S, Yang C, Wan J, Liang L, Yan J, Liu W. Tibetan tea reduces obesity brought on by a high-fat diet and modulates gut flora in mice. Food Sci Nutr 2023; 11:6582-6595. [PMID: 37823111 PMCID: PMC10563754 DOI: 10.1002/fsn3.3607] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/15/2023] [Accepted: 07/18/2023] [Indexed: 10/13/2023] Open
Abstract
It has been shown that Tibetan tea (TT) inhibits obesity and controls lipid metabolism. The fundamental processes by which TT prevents obesity are yet entirely unknown. Consequently, this research aimed to ascertain if TT may prevent obesity by modifying the gut flora. Our research demonstrated that TT prevented mice from gaining weight and accumulating fat due to the high-fat diet (HFD), decreased levels of blood total cholesterol (TC), triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C), and raised levels of high-density lipoprotein cholesterol (HDL-C). Adipogenesis-related genes such as acetyl-Coenzyme A carboxylase 1 (ACC1, LOC107476), fatty acid synthase (Fas, LOC14104), sterol regulatory element-binding protein-1c (SREBP-1c, LOC20787), CCAAT/enhancer-binding protein α (C/EBPα, LOC12606), stearoyl-CoA desaturase 1 (SCD1, LOC20249), and peroxisome proliferator-activated receptor γ (PPARγ, LOC19016) had their expression downregulated by lowering the Firmicutes/Bacteroidetes (F/B) ratio and controlling the number of certain gut bacteria. TT also alleviated HFD-induced abnormalities of the gut microbiota. The Muribaculaceae, Lachnospiraceae NK4A136_group, Alistipes, and Odoribacter families were identified as the major beneficial gut microorganisms using Spearman's correlation analysis. Fecal microbiota transplantation (FMT) demonstrated that TT's anti-obesity and gut microbiota-modulating benefits might be transmitted to mice on an HFD, demonstrating that one of TT's targets for preventing obesity is the gut microbiota. TT also increased the amount of short-chain fatty acids (SCFAs) in the feces, including acetic, propionic, and butyric acids. These results indicate the possible development of TT as a prebiotic to combat obesity and associated disorders. These results suggest that TT may act as a prebiotic against obesity and its associated diseases.
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Affiliation(s)
- Gang He
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
| | - Tangcong Chen
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
| | - Lifen Huang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
| | - Yiyuan Zhang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
| | - Yanjiao Feng
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
| | - Qijun Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
| | - Xiaojing Yin
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
| | - Shaokui Qu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
| | - Chen Yang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
| | - Jianghong Wan
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
- Sichuan Jiang's Tibetan Tea Co., LTDYa'anChina
| | - Li Liang
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
| | - Jun Yan
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
| | - Wei Liu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education DepartmentSichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu UniversityChengduChina
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21
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Li Y, Xu J, Hong Y, Li Z, Xing X, Zhufeng Y, Lu D, Liu X, He J, Li Y, Sun X. Metagenome-wide association study of gut microbiome features for myositis. Clin Immunol 2023; 255:109738. [PMID: 37595937 DOI: 10.1016/j.clim.2023.109738] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/20/2023]
Abstract
PURPOSE The clinical relevance and pathogenic role of gut microbiome in both myositis and its associated interstitial lung disease (ILD) are still unclear. The purpose of this study was to investigate the role of gut microbiome in myositis through comprehensive metagenomic-wide association studies (MWAS). METHODS We conducted MWAS of the myositis gut microbiome in a Chinese cohort by using whole-genome shotgun sequencing of high depth, including 30 myositis patients and 31 healthy controls (HC). Among the myositis patients, 11 developed rapidly progressive interstitial lung disease (RP-ILD) and 10 had chronic ILD (C-ILD). RESULTS Analysis for overall distribution level of the bacteria showed Alistipes onderdonkii, Parabacteroides distasonis and Escherichia coli were upregulated, Lachnospiraceae bacterium GAM79, Roseburia intestinalis, and Akkermansia muciniphila were downregulated in patients with myositis compared to HC. Bacteroides thetaiotaomicron, Parabacteroides distasonis and Escherichia coli were upregulated, Bacteroides A1C1 and Bacteroides xylanisolvens were downregulated in RP-ILD cases compared with C-ILD cases. A variety of biological pathways related to metabolism were enriched in the myositis and HC, RP-ILD and C-ILD comparison. And in the analyses for microbial contribution in metagenomic biological pathways, we have found that E. coli played an important role in the pathway expression in both myositis group and myositis-associated RP-ILD group. Anti-PL-12 antibody, anti-Ro-52 antibody, and anti-EJ antibody were found to have positive correlation with bacterial diversity (Shannon-wiener diversity index and Chao1, richness estimator) between myositis group and control groups. The combination of E. coli and R. intestinalis could distinguish myositis group from HC effectively. R. intestinalis can also be applied in the distinguishment of RP-ILD group vs. C-ILD group in myositis patients. CONCLUSION Our MWAS study first revealed the link between gut microbiome and pathgenesis of myositis, which may help us understand the role of gut microbiome in the etiology of myositis and myositis-associated RP-ILD.
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Affiliation(s)
- Yimin Li
- Department of Rheumatology & Immunology, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Peking University People's Hospital, Beijing, China; Department of Rheumatology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Xu
- Department of Gastroenterology, Clinical Center of Immune-Mediated Digestive Diseases, Institute of Clinical Molecular Biology & Central Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Yixiang Hong
- Department of Rheumatology & Immunology, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Peking University People's Hospital, Beijing, China
| | - Zijun Li
- Department of Rheumatology & Immunology, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Peking University People's Hospital, Beijing, China
| | - Xiaoyan Xing
- Department of Rheumatology & Immunology, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Peking University People's Hospital, Beijing, China
| | - Yunzhi Zhufeng
- Department of Rheumatology & Immunology, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Peking University People's Hospital, Beijing, China
| | - Dan Lu
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xu Liu
- Department of Rheumatology & Immunology, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Peking University People's Hospital, Beijing, China
| | - Jing He
- Department of Rheumatology & Immunology, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Peking University People's Hospital, Beijing, China
| | - Yuhui Li
- Department of Rheumatology & Immunology, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Peking University People's Hospital, Beijing, China.
| | - Xiaolin Sun
- Department of Rheumatology & Immunology, Beijing Key Laboratory for Rheumatism Mechanism and Immune Diagnosis (BZ0135), Peking University People's Hospital, Beijing, China.
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22
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Huang H, Cheng S, Yang X, Liu L, Cheng B, Meng P, Pan C, Wen Y, Jia Y, Liu H, Zhang F. Dissecting the Association between Gut Microbiota and Brain Structure Change Rate: A Two-Sample Bidirectional Mendelian Randomization Study. Nutrients 2023; 15:4227. [PMID: 37836511 PMCID: PMC10574136 DOI: 10.3390/nu15194227] [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: 08/30/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
The connection between the gut microbiota and brain structure changes is still unclear. We conducted a Mendelian randomization (MR) study to examine the bidirectional causality between the gut microbiota (211 taxa, including 131 genera, 35 families, 20 orders, 16 classes and 9 phyla; N = 18,340 individuals) and age-independent/dependent longitudinal changes in brain structure across the lifespan (N = 15,640 individuals aged 4~99 years). We identified causal associations between the gut microbiota and age-independent/dependent longitudinal changes in brain structure, such as family Peptostreptococcaceae with age-independent longitudinal changes of cortical gray matter (GM) volume and genus Faecalibacterium with age-independent average cortical thickness and cortical GM volume. Taking age-independent longitudinal changes in brain structure across the lifespan as exposures, there were causal relationships between the surface area and genus Lachnospiraceae. Our findings may serve as fundamentals for further research on the genetic mechanisms and biological treatment of complex traits and diseases associated with the gut microbiota and the brain structure change rate.
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Affiliation(s)
- Huimei Huang
- Department of Nephrology, Xi’an Children’s Hospital, The Affiliated Children’s Hospital of Xi’an Jiaotong University, Xi’an 710003, China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (S.C.); (X.Y.); (L.L.); (B.C.); (P.M.); (C.P.); (Y.W.); (Y.J.); (H.L.)
