Article
Gastroenterology & Hepatology
Weitong Zhang, Xingjian Chen, Ka-Chun Wong
Summary: The advancement in artificial intelligence and genomics has driven research on intestinal diseases, with new strategies utilizing blood and microbiome data, high-throughput sequencing, and machine learning technologies for more accurate diagnosis.
JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Mauro Giuffre, Rita Moretti, Claudio Tiribelli
Summary: The human gut microbiome is important for human health and is the subject of increasing research. Omics-based methods, such as metagenomics and metabolomics, are commonly used for studying the gut microbiome due to their ability to provide high-throughput and high-resolution data. However, there are challenges in using machine learning-based approaches to analyze the relationship between microbiota and disease, such as small sample sizes and inconsistent experimental protocols. Efforts are being made to address these challenges, including the construction of data repositories and improved data transparency guidelines.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biotechnology & Applied Microbiology
Shaodong Wei, Martin Iain Bahl, Simon Mark Dahl Baunwall, Christian Lodberg Hvas, Tine Rask Licht
Summary: This paper lists various types of dysbiosis indexes identified in the literature, introduces their methodology, categorizes them, and discusses their potential descriptive and clinical applications as well as their limitations. The focus is on the methodological approaches available to determine and quantify the dysbiosis condition, rather than on the implications of dysbiosis for disease.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Medicine, General & Internal
Sultan Imangaliyev, Joerg Schloetterer, Folker Meyer, Christin Seifert
Summary: The study shows that multi-view stacked generalization performs better than using a single best machine learning algorithm on pediatric inflammatory bowel disease and adult colorectal cancer patients' cohorts, achieving the best predictive performance on test sets for both datasets.
Review
Microbiology
Benjamin H. Levine, Jessica M. Hoffman
Summary: The human gut contains trillions of microbes that play a crucial role in various health functions, but they are also associated with numerous diseases. Microbiome transplants offer a potential solution to mitigate these health issues caused by the gut microbiome. This article provides an overview of the gut's functional relationships, highlights the diseases directly affected, and explores the history and applications of microbiome transplants in various diseases.
Article
Gastroenterology & Hepatology
Ishan Manandhar, Ahmad Alimadadi, Sachin Aryal, Patricia B. Munroe, Bina Joe, Xi Cheng
Summary: Despite frequent misdiagnosis of inflammatory bowel diseases (IBD), this study shows promising potential of using supervised machine learning modeling to predictively diagnose different types of IBD using fecal gut microbiome data.
AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY
(2021)
Review
Food Science & Technology
Sevda Zoghi, Amin Abbasi, Fatemah Sadeghpour Heravi, Mohammad Hossein Somi, Zeinab Nikniaz, Seyed Yaghoub Moaddab, Hamed Ebrahimzadeh Leylabadlo
Summary: This article discusses the association between the development of celiac disease and gut microbiota, the effects of infectious agents, especially the recent Covid-19 infection in celiac disease patients, and the efficacy of potential therapeutic approaches. Scientific literature suggests that microbiome-based therapy can improve the symptoms and quality of life of celiac disease patients, but the full potential of microbiota-based techniques requires further research.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2022)
Review
Microbiology
Kimberley Parkin, Claus T. Christophersen, Valerie Verhasselt, Matthew N. Cooper, David Martino
Summary: Dysbiosis of the gut microbiome can impact the nervous and immune systems, contributing to inflammatory diseases. Environmental factors during infancy, such as delivery route, antibiotic exposure, and diet, play crucial roles in the development and dysbiosis of the gut microbiome.
Article
Food Science & Technology
Tiantian Li, Shimeng Huang, Jun Wang, Peng Yin, Hujun Liu, Changpo Sun
Summary: The study found that FB1 can lead to degradation of intestinal barrier function, disturbance of cecal and fecal microbiota composition, and inhibition of short chain fatty acid production. Alginate oligosaccharides (AOS) can significantly alleviate FB1-induced damage to the intestine by promoting the growth of beneficial microbes and increasing the production of short chain fatty acids, thereby reducing gut microbial dysbiosis.
FOOD RESEARCH INTERNATIONAL
(2022)
Article
Gastroenterology & Hepatology
Barbara Olendzki, Vanni Bucci, Caitlin Cawley, Rene Maserati, Margaret McManus, Effie Olednzki, Camilla Madziar, David Chiang, Doyle Ward, Randall Pellish, Christine Foley, Shakti Bhattarai, Beth A. McCormick, Ana Maldonado-Contreras
Summary: This study aims to investigate the impact of specific foods on the intestinal microbiome in patients with IBD and explore the interactions between diet and immunity to provide personalized nutrition guidance for IBD patients with dysbiosis-related conditions.
Review
Nutrition & Dietetics
Eleuterio A. Sanchez Romero, Erika Melendez Oliva, Jose Luis Alonso Perez, Sebastian Martin Perez, Silvia Turroni, Lorenzo Marchese, Jorge Hugo Villafane
Summary: This study aimed to review the association between gut microbiome and pain in OA patients and found only three out of 2084 studies supported a relationship, but the results were not conclusive. It also highlighted the lack of high-quality studies and significant technique disparities, making it impossible to draw firm conclusions on the topic.
