Article
Microbiology
Jue Xu, Yue Lan, Xinqi Wang, Ke Shang, Xu Liu, Jiao Wang, Jing Li, Bisong Yue, Meiying Shao, Zhenxin Fan
Summary: Through multi-omics analysis, we found significant changes in the oral and gut microbiomes of aged Chinese rhesus macaques (CRs), including a decrease in probiotic abundance and an increase in pathogenic bacterial abundance. We also identified multiple metabolic issues, immunological disorders, and oral and gut diseases in aged CRs. Tryptophan metabolism was found to be critical for the physiological health of aged CRs.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Gastroenterology & Hepatology
Consuelo Sauceda, Charlie Bayne, Khadijeh Sudqi, Antonio Gonzalez, Parambir S. Dulai, Rob Knight, David J. Gonzalez, Carlos G. Gonzalez
Summary: Inflammatory Bowel Disease (IBD) is a chronic immune-mediated inflammatory disease of the gastrointestinal tract that is increasing in public burden. Stool-based multi-omics is a promising approach for characterizing host-gut microbiome interactions and advancing IBD research and precision medicine. This review highlights the historical and recent findings from stool-based multi-omic studies and discusses common pitfalls, issues, and limitations for future research.
Article
Health Care Sciences & Services
Marianthi Logotheti, Panagiotis Agioutantis, Paraskevi Katsaounou, Heleni Loutrari
Summary: Asthma is a multifactorial inflammatory disorder with diverse clinical manifestations. Microbiota dysbiosis may lead to chronic inflammation, including in conditions like asthma. By integrating microbiome analysis, there is potential for a better understanding of asthma complexity and improving treatment options.
JOURNAL OF PERSONALIZED MEDICINE
(2021)
Article
Immunology
Lei Chen, Sai Wang, Yupeng Zhang, Ye Li, Xiangbin Zhang, Junyi Ma, Xuelun Zou, TianXing Yao, Si Li, Junyou Chen, Huifang Zhou, Lianxu Wu, Yanhong Zhou, Le Zhang
Summary: The gut microbiome and its metabolites are associated with the severity of intracerebral hemorrhage (ICH), suggesting their potential as therapeutic targets.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Gastroenterology & Hepatology
Kathie A. Mihindukulasuriya, Ruben A. T. Mars, Abigail J. Johnson, Tonya Ward, Sambhawa Priya, Heather R. Lekatz, Krishna R. Kalari, Lindsay Droit, Tenghao Zheng, Ran Blekhman, Mauro D'Amato, Gianrico Farrugia, Dan Knights, Scott A. Handley, Purna C. Kashyap
Summary: The gut virome is stable over time but varies among subsets of patients with IBS. Specific changes in phage populations were identified in different IBS subsets, and they were correlated with bacterial composition and diet.
Review
Immunology
Shivani Singh, Jake G. Natalini, Leopoldo N. Segal
Summary: In recent years, our understanding of the microbial world within us has been revolutionized by culture-independent techniques. Advances in bioinformatics have enabled comprehensive analysis of the role of the human microbiome in different conditions. Despite challenges in lower airway research, new approaches will facilitate further progress.
MUCOSAL IMMUNOLOGY
(2022)
Review
Cardiac & Cardiovascular Systems
Chaoying Zhan, Tong Tang, Erman Wu, Yuxin Zhang, Mengqiao He, Rongrong Wu, Cheng Bi, Jiao Wang, Yingbo Zhang, Bairong Shen
Summary: Myocardial infarction is a cardiovascular disease with unclear etiological mechanism. Omics technologies have provided new opportunities for studying its molecular mechanism and identifying biomarkers. The multi-omics approach can reveal the interaction network among molecules and overcome the limitations of single-omics approaches.
FRONTIERS IN CARDIOVASCULAR MEDICINE
(2023)
Review
Biochemistry & Molecular Biology
Qing Wang
Summary: Bacteriophage-eukaryotic cell interaction forms the basis of Phage Display technology, enabling the study of protein interactions and personalized cancer therapeutics. The direct connection between proteins and their encoding DNA provides valuable insights into cancer mutations.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Microbiology
Ling Xu, Grady Pierroz, Heidi M-L Wipf, Cheng Gao, John W. Taylor, Peggy G. Lemaux, Devin Coleman-Derr
Summary: Holo-omics studies can provide a comprehensive perspective of molecular networks within the plant microbiome system and offer important opportunities for improving plant fitness. However, challenges such as the lack of vetted analytical frameworks, publicly available tools, and technical expertise hinder the advancement of holo-omics research.