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (S.C.); (X.Y.); (L.L.); (B.C.); (P.M.); (C.P.); (Y.W.); (Y.J.); (H.L.)
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (S.C.); (X.Y.); (L.L.); (B.C.); (P.M.); (C.P.); (Y.W.); (Y.J.); (H.L.)
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (S.C.); (X.Y.); (L.L.); (B.C.); (P.M.); (C.P.); (Y.W.); (Y.J.); (H.L.)
| | - Peilin Meng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (S.C.); (X.Y.); (L.L.); (B.C.); (P.M.); (C.P.); (Y.W.); (Y.J.); (H.L.)
| | - Chuyu Pan
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (S.C.); (X.Y.); (L.L.); (B.C.); (P.M.); (C.P.); (Y.W.); (Y.J.); (H.L.)
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (S.C.); (X.Y.); (L.L.); (B.C.); (P.M.); (C.P.); (Y.W.); (Y.J.); (H.L.)
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (S.C.); (X.Y.); (L.L.); (B.C.); (P.M.); (C.P.); (Y.W.); (Y.J.); (H.L.)
| | - Huan Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (S.C.); (X.Y.); (L.L.); (B.C.); (P.M.); (C.P.); (Y.W.); (Y.J.); (H.L.)
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi’an Jiaotong University, Xi’an 710061, China; (S.C.); (X.Y.); (L.L.); (B.C.); (P.M.); (C.P.); (Y.W.); (Y.J.); (H.L.)
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23
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Sun Z, Liu J, Zhang M, Wang T, Huang S, Weiss ST, Liu YY. Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites. Nat Commun 2023; 14:5321. [PMID: 37658057 PMCID: PMC10474111 DOI: 10.1038/s41467-023-41099-8] [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: 05/29/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023] Open
Abstract
Accurate species identification and abundance estimation are critical for the interpretation of whole metagenome sequencing (WMS) data. Yet, existing metagenomic profilers suffer from false-positive identifications, which can account for more than 90% of total identified species. Here, by leveraging species-specific Type IIB restriction endonuclease digestion sites as reference instead of universal markers or whole microbial genomes, we present a metagenomic profiler, MAP2B (MetAgenomic Profiler based on type IIB restriction sites), to resolve those issues. We first illustrate the pitfalls of using relative abundance as the only feature in determining false positives. We then propose a feature set to distinguish false positives from true positives, and using simulated metagenomes from CAMI2, we establish a false-positive recognition model. By benchmarking the performance in metagenomic profiling using a simulation dataset with varying sequencing depth and species richness, we illustrate the superior performance of MAP2B over existing metagenomic profilers in species identification. We further test the performance of MAP2B using real WMS data from an ATCC mock community, confirming its superior precision against sequencing depth. Finally, by leveraging WMS data from an IBD cohort, we demonstrate the taxonomic features generated by MAP2B can better discriminate IBD and predict metabolomic profiles.
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Affiliation(s)
- Zheng Sun
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jiang Liu
- Qingdao OE Biotechnology Company Limited, Qingdao, Shandong, China
| | - Meng Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
| | - Tong Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
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24
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Peng W, Qiao H, Mo L, Guo Y. Progress in the diagnosis of lymph node metastasis in rectal cancer: a review. Front Oncol 2023; 13:1167289. [PMID: 37519802 PMCID: PMC10374255 DOI: 10.3389/fonc.2023.1167289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Historically, the chief focus of lymph node metastasis research has been molecular and clinical studies of a few essential pathways and genes. Recent years have seen a rapid accumulation of massive omics and imaging data catalyzed by the rapid development of advanced technologies. This rapid increase in data has driven improvements in the accuracy of diagnosis of lymph node metastasis, and its analysis further demands new methods and the opportunity to provide novel insights for basic research. In fact, the combination of omics data, imaging data, clinical medicine, and diagnostic methods has led to notable advances in our basic understanding and transformation of lymph node metastases in rectal cancer. Higher levels of integration will require a concerted effort among data scientists and clinicians. Herein, we review the current state and future challenges to advance the diagnosis of lymph node metastases in rectal cancer.
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Affiliation(s)
- Wei Peng
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- School of Public Health and Health Management, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Huimin Qiao
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- School of Public Health and Health Management, Gannan Medical University, Ganzhou, Jiangxi, China
| | - Linfeng Mo
- School of Health and Medicine, Guangzhou Huashang Vocational College, Guangzhou, Guangdong, China
| | - You Guo
- Medical Big Data and Bioinformatics Research Centre, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
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25
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Tian C, Li J, Bao Y, Gao L, Song L, Li K, Sun M. Ursolic acid ameliorates obesity of mice fed with high-fat diet via alteration of gut microbiota and amino acid metabolism. Front Microbiol 2023; 14:1183598. [PMID: 37485499 PMCID: PMC10359042 DOI: 10.3389/fmicb.2023.1183598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023] Open
Abstract
Obesity has been regarded as one of the major health problems worldwide. Studies demonstrated that ursolic acid (UA) can significantly ameliorate the progress of obesity. However, whether the effect of UA on obesity depends on the regulation of gut microbiota and metabolism is uncertain. To investigate the regulatory role of UA in obese mice from the perspective of intestinal microbiome and metabolomics analyses, an obese mice model was established with a high-fat diet, and the effect of UA on obesity was evaluated. The alterations of gut microbiota and metabolism related to obesity were evaluated by bioinformatic analysis. The results of the gut microbiota analysis showed that UA intervention could shift the Firmicutes to Bacteroidetes ratio at the phylum level and increase in the genera of Lactobacillus, Bacteroides, and Akkermansia. Additionally, metabolomics analysis showed that the beneficial influence of UA on obesity partly depended on amino acid metabolism. The current study demonstrated the roles of UA in the anti-obesity process, which depends in part on alterations in the gut microbiota and metabolism. Therefore, our findings highlight the potential therapeutic effect of UA on the improvement of diet-induced obesity in humans.
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Affiliation(s)
- Chunfeng Tian
- School of Public Health, Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, China
| | - Jie Li
- School of Public Health, Jiamusi University, Jiamusi, China
| | - Yan Bao
- School of Public Health, Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, China
- Institute of Nutrition and Food Health, Baotou Medical College, Baotou, China
| | - Long Gao
- School of Public Health, Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, China
| | - Lixin Song
- Baotou Disease Prevention Control Center, Baotou, China
| | - Kai Li
- School of Public Health, Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, China
| | - Ming Sun
- School of Public Health, Baotou Medical College, Inner Mongolia University of Science and Technology, Baotou, China
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26
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Guiducci L, Nicolini G, Forini F. Dietary Patterns, Gut Microbiota Remodeling, and Cardiometabolic Disease. Metabolites 2023; 13:760. [PMID: 37367916 DOI: 10.3390/metabo13060760] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/28/2023] Open
Abstract
The cardiovascular and metabolic disorders, collectively known as cardiometabolic disease (CMD), are high morbidity and mortality pathologies associated with lower quality of life and increasing health-care costs. The influence of the gut microbiota (GM) in dictating the interpersonal variability in CMD susceptibility, progression and treatment response is beginning to be deciphered, as is the mutualistic relation established between the GM and diet. In particular, dietary factors emerge as pivotal determinants shaping the architecture and function of resident microorganisms in the human gut. In turn, intestinal microbes influence the absorption, metabolism, and storage of ingested nutrients, with potentially profound effects on host physiology. Herein, we present an updated overview on major effects of dietary components on the GM, highlighting the beneficial and detrimental consequences of diet-microbiota crosstalk in the setting of CMD. We also discuss the promises and challenges of integrating microbiome data in dietary planning aimed at restraining CMD onset and progression with a more personalized nutritional approach.