Article
Nutrition & Dietetics
Awad Mahalhal, Alessandra Frau, Michael D. Burkitt, Umer Z. Ijaz, Christopher A. Lamb, John C. Mansfield, Stephen Lewis, D. Mark Pritchard, Chris S. Probert
Summary: This study demonstrates differential and unique influences of ferric maltol and ferrous sulphate supplements on intestinal microbiota. FS treatment led to an increase in five genera, but FM was not associated with any measurable change. The severity of DSS-induced colitis was greater with FSS than FMS.
Article
Gastroenterology & Hepatology
Aleksandra Kovaleva, Elena Poluektova, Roman Maslennikov, Anna Karchevskaya, Oleg Shifrin, Andrey Kiryukhin, Aleksandr Tertychnyy, Leonid Kovalev, Marina Kovaleva, Olga Lobanova, Anna Kudryavtseva, George Krasnov, Vladimir Ivashkin
Summary: This study found that patients with IDFO had increased biomarkers of intestinal barrier disorders at multiple levels. These disruptions were associated with the severity of clinical symptoms and changes in the gut microbiota.
DIGESTIVE DISEASES AND SCIENCES
(2023)
Article
Gastroenterology & Hepatology
Roman Maslennikov, Vladimir Ivashkin, Irina Efremova, Elena Poluektova, Anna Kudryavtseva, George Krasnov
Summary: This study found a relationship between small intestinal bacterial overgrowth (SIBO) and gut dysbiosis in patients with cirrhosis. Patients with SIBO had higher levels of Firmicutes and Fusobacteria, and lower levels of Bacteroidetes compared to patients without SIBO. However, gut dysbiosis and SIBO are likely independent disorders in cirrhosis.
WORLD JOURNAL OF GASTROENTEROLOGY
(2022)
Review
Biochemistry & Molecular Biology
Mattia Di Stefano, Simona Santonocito, Alessandro Polizzi, Rodolfo Mauceri, Giuseppe Troiano, Antonino Lo Giudice, Alessandra Romano, Marco Mascitti, Gaetano Isola
Summary: The human body is colonized by a diverse microbial community known as the microbiota, which plays a crucial role in influencing human health throughout life. The oral microbiota forms complex biofilms and interactions, contributing to the host's resistance to antimicrobial agents and maintaining a balanced symbiotic relationship. Understanding the functions and interactions of the microbiota is essential for developing diagnostic, therapeutic, and preventive strategies. This review focuses on the connection between the oral and gut microbiomes, and how alterations in these microbial communities can lead to oral and intestinal illnesses, as well as the potential role of probiotics in ameliorating inflammation and microbial dysbiosis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Senying Lai, Longhao Jia, Balakrishnan Subramanian, Shaojun Pan, Jinglong Zhang, Yanqi Dong, Wei-Hua Chen, Xing-Ming Zhao
Summary: Extrachromosomal mobile genetic elements (eMGEs), such as phages and plasmids, are important for genome evolution and shaping microbial communities, but are still poorly understood. The mMGE catalog contains comprehensive annotations and prevalence calculations for over 500,000 non-redundant eMGEs from diverse human metagenomic samples. Users can browse, query, and access all contents easily through a user-friendly interface and a BLAST server.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Liting Song, Shaojun Pan, Zichao Zhang, Longhao Jia, Wei-Hua Chen, Xing-Ming Zhao
Summary: The human brain, the most complex organ, can now be dissected at the single-cell level with the help of single-cell RNA sequencing technologies. STAB, a database containing single-cell transcriptomes from multiple brain regions and developmental periods, provides insights into cell compositions, regional differences, and temporal dynamics in the human brain, aiding in understanding brain development and neuropsychiatric disorders.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Sanathoi Gurumayum, Puzi Jiang, Xiaowen Hao, Tulio L. Campos, Neil D. Young, Pasi K. Korhonen, Robin B. Gasser, Peer Bork, Xing-Ming Zhao, Li-jie He, Wei-Hua Chen
Summary: OGEE is an online database focusing on gene essentiality, providing data for 91 species and expanding collection of human essential genes for cancer research. It includes experimentally tested gene essentiality data and associated gene properties, allowing researchers to study the complex interplays between gene functions and environmental/experimental perturbations.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Yanze Li, Wenming Cao, Na L. Gao, Xing-Ming Zhao, Wei-Hua Chen
Summary: This study aimed to identify human gut microbes that undergo significant and consistent changes after transplantation into germ-free mice. The results showed that only about 47% of the human gut microbes could be re-established at the species level in mice, and more than 1/3 of them underwent significant changes. Most of the microbes that underwent significant changes were consistent across multiple experimental settings, providing important information for researchers using mice in gut microbiota studies.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Die Dai, Jiaying Zhu, Chuqing Sun, Min Li, Jinxin Liu, Sicheng Wu, Kang Ning, Li-Jie He, Xing-Ming Zhao, Wei-Hua Chen
Summary: GMrepo is a curated database of human gut metagenomes aimed at increasing data reusability and accessibility, and enabling cross-project and phenotype comparisons. The latest version, GMrepo v2, includes more projects and samples obtained through different sequencing methods. Various disease markers have been identified and compared across datasets to facilitate the discovery of consistent microbial markers.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Hanbo Jin, Guoru Hu, Chuqing Sun, Yiqian Duan, Zhenmo Zhang, Zhi Liu, Xing-Ming Zhao, Wei-Hua Chen
Summary: mBodyMap is a curated database for microbes across the human body, aiming to promote the reusability of human-associated metagenomic data and assist with the identification of disease-associated microbes. It organizes samples based on their association with human diseases and body sites to enable cross-dataset integration and comparison, providing pre-computed abundances and prevalence data for users to access.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Menglu Jin, Jingchao Chen, Xueyang Zhao, Guoru Hu, Hailei Wang, Zhi Liu, Wei-Hua Chen
Summary: Bacteriophages are effective alternatives to traditional antimicrobial agents and can modulate the gut microbiota. Researchers engineered a phage to specifically target and eliminate a pathogenic strain of Escherichia coli, showing enhanced killing ability without affecting other strains or causing resistance. This study highlights the potential of engineered phages for targeted treatment and the prevention of antimicrobial resistance.