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Affiliation(s)
- Letizia Guiducci
- CNR Institute of Clinical Physiology, Via Moruzzi 1, 56124 Pisa, Italy
| | | | - Francesca Forini
- CNR Institute of Clinical Physiology, Via Moruzzi 1, 56124 Pisa, Italy
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27
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Olek K, Kuczaj AA, Warwas S, Hrapkowicz T, Przybyłowski P, Tanasiewicz M. Gut Microbiome in Patients after Heart Transplantation-Current State of Knowledge. Biomedicines 2023; 11:1588. [PMID: 37371683 DOI: 10.3390/biomedicines11061588] [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: 03/31/2023] [Revised: 05/13/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
The human gut microbiota include over 10 trillion microorganisms, such as bacteria, fungi, viruses, archaea, and protozoa. Many reports indicate the strong correlation between dysbiosis and the severity of cardiovascular diseases. Microbiota seem to interact with the host's alloimmunity and may have an immunomodulatory role in graft rejection processes. In our study, we present the current state of the knowledge of microbiota in heart transplant recipients. We present up-to-date microbiota diagnostic methods, interactions between microbiota and immunosuppressive drugs, the immunomodulatory effects of dysbiosis, and the available strategies (experimental and clinical strategies) to modulate host microbiota.
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Affiliation(s)
- Katarzyna Olek
- Department of Dental Propedeutics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-800 Zabrze, Poland
| | - Agnieszka Anna Kuczaj
- Department of Cardiac Surgery, Transplantology, Vascular and Endovascular Surgery, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, M.C. Sklodowskiej 9, 41-800 Zabrze, Poland
| | - Szymon Warwas
- Students' Scientific Association Affiliated with the Department of Cardiac, Vascular and Endovascular Surgery and Transplantology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-808 Zabrze, Poland
| | - Tomasz Hrapkowicz
- Department of Cardiac Surgery, Transplantology, Vascular and Endovascular Surgery, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, M.C. Sklodowskiej 9, 41-800 Zabrze, Poland
| | - Piotr Przybyłowski
- Department of Cardiac Surgery, Transplantology, Vascular and Endovascular Surgery, Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, M.C. Sklodowskiej 9, 41-800 Zabrze, Poland
| | - Marta Tanasiewicz
- Department of Conservative Dentistry and Endodontics, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 41-800 Zabrze, Poland
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Lin Q, Guan SW, Yu HB. Immuno-oncology-microbiome axis of gastrointestinal malignancy. World J Gastrointest Oncol 2023; 15:757-775. [PMID: 37275452 PMCID: PMC10237027 DOI: 10.4251/wjgo.v15.i5.757] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/15/2023] [Accepted: 04/14/2023] [Indexed: 05/12/2023] Open
Abstract
Research on the relationship between the microbiome and cancer has been controversial for centuries. Recent works have discovered that the intratumor microbiome is an important component of the tumor microenvironment (TME). Intratumor bacteria, the most studied intratumor microbiome, are mainly localized in tumor cells and immune cells. As the largest bacterial reservoir in human body, the gut microbiome may be one of the sources of the intratumor microbiome in gastrointestinal malignancies. An increasing number of studies have shown that the gut and intratumor microbiome play an important role in regulating the immune tone of tumors. Moreover, it has been recently proposed that the gut and intratumor microbiome can influence tumor progression by modulating host metabolism and the immune and immune tone of the TME, which is defined as the immuno-oncology-microbiome (IOM) axis. The proposal of the IOM axis provides a new target for the tumor microbiome and tumor immunity. This review aims to reveal the mechanism and progress of the gut and intratumor microbiome in gastrointestinal malignancies such as esophageal cancer, gastric cancer, liver cancer, colorectal cancer and pancreatic cancer by exploring the IOM axis. Providing new insights into the research related to gastrointestinal malignancies.
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Affiliation(s)
- Quan Lin
- Department of Surgery, Wenzhou Central Hospital, The Dingli Clinical Institute of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China
| | - Shi-Wei Guan
- Department of Surgery, Wenzhou Central Hospital, The Dingli Clinical Institute of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China
| | - Hai-Bo Yu
- Department of Surgery, Wenzhou Central Hospital, The Dingli Clinical Institute of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China
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Tomofuji Y, Sonehara K, Kishikawa T, Maeda Y, Ogawa K, Kawabata S, Nii T, Okuno T, Oguro-Igashira E, Kinoshita M, Takagaki M, Yamamoto K, Kurakawa T, Yagita-Sakamaki M, Hosokawa A, Motooka D, Matsumoto Y, Matsuoka H, Yoshimura M, Ohshima S, Nakamura S, Inohara H, Kishima H, Mochizuki H, Takeda K, Kumanogoh A, Okada Y. Reconstruction of the personal information from human genome reads in gut metagenome sequencing data. Nat Microbiol 2023:10.1038/s41564-023-01381-3. [PMID: 37188815 DOI: 10.1038/s41564-023-01381-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/12/2023] [Indexed: 05/17/2023]
Abstract
Human DNA present in faecal samples can result in a small number of human reads in gut shotgun metagenomic sequencing data. However, it is presently unclear how much personal information can be reconstructed from such reads, and this has not been quantitatively evaluated. Such a quantitative evaluation is necessary to clarify the ethical concerns related to data sharing and to enable efficient use of human genetic information in stool samples, such as for research and forensics. Here we used genomic approaches to reconstruct personal information from the faecal metagenomes of 343 Japanese individuals with associated human genotype data. Genetic sex could be accurately predicted based on the sequencing depth of sex chromosomes for 97.3% of the samples. Individuals could be re-identified from the matched genotype data based on human reads recovered from the faecal metagenomic data with 93.3% sensitivity using a likelihood score-based method. This method also enabled us to predict the ancestries of 98.3% of the samples. Finally, we performed ultra-deep shotgun metagenomic sequencing of five faecal samples as well as whole-genome sequencing of blood samples. Using genotype-calling approaches, we demonstrated that the genotypes of both common and rare variants could be reconstructed from faecal samples. This included clinically relevant variants. Our approach can be used to quantify personal information contained within gut metagenome data.
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Affiliation(s)
- Yoshihiko Tomofuji
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
| | - Kyuto Sonehara
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshihiro Kishikawa
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Head and Neck Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kotaro Ogawa
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Shuhei Kawabata
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Takuro Nii
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Tatsusada Okuno
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Eri Oguro-Igashira
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Makoto Kinoshita
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Masatoshi Takagaki
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Pediatrics, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Takashi Kurakawa
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Mayu Yagita-Sakamaki
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Akiko Hosokawa
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Neurology, Suita Municipal Hospital, Suita, Japan
| | - Daisuke Motooka
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Hidetoshi Matsuoka
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Maiko Yoshimura
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Shiro Ohshima
- Department of Rheumatology and Allergology, NHO Osaka Minami Medical Center, Kawachinagano, Japan
| | - Shota Nakamura
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
| | - Hidenori Inohara
- Department of Otorhinolaryngology-Head and Neck Surgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Haruhiko Kishima
- Department of Neurosurgery, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Hideki Mochizuki
- Department of Neurology, Graduate School of Medicine, Osaka University, Suita, Japan
| | - Kiyoshi Takeda
- Laboratory of Immune Regulation, Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan
- WPI Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Graduate School of Medicine, Osaka University, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- Laboratory of Statistical Immunology, WPI Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Center for Infectious Disease Education and Research, Osaka University, Suita, Japan.
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Wang D, Ma Q, Lin H, Zhou J, Yuan S, Ma B, Bai Y, Qu J. Enhancement of micropollutant biotransformation by adding manganese sand in constructed wetlands. Heliyon 2023; 9:e15092. [PMID: 37089304 PMCID: PMC10119567 DOI: 10.1016/j.heliyon.2023.e15092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/07/2023] Open
Abstract
Recent investigations have shown that the addition of manganese (Mn) sand to constructed wetlands (i.e., Mn-amended CWs) can improve the performance of organic micropollutants (MPs) removal. In addition to the direct oxidation and adsorption of Mn oxides, the indirect role of Mn oxides in MP biotransformation is crucial to the removal of MPs but has seldom been referred to. Herein, we constructed lab-scale CWs with or without the addition of natural Mn sand (∼35% Mn oxides) to decipher the influence of Mn oxides on the biotransformation of the six selected MPs which commonly existed in the wastewater. The experimental results showed that the addition of Mn sand to CWs can improve the removal of MPs (8.48% atrazine, 13.16% atenolol, and 6.27% sulfamethoxazole [pairwise Wilcoxon test p < 0.05]). Combining the detection of transformation products and metagenomic sequencing, we found that the enhanced removal of atrazine in the Mn-amended CWs was mainly due to the bioaugmented hydroxylation process. The enrichment of biotransformation-related genes and associated microbes of atenolol and sulfamethoxazole in Mn-amended CWs indicated that the addition of Mn sand to CWs can strengthen the biotransformation of MPs. Furthermore, we found that these MP-biodegrading microbes were widely present in the full-scale CWs. Overall, our research provides fundamental information and insights for further application of Mn-amended CWs in MP removal.