MICROBIOLOGY SPECTRUM
(2022)
Article
Gastroenterology & Hepatology
Min Li, Jinxin Liu, Jiaying Zhu, Huarui Wang, Chuqing Sun, Na L. Gao, Xing-Ming Zhao, Wei-Hua Chen
Summary: Cross-cohort validation of gut microbiome-based machine-learning classifiers for 20 diseases was systematically evaluated. High predictive accuracies were obtained in intra-cohort validation using single-cohort classifiers (around 0.77 AUC), except for intestinal diseases (around 0.73 AUC) in cross-cohort validation. Combined-cohort classifiers trained on samples from multiple cohorts were then built to improve validation of non-intestinal diseases, and the required sample size to achieve >0.7 validation accuracies was estimated. Higher validation performance was observed for classifiers using metagenomic data compared to 16S amplicon data in intestinal diseases. Marker Similarity Index was used to quantify cross-cohort marker consistency and similar trends were observed. Overall, the results support the gut microbiome as an independent diagnostic tool for intestinal diseases and reveal strategies to improve cross-cohort performance based on identified determinants of consistent cross-cohort gut microbiome alterations.
Article
Microbiology
Xueyang Zhao, Chuqing Sun, Menglu Jin, Jingchao Chen, Lulu Xing, Jin Yan, Hailei Wang, Zhi Liu, Wei-Hua Chen
Summary: In this study, the first gut phage of Lactiplantibacillus plantarum, Gut-P1, was reported. It was found to be highly prevalent in the human gut and strongly inhibits the growth of L. plantarum, potentially impeding its application in humans. Interestingly, Gut-P1 was identified only in enrichment culture, indicating the limitations of bulk sequencing in detecting low-abundance but prevalent phages and highlighting the unexplored diversity of the human gut virome.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Zi-Xin Qin, Guo-Zhong Chen, Qian-Qian Yang, Ying-Jian Wu, Chu-Qing Sun, Xiao-Man Yang, Mei Luo, Chun-Rong Yi, Jun Zhu, Wei-Hua Chen, Zhi Liu
Summary: We integrated RNA-seq data for laboratory studies with clinical microarray data for the first time, obtaining interactions between V. cholerae genes, comparing similarity between clinical human samples and current experimental conditions, and uncovering major functional modules under different conditions. By integrating transcriptome data, we identified active or silent genes and important functional modules of V. cholerae. Analysis of hub genes in functional modules revealed uniqueness of clinical human samples, but also similarity with specific expression patterning and treatment groups. Novel protein interactions were discovered within transposon functional modules through protein-protein interaction analysis.
MICROBIOLOGY SPECTRUM
(2023)
Article
Mathematical & Computational Biology
Yuhao Chi, Ruicheng Qi, Yue Zhou, Huige Tong, Hanbo Jin, Christoph W. Turck, Wei-Hua Chen, Guang-Zhong Wang
Summary: A database called scBrainMap has been developed to identify and characterize different types of brain cells and their genetic markers. It contains information from 6,577,222 single cells across 14 species, 124 brain regions, and 20 disease states. The database enables customized queries for exploring the role of cell types in brain function.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2023)
Article
Gastroenterology & Hepatology
Jiaying Zhu, Chuqing Sun, Min Li, Guoru Hu, Xing-Ming Zhao, Wei-Hua Chen
Summary: This study aims to compare the effects of proton pump inhibitors (PPIs) and histamine-2 receptor antagonists (H2RAs) on the gut microbiota. The results showed that PPIs had a greater impact on the gut microbiome and oral-to-gut transmission compared to H2RAs. PPI usage led to a significant increase in both the number and total abundance of oral species present in the gut, and gut microbiome-based machine learning classifiers could accurately distinguish PPI users from non-PPI users.