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31
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Zhu L, Zhang J, Yang H, Li G, Li H, Deng Z, Zhang B. Propolis polyphenols: A review on the composition and anti-obesity mechanism of different types of propolis polyphenols. Front Nutr 2023; 10:1066789. [PMID: 37063322 PMCID: PMC10102383 DOI: 10.3389/fnut.2023.1066789] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/14/2023] [Indexed: 04/03/2023] Open
Abstract
Obesity, one of the most common nutritional diseases worldwide, can lead to dyslipidemia, high blood sugar, high blood pressure, and inflammation. Some drugs have been developed to ameliorate obesity. However, these drugs may cause serious side effects. Therefore, there is an urgent need for alternative “natural” remedies including propolis. Studies have found that propolis has excellent anti-obesity activity in in vitro and in vivo models during the past decades, of which polyphenols are the key component in regulating weight loss. This review focused on the different polyphenol compositions of propolis from different regions and plants, the evidence for the anti-obesity effects of different types of propolis and its derivatives, discussed the impact of propolis polyphenols on obesity related signal pathways, and proposed the molecular mechanism of how propolis polyphenols affect these signal pathways. For example, propolis and its derivatives regulate lipid metabolism related proteins, such as PPARα, PPARγ, SREBP-1&2, and HMG CoA etc., destroy the formation of CREB/CRTC2 transcription complex, activate Nrf2 pathway or inhibit protein kinase IKK ε/TBK1, thereby affecting fat production and lipid metabolism; The effects of propolis on adipokines (adiponectin, leptin and inflammatory factors) were discussed. Additionally, the mechanism of polyphenols in propolis promoting the browning of adipose tissues and the relationship between intestinal microorganisms was summarized. These information may be of value to better understand how specific propolis polyphenols interact with specific signaling pathways and help guide the development of new drugs to combat obesity and related metabolic diseases.
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Affiliation(s)
- Liuying Zhu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Jinwu Zhang
- Nanchang Concentric Purple Nest Biological Engineering Co., Ltd., Nanchang, China
| | - Hui Yang
- Nanchang Concentric Purple Nest Biological Engineering Co., Ltd., Nanchang, China
| | - Guangyan Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- Nanchang Concentric Purple Nest Biological Engineering Co., Ltd., Nanchang, China
| | - Hongyan Li
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Zeyuan Deng
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
| | - Bing Zhang
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China
- *Correspondence: Bing Zhang,
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Yuzefpolskaya M, Bohn B, Ladanyi A, Khoruts A, Colombo PC, Demmer RT. Oral and gut microbiome alterations in heart failure: Epidemiology, pathogenesis and response to advanced heart failure therapies. J Heart Lung Transplant 2023; 42:291-300. [PMID: 36586790 DOI: 10.1016/j.healun.2022.12.009] [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: 09/27/2022] [Revised: 11/18/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Despite significant advances in therapies, heart failure (HF) remains a progressive disease that, once advanced, is associated with significant death and disability. Cardiac replacement therapies with left ventricular assist device (LVAD) and heart transplantation (HT) are the only treatment options for advanced HF, while lifesaving they can also be lifespan limiting due to the associated complications. Systemic inflammation is mechanistically important in HF pathophysiology and progression. However, directly targeting inflammation in HF has not been beneficial thus far. These failed attempts at therapeutics might be related to our limited understanding of the factors that cause inflammation in HF, and, therefore, to our inability to investigate these triggers in interventional studies. Observational studies have consistently demonstrated associations between alterations in the digestive (gut and oral) microbiome, inflammation and HF risk and progression. Additionally, recent data indicate that these microbial perturbations persist following LVAD and HT, along with residual inflammation and oxidative stress. Furthermore, there is rising recognition of the critical contribution of the microbiome to the metabolism of immunosuppressive drugs after HT. Cumulatively, these findings might posit a mechanistic link between microbiome alterations, systemic inflammation, and adverse outcomes in HF patients before and after cardiac replacement therapies. This review (1) provides an update on available data linking changes in digestive tract microbiota, inflammation, and oxidative stress, to HF pathogenesis and progression; (2) describes evolution of these relationships following LVAD and HT; and (3) outlines present and future intervention strategies that can manipulate the microbiome and possibly modify HF disease trajectory.
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Affiliation(s)
- Melana Yuzefpolskaya
- Division of Cardiovascular Medicine, Columbia University Irving Medical Center, New York City, New York.
| | - Bruno Bohn
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Annamaria Ladanyi
- Division of Cardiovascular Medicine, Columbia University Irving Medical Center, New York City, New York
| | - Alexander Khoruts
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine University of Minnesota, Minneapolis, Minnesota
| | - Paolo C Colombo
- Division of Cardiovascular Medicine, Columbia University Irving Medical Center, New York City, New York
| | - Ryan T Demmer
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, Minnesota; Division of Epidemiology, Mailman School of Public Health, Columbia University Irving Medical Center, New York, New York
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Phenolics from noni (Morinda citrifolia L.) fruit alleviate obesity in high fat diet-fed mice via modulating the gut microbiota and mitigating intestinal damage. Food Chem 2023; 402:134232. [DOI: 10.1016/j.foodchem.2022.134232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 08/27/2022] [Accepted: 09/11/2022] [Indexed: 11/22/2022]
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Zhou W, Weng Y, Liu Q, Wang C, Zhang YQ, Zhang X, Ye A. Dietary administration with hydrolyzed silk sericin improves the intestinal health of diabetic rats. Front Microbiol 2023; 14:1074892. [PMID: 36960285 PMCID: PMC10027739 DOI: 10.3389/fmicb.2023.1074892] [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: 11/04/2022] [Accepted: 02/06/2023] [Indexed: 03/09/2023] Open
Abstract
Type II diabetes (T2D) is a global epidemic disease with an increased incidence and prevalence. Gut microbiota plays an important role in controlling T2D development. Dietary administration of prebiotics, probiotics, and drugs, including metformin, showed the regulatory impact on the change of gut microbiota, which is associated with the improvement of glucose tolerance. In this study, silk sericin was manufactured into hydrolyzed sericin peptide (HSP) powders as a dietary additive to investigate the effect on the gut microbiota of T2D model rats. The results indicated that the HSP-augmented dietary administration lowers the fast glucose level of diabetic rats, and HSP augmentation induces a change in the gut microbiota composition of T2D model rats toward the normal rats. Some key taxa, including Lactobacillus gasseri, were suggested to be involved in controlling T2D development. This finding provides new insight into developing sericin as functional food or therapeutic prebiotics against T2D in clinical practice.
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Affiliation(s)
- Wenlin Zhou
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yujie Weng
- Department of Biological Sciences, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Qian Liu
- Department of Biological Sciences, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Chonglong Wang
- Department of Biological Sciences, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Yu-Qing Zhang
- Department of Biological Sciences, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Xing Zhang
- Department of Biological Sciences, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
- Xing Zhang
| | - Aihong Ye
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Aihong Ye
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Wang Y, Chen J, Wang X, Guo C, Peng X, Liu Y, Li T, Du J. Novel investigations in retinoic-acid-induced cleft palate about the gut microbiome of pregnant mice. Front Cell Infect Microbiol 2022; 12:1042779. [PMID: 36590585 PMCID: PMC9798234 DOI: 10.3389/fcimb.2022.1042779] [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: 09/16/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction Cleft palate (CP) is one of the most common congenital birth defects in the craniofacial region, retinoic acid (RA) gavage is the most common method for inducing cleft palate model. Although several mechanisms have been proposed to illuminate RA-induced cleft palate during embryonic development, these findings are far from enough. Many efforts remain to be devoted to studying the etiology and pathogenesis of cleft palate. Recent research is gradually shifting the focus to the effect of retinoic acid on gut microbiota. However, few reports focus on the relationship between the occurrence of CP in embryos and gut microbiota. Methods In our research, we used RA to induce cleft palate model for E10.5 the feces of 5 RA-treated pregnant mice and 5 control pregnant mice were respectively metagenomics analysis. Results Compared with the control group, Lactobacillus in the gut microbiome the RA group was significantly increased. GO, KEGG and CAZy analysis of differentially unigenes demonstrated the most abundant metabolic pathway in different groups, lipopolysaccharide biosynthesis, and histidine metabolism. Discussion Our findings indicated that changes in the maternal gut microbiome palatal development, which might be related to changes in Lactobacillus and These results provide a new direction in the pathogenesis of CP induced by RA.
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Affiliation(s)
- Yijia Wang
- Laboratory of Orofacial Development, Capital Medical University School of Stomatology, Beijing, China,Laboratory of Molecular Signaling and Stem Cells Therapy, Capital Medical University School of Stomatology, Beijing, China,Molecular Laboratory for Gene Therapy and Tooth Regeneration, Capital Medical University School of Stomatology, Beijing, China,Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Jing Chen
- Laboratory of Orofacial Development, Capital Medical University School of Stomatology, Beijing, China,Laboratory of Molecular Signaling and Stem Cells Therapy, Capital Medical University School of Stomatology, Beijing, China,Molecular Laboratory for Gene Therapy and Tooth Regeneration, Capital Medical University School of Stomatology, Beijing, China,Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Xiaotong Wang
- Laboratory of Orofacial Development, Capital Medical University School of Stomatology, Beijing, China,Laboratory of Molecular Signaling and Stem Cells Therapy, Capital Medical University School of Stomatology, Beijing, China,Molecular Laboratory for Gene Therapy and Tooth Regeneration, Capital Medical University School of Stomatology, Beijing, China,Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Cui Guo
- Department of Geriatric Dentistry, Capital Medical University School of Stomatology, Beijing, China
| | - Xia Peng
- Laboratory of Orofacial Development, Capital Medical University School of Stomatology, Beijing, China,Laboratory of Molecular Signaling and Stem Cells Therapy, Capital Medical University School of Stomatology, Beijing, China,Molecular Laboratory for Gene Therapy and Tooth Regeneration, Capital Medical University School of Stomatology, Beijing, China,Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Ying Liu
- Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China,Laboratory of Oral Microbiology, Capital Medical University School of Stomatology, Beijing, China
| | - Tianli Li
- Laboratory of Orofacial Development, Capital Medical University School of Stomatology, Beijing, China,Laboratory of Molecular Signaling and Stem Cells Therapy, Capital Medical University School of Stomatology, Beijing, China,Molecular Laboratory for Gene Therapy and Tooth Regeneration, Capital Medical University School of Stomatology, Beijing, China,Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China
| | - Juan Du
- Laboratory of Orofacial Development, Capital Medical University School of Stomatology, Beijing, China,Laboratory of Molecular Signaling and Stem Cells Therapy, Capital Medical University School of Stomatology, Beijing, China,Molecular Laboratory for Gene Therapy and Tooth Regeneration, Capital Medical University School of Stomatology, Beijing, China,Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Beijing, China,Department of Geriatric Dentistry, Capital Medical University School of Stomatology, Beijing, China,*Correspondence: Juan Du,
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Ruscheweyh HJ, Milanese A, Paoli L, Karcher N, Clayssen Q, Keller MI, Wirbel J, Bork P, Mende DR, Zeller G, Sunagawa S. Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments. MICROBIOME 2022; 10:212. [PMID: 36464731 PMCID: PMC9721005 DOI: 10.1186/s40168-022-01410-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic data generally depend on the deposition of sequenced and taxonomically annotated genomes, usually from cultures of isolated strains, in reference databases (reference genomes). However, the majority of microorganisms have not been cultured yet. Thus, a substantial fraction of microbial community members remains unaccounted for during taxonomic profiling, particularly in samples from underexplored environments. To address this issue, we developed the mOTU profiler, a tool that enables reference genome-independent species-level profiling of metagenomes. As such, it supports the identification and quantification of both "known" and "unknown" species based on a set of select marker genes. RESULTS We present mOTUs3, a command line tool that enables the profiling of metagenomes for >33,000 species-level operational taxonomic units. To achieve this, we leveraged the reconstruction of >600,000 draft genomes, most of which are metagenome-assembled genomes (MAGs), from diverse microbiomes, including soil, freshwater systems, and the gastrointestinal tract of ruminants and other animals, which we found to be underrepresented by reference genomes. Overall, two thirds of all species-level taxa lacked a reference genome. The cumulative relative abundance of these newly included taxa was low in well-studied microbiomes, such as the human body sites (6-11%). By contrast, they accounted for substantial proportions (ocean, freshwater, soil: 43-63%) or even the majority (pig, fish, cattle: 60-80%) of the relative abundance across diverse non-human-associated microbiomes. Using community-developed benchmarks and datasets, we found mOTUs3 to be more accurate than other methods and to be more congruent with 16S rRNA gene-based methods for taxonomic profiling. Furthermore, we demonstrate that mOTUs3 increases the resolution of well-known microbial groups into species-level taxa and helps identify new differentially abundant taxa in comparative metagenomic studies. CONCLUSIONS We developed mOTUs3 to enable accurate species-level profiling of metagenomes. Compared to other methods, it provides a more comprehensive view of prokaryotic community diversity, in particular for currently underexplored microbiomes. To facilitate comparative analyses by the research community, it is released with >11,000 precomputed profiles for publicly available metagenomes and is freely available at: https://github.com/motu-tool/mOTUs . Video Abstract.
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Affiliation(s)
- Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Alessio Milanese
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Nicolai Karcher
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Quentin Clayssen
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
| | - Marisa Isabell Keller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Jakob Wirbel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Peer Bork
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
- Max Delbrück Centre for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
- Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Daniel R. Mende
- Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, 8093 Zürich, Switzerland
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Zhang S, Deng F, Chen J, Chen F, Wu Z, Li L, Hou K. Fecal microbiota transplantation treatment of autoimmune-mediated type 1 diabetes: A systematic review. Front Cell Infect Microbiol 2022; 12:1075201. [PMID: 36530444 PMCID: PMC9751335 DOI: 10.3389/fcimb.2022.1075201] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022] Open
Abstract
There is a strong link between fecal microbiota and the development of type 1 diabetes. As an emerging therapeutic modality, fecal microbiota transplantation has been shown to be safe and effective in the treatment of many intestinal and extraintestinal diseases. Various studies have found that fecal microbiota transplantation can treat diseases by correcting patients' immune disorders. Besides, many studies have found that fecal microbiota transplantation can improve glycemic control and insulin resistance in diabetic patients. Therefore, this paper reviews the mechanism of action of fecal microbiota transplantation on autoimmune-mediated T1DM and the current research progress, feasibility, and issues that need to be addressed in the future development of fecal microbiota transplantation in the treatment of autoimmune-mediated T1DM.
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Affiliation(s)
- Shuo Zhang
- Shantou University Medical College, Shantou, China
- Department of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Feiying Deng
- Shantou University Medical College, Shantou, China
- Department of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Jingxian Chen
- Department of Endocrine and Metabolic Diseases, Longhu People’s Hospital, Shantou, China
- School of Public Health, Shantou University, Shantou, China
| | - Fengwu Chen
- Department of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Department of Endocrine and Metabolic Diseases, Longhu People’s Hospital, Shantou, China
| | - Zezhen Wu
- Shantou University Medical College, Shantou, China
- Department of Endocrine and Metabolic Diseases, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Liping Li
- School of Public Health, Shantou University, Shantou, China
| | - Kaijian Hou
- Department of Endocrine and Metabolic Diseases, Longhu People’s Hospital, Shantou, China
- School of Public Health, Shantou University, Shantou, China
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Plaza-Díaz J, Manzano M, Ruiz-Ojeda FJ, Giron MD, Salto R, López-Pedrosa JM, Santos-Fandila A, Garcia-Corcoles MT, Rueda R, Gil Á. Intake of slow-digesting carbohydrates is related to changes in the microbiome and its functional pathways in growing rats with obesity induced by diet. Front Nutr 2022; 9:992682. [PMID: 36532542 PMCID: PMC9748084 DOI: 10.3389/fnut.2022.992682] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/02/2022] [Indexed: 08/17/2023] Open
Abstract
INTRODUCTION The main cause of insulin resistance in childhood is obesity, which contributes to future comorbidities as in adults. Although high-calorie diets and lack of exercise contribute to metabolic disease development, food quality rather than the quantity of macronutrients is more important than food density. The purpose of the present study was to examine the effects of changing the quality of carbohydrates from rapidly to slowly digestible carbohydrates on the composition of the gut microbiota and the profiles of the functional pathways in growing rats with obesity due to a high-fat diet (HFD). METHODS During the course of 4 weeks, rats growing on an HFD-containing carbohydrates with different digestive rates were fed either HFD-containing carbohydrates with a rapid digestion rate (OBE group) or HFD-containing carbohydrates with a slow digestion rate (OBE-ISR group). A non-obese group (NOB) was included as a reference, and rats were fed on a rodent standard diet (AIN93G). An analysis of gut microbiota was conducted using 16S rRNA-based metagenomics; a linear mixed-effects model (LMM) was used to determine changes in abundance between baseline and 4 weeks of treatment, and functional pathways were identified. Gut microbiota composition at bacterial diversity and relative abundance, at phylum and genus levels, and functional profiles were analyzed by integrating the Integrated Microbial Genomes (IMG) database. RESULTS The groups showed comparable gut microbiota at baseline. At the end of the treatment, animals from the ISR group exhibited differences at the phylum levels by decreasing the diversity of Fisher's index and Firmicutes (newly named as Bacillota), and increasing the Pielou's evenness and Bacteroidetes (newly named as Bacteroidota); at the genus level by increasing Alistipes, Bifidobacterium, Bacteroides, Butyricimonas, Lachnoclostridium, Flavonifractor, Ruminiclostridium 5, and Faecalibaculum and decreasing Muribaculum, Blautia, and Ruminiclostridium 9. Remarkably, relative abundances of genera Tyzzerella and Angelakisella were higher in the OBE group compared to NOB and OBE-ISR groups. In addition, some microbiota carbohydrate metabolism pathways such as glycolysis, glucuronic acid degradation, pentose phosphate pathway, methanogenesis, and fatty acid biosynthesis exhibited increased activity in the OBE-ISR group after the treatment. Higher levels of acetate and propionate were found in the feces of the ISR group compared with the NOB and OBE groups. CONCLUSION The results of this study demonstrate that replacing rapidly digestible carbohydrates with slowly digestible carbohydrates within an HFD improve the composition of the gut microbiota. Consequently, metabolic disturbances associated with obesity may be prevented.
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Affiliation(s)
- Julio Plaza-Díaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
- Instituto de Investigación Biosanitaria de Granada (ibs.Granada), Complejo Hospitalario Universitario de Granada, Granada, Spain
| | | | - Francisco Javier Ruiz-Ojeda
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.Granada), Complejo Hospitalario Universitario de Granada, Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix”, Biomedical Research Centre, University of Granada, Granada, Spain
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Center Munich, Munich, Germany
| | - Maria D. Giron
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
| | - Rafael Salto
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
| | | | | | | | | | - Ángel Gil
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.Granada), Complejo Hospitalario Universitario de Granada, Granada, Spain
- Institute of Nutrition and Food Technology “José Mataix”, Biomedical Research Centre, University of Granada, Granada, Spain
- CIBER Physiopathology of Obesity and Nutrition, Instituto de Salud Carlos III, Madrid, Spain
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Gaba FI, González RC, Martïnez RG. The Role of Oral Fusobacterium nucleatum in Female Breast Cancer: A Systematic Review and Meta-Analysis. Int J Dent 2022; 2022:1876275. [PMID: 36466367 PMCID: PMC9711985 DOI: 10.1155/2022/1876275] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/17/2022] [Accepted: 11/01/2022] [Indexed: 02/06/2024] Open
Abstract
INTRODUCTION Breast cancer is the world's most prevalent malignancy, with an increasing incidence and a predisposition for postpubertal females from all cultural and ethnic backgrounds. More recently, oral Fusobacterium nucleatum species have been observed in cancerous human breast tissue, drawing attention to the role of microbes in cancer pathogenesis. OBJECTIVES Investigating oral Fusobacterium nucleatum species as potential biomarkers for female-specific breast cancer. METHODS A systematic search in The Central Register of Controlled Trials, EMBASE, EBSCO, NCBI, and MEDLINE databases was undertaken from the 1st January, 1983-31st March, 2022. Articles included were in English and based on women between the ages of 18-96 years with confirmed gingivitis/periodontal disease and breast cancer diagnoses from registered specialists. Authors extracted data independently, and a meta-analysis of risk estimations measuring associations between oral Fusobacterium nucleatum species and female-specific breast cancer was elucidated via calculated relative risks and 95% confidence intervals. RESULTS AXIS tool analysis revealed 78.70% of articles with a positive correlation between oral Fusobacterium nucleatum and female-specific breast cancer. The risk of breast cancer development increased with significant levels of oral Fusobacterium nucleatum due to gingivitis/periodontitis (relative risk = 1.78, 95% confidence interval = 1.63-1.91). Low-moderate statistical heterogeneity was found (I 2 = 41.39%; P = 0.02), and the importance of periodontal status on breast cancer pathogenesis was determined (relative risk = 1.24, 95% confidence interval = 1.01-1.30). CONCLUSIONS Oral Fusobacterium nucleatum species are a risk factor for breast cancer development, thus elevating their biomarker potentiality.
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Affiliation(s)
- Fariah I. Gaba
- Mondzorg Scheveningen, Renbaanstraat 75, 2586 EZ, The Hague, Netherlands
| | - Raquel Carcelén González
- Faculty of Health and Science, CEU Cardenal Herrera University, Carrer Lluís Vives 1, 46115 Alfara del Patriarca, Valencia, Spain
| | - Raquel González Martïnez
- CIMEV Institute in Spain, Periodontics and Oral Surgery at the Faculty of Health and Science, CEU Cardenal Herrera University, Carrer Lluís Vives 1, 46115 Alfara del Patriarca, Valencia, Spain
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Tsimpiris A, Tsolianos I, Grigoriadis A, Moschos I, Goulis DG, Kouklakis G. Association of Chronic Periodontitis with Helicobacter pylori Infection in Stomach or Mouth: A Systematic Review and Meta-Analysis. Eur J Dent 2022. [DOI: 10.1055/s-0042-1756690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
Helicobacter pylori (H. pylori) infection and periodontitis are both inflammatory conditions associated with systemic diseases. Researchers have attempted to investigate the correlation between them. This systematic review and meta-analyses were conducted to investigate the association of H. pylori infection in the stomach and/or in subgingival plaque and gingival crevicular fluid with chronic periodontitis. The protocol was created according to the Preferred Reporting Items for Systematic review and Meta-Analysis Protocols (PRISMA-P) statement. The study was designed according to the Cochrane criteria. A comprehensive literature search was performed in MEDLINE, Scopus, and CENTRAL, combined with hand-searching and assessment of gray literature. The meta-analysis of the included studies was made by the Review Manager (RevMan) 5.4 software. The effect measure of the outcome was odds ratios with 95% confidence intervals. Heterogeneity was assessed by chi-square and I2. Four observational studies involving 818 subjects were included in this meta-analysis. The odds of oral H. pylori presence were higher in patients with chronic periodontitis, compared to healthy controls, with an odds ratio of 1.87 (95% confidence interval 0.85–4.10; p = 0.12). The odds of the presence of H. pylori in the stomach also were higher in patients with chronic periodontitis, with an odds ratio of 1.80 (95% confidence interval 0.82–3.95; p = 0.15). There is no evidence for an association between chronic periodontitis and the prevalence of H. pylori, detected either in subgingival plaque and gingival crevicular fluid or in the stomach.
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Affiliation(s)
- Athanasios Tsimpiris
- Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Dental Sector, 424 General Military Training Hospital, Thessaloniki, Greece
| | - Ioannis Tsolianos
- Dental School, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Andreas Grigoriadis
- Dental Sector, 424 General Military Training Hospital, Thessaloniki, Greece
- Department of Preventive Dentistry, Periodontology and Implant Biology, Dental School, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Moschos
- Department of Nursing, International Hellenic University, Thessaloniki, Greece
| | - Dimitrios G. Goulis
- 1st Department of Obstetrics and Gynecology, Unit of Reproductive Endocrinology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios Kouklakis
- A΄ Department of Pathology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
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Numberger D, Zoccarato L, Woodhouse J, Ganzert L, Sauer S, Márquez JRG, Domisch S, Grossart HP, Greenwood AD. Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 845:157321. [PMID: 35839872 DOI: 10.1016/j.scitotenv.2022.157321] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Freshwater ecosystems are characterized by complex and highly dynamic microbial communities that are strongly structured by their local environment and biota. Accelerating urbanization and growing city populations detrimentally alter freshwater environments. To determine differences in freshwater microbial communities associated with urbanization, full-length 16S rRNA gene PacBio sequencing was performed in a case study from surface waters and sediments from a wastewater treatment plant, urban and rural lakes in the Berlin-Brandenburg region, Northeast Germany. Water samples exhibited highly habitat specific bacterial communities with multiple genera showing clear urban signatures. We identified potentially harmful bacterial groups associated with environmental parameters specific to urban habitats such as Alistipes, Escherichia/Shigella, Rickettsia and Streptococcus. We demonstrate that urbanization alters natural microbial communities in lakes and, via simultaneous warming and eutrophication and creates favourable conditions that promote specific bacterial genera including potential pathogens. Our findings are evidence to suggest an increased potential for long-term health risk in urbanized waterbodies, at a time of rapidly expanding global urbanization. The results highlight the urgency for undertaking mitigation measures such as targeted lake restoration projects and sustainable water management efforts.
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Affiliation(s)
- Daniela Numberger
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany; Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany
| | - Luca Zoccarato
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany; University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Computational Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Jason Woodhouse
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany
| | - Lars Ganzert
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany; GFZ German Research Centre for Geosciences, Helmholtz Centre Potsdam, Section 3.7 Geomicrobiology, Telegrafenberg C-422, 14473 Potsdam, Germany
| | - Sascha Sauer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 16775, 13125 Berlin, Germany
| | | | - Sami Domisch
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 310, 12587 Berlin, Germany
| | - Hans-Peter Grossart
- Leibniz Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany; University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Altensteinstrasse 32, 14195 Berlin, Germany.
| | - Alex D Greenwood
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, 10315 Berlin, Germany; Freie Universität Berlin, Department of Veterinary Medicine, Institute for Virology, Robert von Ostertag-Strasse 7-13, 14163 Berlin, Germany
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Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians. Nat Commun 2022; 13:6044. [PMID: 36229545 PMCID: PMC9561172 DOI: 10.1038/s41467-022-33782-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/27/2022] [Indexed: 12/24/2022] Open
Abstract
Despite extensive efforts to address it, the vastness of uncharacterized 'dark matter' microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.
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Liu N, Song Z, Jin W, Yang Y, Sun S, Zhang Y, Zhang S, Liu S, Ren F, Wang P. Pea albumin extracted from pea (Pisum sativum L.) seed protects mice from high fat diet-induced obesity by modulating lipid metabolism and gut microbiota. J Funct Foods 2022. [DOI: 10.1016/j.jff.2022.105234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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The Study of Soil Bacterial Diversity and the Influence of Soil Physicochemical Factors in Meltwater Region of Ny-Ålesund, Arctic. Microorganisms 2022; 10:microorganisms10101913. [PMID: 36296189 PMCID: PMC9611652 DOI: 10.3390/microorganisms10101913] [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: 08/25/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Global climate change has caused the changes of the ecological environment in the Arctic region, including sea ice melting, runoff increase, glacial lake expansion, and a typical meltwater area has formed in the Arctic coastal area. In this study, the meltwater areas near six different characteristic areas of Ny-Ålesund in 2018 were taken as the research objects, and high-throughput sequencing of V3–V4 regions of all samples were performed using 16S rDNA. Among the soil samples of six glacial meltwater areas in Ny-Ålesund, Arctic, the meltwater area near the reservoir bay had the highest bacterial abundance, and the meltwater area near the sand had the lowest one. The dominant phyla in soil samples were Proteobacteria, Actinobacteria, Acidobacteria. The NH4+-N content in intertidal soil was higher than that in subtidal soil. Through WGCNA analysis and LEFSE analysis, it was found that the core bacteria significantly related to NH4+-N were basically distributed in the intertidal area. For example, Nitrosomonadaceae, Nitrospira and Sphingomonas were the core bacteria showed significant different abundance in the intertidal area, which have the ability to metabolize NH4+-N. Our findings suggest that NH4+-N plays an important role in soil bacterial community structure in the Arctic meltwater areas.
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Zhang N, Peng Y, Zhao L, He P, Zhu J, Liu Y, Liu X, Liu X, Deng G, Zhang Z, Feng M. Integrated Analysis of Gut Microbiome and Lipid Metabolism in Mice Infected with Carbapenem-Resistant Enterobacteriaceae. Metabolites 2022; 12:metabo12100892. [PMID: 36295794 PMCID: PMC9609999 DOI: 10.3390/metabo12100892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/15/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022] Open
Abstract
The disturbance in gut microbiota composition and metabolism has been implicated in the process of pathogenic bacteria infection. However, the characteristics of the microbiota and the metabolic interaction of commensals−host during pathogen invasion remain more than vague. In this study, the potential associations of gut microbes with disturbed lipid metabolism in mice upon carbapenem-resistant Escherichia coli (CRE) infection were explored by the biochemical and multi-omics approaches including metagenomics, metabolomics and lipidomics, and then the key metabolites−reaction−enzyme−gene interaction network was constructed. Results showed that intestinal Erysipelotrichaceae family was strongly associated with the hepatic total cholesterol and HDL-cholesterol, as well as a few sera and fecal metabolites involved in lipid metabolism such as 24, 25-dihydrolanosterol. A high-coverage lipidomic analysis further demonstrated that a total of 529 lipid molecules was significantly enriched and 520 were depleted in the liver of mice infected with CRE. Among them, 35 lipid species showed high correlations (|r| > 0.8 and p < 0.05) with the Erysipelotrichaceae family, including phosphatidylglycerol (42:2), phosphatidylglycerol (42:3), phosphatidylglycerol (38:5), phosphatidylcholine (42:4), ceramide (d17:1/16:0), ceramide (d18:1/16:0) and diacylglycerol (20:2), with correlation coefficients higher than 0.9. In conclusion, the systematic multi-omics study improved the understanding of the complicated connection between the microbiota and the host during pathogen invasion, which thereby is expected to lead to the future discovery and establishment of novel control strategies for CRE infection.
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Affiliation(s)
- Ning Zhang
- School of Chemistry and Chemical Engineering, Shanghai Engineering Research Center for Pharmaceutical Intelligent Equipment, Shanghai Frontiers Science Research Center for Druggability of Cardiovascular Noncoding RNA, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Yuanyuan Peng
- School of Chemistry and Chemical Engineering, Shanghai Engineering Research Center for Pharmaceutical Intelligent Equipment, Shanghai Frontiers Science Research Center for Druggability of Cardiovascular Noncoding RNA, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Linjing Zhao
- School of Chemistry and Chemical Engineering, Shanghai Engineering Research Center for Pharmaceutical Intelligent Equipment, Shanghai Frontiers Science Research Center for Druggability of Cardiovascular Noncoding RNA, Shanghai University of Engineering Science, Shanghai 201620, China
- Correspondence: ; Tel.: +86-21-6779-1214
| | - Peng He
- Minhang Hospital & School of Pharmacy, Fudan University, Shanghai 200433, China
- Shanghai Engineering Research Center of Immunotherapeutic, Shanghai 201203, China
| | - Jiamin Zhu
- School of Chemistry and Chemical Engineering, Shanghai Engineering Research Center for Pharmaceutical Intelligent Equipment, Shanghai Frontiers Science Research Center for Druggability of Cardiovascular Noncoding RNA, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Yumin Liu
- Instrumental Analysis Centre, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xijian Liu
- School of Chemistry and Chemical Engineering, Shanghai Engineering Research Center for Pharmaceutical Intelligent Equipment, Shanghai Frontiers Science Research Center for Druggability of Cardiovascular Noncoding RNA, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Xiaohui Liu
- School of Chemistry and Chemical Engineering, Shanghai Engineering Research Center for Pharmaceutical Intelligent Equipment, Shanghai Frontiers Science Research Center for Druggability of Cardiovascular Noncoding RNA, Shanghai University of Engineering Science, Shanghai 201620, China
| | - Guoying Deng
- Trauma Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Zhong Zhang
- Nursing Department, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 201620, China
| | - Meiqing Feng
- Minhang Hospital & School of Pharmacy, Fudan University, Shanghai 200433, China
- Shanghai Engineering Research Center of Immunotherapeutic, Shanghai 201203, China
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Wang X, Pang K, Wang J, Zhang B, Liu Z, Lu S, Xu X, Zhu L, Zhou Z, Niu M, Gao J, Li J, Zhao F, Wu J. Microbiota dysbiosis in primary Sjögren's syndrome and the ameliorative effect of hydroxychloroquine. Cell Rep 2022; 40:111352. [PMID: 36103827 DOI: 10.1016/j.celrep.2022.111352] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 06/17/2022] [Accepted: 08/23/2022] [Indexed: 11/03/2022] Open
Abstract
The human microbiome plays an important role in autoimmune diseases. However, there is limited knowledge regarding the microbiota in individuals with primary Sjögren's syndrome (pSS). Here, we perform 16S ribosomal RNA gene sequencing of fecal, oral, and vaginal samples from a cohort of 133 individuals with pSS, 56 with non-pSS, and 40 healthy control (HC) individuals. Dysbiosis in the gut, oral, and vaginal microbiome is evident in patients with pSS, and oral samples demonstrate the greatest extent of microbial variation. Multiple key indicator bacteria and clinical characteristics are identified across different body sites, implying that microbial dysbiosis has important roles in the pathogenesis of pSS. Furthermore, we observe pSS-like dysbiosis in individuals with pre-clinical pSS or non-pSS-related disease, revealing that microbial shifts could appear prior to pSS. After hydroxychloroquine (HCQ) treatment, microbial dysbiosis in individuals with pSS is partially resolved, although the microbiota composition remain disordered. These results contribute to the overall understanding of the relationship between the microbiome and pSS.
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Affiliation(s)
- Xiaobing Wang
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Affiliated Hospital of Naval Medical University, Shanghai 200003, China; Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Kun Pang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinfeng Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100091, China
| | - Bing Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Saisai Lu
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xin Xu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Lingxiao Zhu
- Rheumatology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Zihao Zhou
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Miaomiao Niu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Jianxia Gao
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Jianmin Li
- Pathology Department, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China.
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Identification of microbial features in multivariate regression under false discovery rate control. Comput Stat Data Anal 2022. [DOI: 10.1016/j.csda.2022.107621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Boyraz A, Pawlowsky-Glahn V, Egozcue JJ, Acar AC. Principal microbial groups: compositional alternative to phylogenetic grouping of microbiome data. Brief Bioinform 2022; 23:6675749. [PMID: 36007229 DOI: 10.1093/bib/bbac328] [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: 02/01/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Statistical and machine learning techniques based on relative abundances have been used to predict health conditions and to identify microbial biomarkers. However, high dimensionality, sparsity and the compositional nature of microbiome data represent statistical challenges. On the other hand, the taxon grouping allows summarizing microbiome abundance with a coarser resolution in a lower dimension, but it presents new challenges when correlating taxa with a disease. In this work, we present a novel approach that groups Operational Taxonomical Units (OTUs) based only on relative abundances as an alternative to taxon grouping. The proposed procedure acknowledges the compositional data making use of principal balances. The identified groups are called Principal Microbial Groups (PMGs). The procedure reduces the need for user-defined aggregation of $\textrm{OTU}$s and offers the possibility of working with coarse group of $\textrm{OTU}$s, which are not present in a phylogenetic tree. PMGs can be used for two different goals: (1) as a dimensionality reduction method for compositional data, (2) as an aggregation procedure that provides an alternative to taxon grouping for construction of microbial balances afterward used for disease prediction. We illustrate the procedure with a cirrhosis study data. PMGs provide a coherent data analysis for the search of biomarkers in human microbiota. The source code and demo data for PMGs are available at: https://github.com/asliboyraz/PMGs.
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Affiliation(s)
- Aslı Boyraz
- Department of Computer Programming, Recep Tayyip Erdoğan University, Ardeşen Vocational School, Rize, 53400, Turkey
| | - Vera Pawlowsky-Glahn
- Department of Computer Sciences, Applied Mathematics and Statistics, University of Girona, Campus Montilivi, 17003 Girona, Spain
| | - Juan José Egozcue
- Department of Civil and Environmental Engineering, Universitat Politécnica de Catalunya, Barcelona, 08034, Spain
| | - Aybar Can Acar
- Department of Medical Informatics, Middle East Technical University, Ankara Turkey
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Khan MN, Khan SI, Rana MI, Ayyaz A, Khan MY, Imran M. Intermittent fasting positively modulates human gut microbial diversity and ameliorates blood lipid profile. Front Microbiol 2022; 13:922727. [PMID: 36081793 PMCID: PMC9445987 DOI: 10.3389/fmicb.2022.922727] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Aim The aim was to evaluate the impact of intermittent fasting (IF) on human body mass index (BMI) and serum lipid profile thorough constructive rectification of gut microbiota. Methods and results Fourteen healthy women and thirty-one men were included in the study. Their blood and fecal samples were collected before and at the end of the study. Blood parameters, anthropometric values, and gut microbiology were noted to investigate the impact of intermittent fasting (IF) on human gut microbiota and physiology. Our data revealed that IF reduces the body weight and improves blood lipid profile, such as increasing high-density lipoprotein (HDL) and decreasing total cholesterol, triglycerides, and low- and very low-density lipoprotein levels. IF also decreases culturable aerobic bacterial count and increased fungal count. It was also found that the gut metagenome is altered considerably after IF. The human fecal bacterial diversity exhibited significant changes in decreased overall bacterial population, increased bacterial diversity (alpha diversity), and promoted evenness within the bacterial population at the species level. Anti-inflammatory bacteria Lactobacillus and Bifidobacterium were favorably increased, while pathogenic bacteria were decreased. Conclusion Collectively, these results indicated that IF could improve lipid profile and body weight in humans, and the potential mechanisms might be via regulating gut microbiota. Significance and impact of the study We demonstrated for the first time that IF improved body weight and blood lipid profile, indicating that IF could mitigate gut microbiota in humans.
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Affiliation(s)
- Muhammad Nadeem Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Sidra Irshad Khan
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Madeeha Ilyas Rana
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
| | - Arshad Ayyaz
- Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Muhammad Yousaf Khan
- Department of Pathology, Pakistan Institute of Medical Sciences (PIMS), Islamabad, Pakistan
| | - Muhammad Imran
- Department of Microbiology, Faculty of Biological Sciences, Quaid-I-Azam University, Islamabad, Pakistan
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Insoluble and Soluble Dietary Fibers from Kiwifruit (Actinidia deliciosa) Modify Gut Microbiota to Alleviate High-Fat Diet and Streptozotocin-Induced TYPE 2 Diabetes in Rats. Nutrients 2022; 14:nu14163369. [PMID: 36014875 PMCID: PMC9414595 DOI: 10.3390/nu14163369] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/30/2022] Open
Abstract
This study aims to examine the anti-diabetic properties of insoluble and soluble dietary fibers from kiwifruit (KIDF and KSDF) in rats with type 2 diabetes mellitus (T2DM) resulting from a high-fat diet (HFD) and streptozotocin (STZ). Both KIDF and KSDF treatments for four weeks remarkably decreased body weight and increased satiety. In addition, the blood glucose level and circulatory lipopolysaccharide (LPS) content were decreased, while the insulin resistance, inflammatory status, and lipid profiles improved. These anti-diabetic effects might be related to the regulation of gut microbiota and increased SCFA content. The key microbial communities of KIDF and KSDF were different. Furthermore, the KIDF treatment increased the level of total SCFAs and isobutyric acid, while KSDF increased the levels of total SCFAs and butyric acid. The association between critical species and SCFA and between SCFA and biochemical parameters indicated that the mechanisms of KIDF and KSDF on T2DM might be different.
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