Article
Microbiology
Zhengzheng Yan, Boxuan Chen, Yuqiong Yang, Xinzhu Yi, Mingyuan Wei, Gertrude Ecklu-Mensah, Mary M. Buschmann, Haiyue Liu, Jingyuan Gao, Weijie Liang, Xiaomin Liu, Junhao Yang, Wei Ma, Zhenyu Liang, Fengyan Wang, Dandan Chen, Lingwei Wang, Weijuan Shi, Martin R. Stampfli, Pan Li, Shenhai Gong, Xia Chen, Wensheng Shu, Emad M. El-Omar, Jack A. Gilbert, Martin J. Blaser, Hongwei Zhou, Rongchang Chen, Zhang Wang
Summary: Multi-omics analyses of sputum samples from patients with COPD reveal the potential therapeutic targets of host-microbe interactions. The study explores the mechanistic role of the airway microbiome in COPD and identifies specific microbial metabolic products associated with host gene expression. Further experiments show that these microbial metabolites can mitigate neutrophilic inflammation and lung function decline through macrophage-epithelial cell cross-talk.
NATURE MICROBIOLOGY
(2022)
Article
Immunology
Ying Chen, Yunchao Huang, Xiaojie Ding, Zhenlin Yang, Liang He, Mingjie Ning, Zhenghong Yang, Daqian He, Lijuan Yang, Zhangyi Liu, Yan Chen, Guangjian Li
Summary: This study investigated the influence of familial lung cancer (FLC) and indoor air pollution (IAP) on the lung microbiome of lung cancer patients, and compared host gene expression patterns with their microbiome. The results showed that the lung microbiome of lung cancer patients was associated with factors such as gender, age, blood type, histology type, TNM stage, smoking, and IAP. Smoking and IAP were found to significantly decrease the biodiversity of specific microbes. RNA-seq analysis highlighted gene pathways associated with carcinogenesis and compromised immune system. The findings provide useful information for studying the interaction between environmental carcinogens, population genetic background, and the diversified lung microbiome.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Microbiology
Gouxin Huang, Raees Khan, Yilin Zheng, Ping-Chin Lee, Qingnan Li, Imran Khan
Summary: Research in the field of gut microbiota has shown that these microbes play a crucial role in human health, affecting drug efficacy and toxicity. Intra-individual variability of gut microbiota can result in biased drug responses. Various methods, such as prebiotic and probiotic interventions, can be used to treat diseases by altering gut microbiota composition.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Samradhi Singh, Devojit Kumar Sarma, Vinod Verma, Ravinder Nagpal, Manoj Kumar
Summary: Personalized medicine utilizing omics approaches has the potential to treat metabolic disorders. By analyzing various data from patients, doctors can identify diagnostic and predictive biomarkers and develop individualized treatment plans. Incorporating advanced technologies like artificial intelligence and machine learning enables data consolidation for decision-making and the establishment of ethical protocols.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
(2023)
Article
Microbiology
Shi Huang, Tao He, Feng Yue, Xiujun Xu, Lijiang Wang, Pengfei Zhu, Fei Teng, Zheng Sun, Xiaohui Liu, Gongchao Jing, Xiaoquan Su, Lijian Jin, Jiquan Liu, Jian Xu
Summary: The research identified periodontitis-like microbiome dysbiosis in an asymptomatic suboptimal health (SoH) stage as early as 24 to 72 h after oral-hygiene pause. The SoH stage features a swift, full activation of multiple salivary cytokines but a steep synergetic decrease of plaque-derived betaine and Rothia spp. The microbial ecology during early gingivitis is highly similar to that in periodontitis under both taxonomical and functional contexts. Unexpectedly, exposures to gingivitis can accelerate over 10-fold the normal rate of oral microbiota aging.
Review
Food Science & Technology
Anastasios Tsoungos, Violeta Pemaj, Aleksandra Slavko, John Kapolos, Marina Papadelli, Konstantinos Papadimitriou
Summary: This review explores recent advances in table olive research through omics and meta-omics approaches, offering insights into the genomic, metagenomic, and metabolomic analysis of the microbial community in table olives. These methods hold the promise of groundbreaking advances in table olive processing technology.
Article
Biochemical Research Methods
Barry Lorbetskie, Taryn White, Marybeth Creskey, Xu Zhang, Michel Girard, Roger Y. Tam, Simon Sauve, Huixin Lu
Summary: Protein-based vaccines are important in combating the COVID-19 pandemic. This study developed a selective reversed-phase HPLC method for the bioanalytical assessment of the S-protein in COVID-19 vaccines, allowing efficient separation of the intact S-protein monomer from its subunits.
JOURNAL OF CHROMATOGRAPHY A
(2022)
Article
Microbiology
Caitlin M. A. Simopoulos, Zhibin Ning, Leyuan Li, Mona M. Khamis, Xu Zhang, Mathieu Lavallee-Adam, Daniel Figeys
Summary: Metaproteomics is a useful tool for studying microbial communities, but the data acquisition process can be time-consuming and resource-intensive. In this study, the researchers developed a computational framework called MetaProClust-MS1 to prioritize samples for follow-up analysis using tandem mass spectrometry (MS/MS). The framework successfully identified microbial responses and disease diagnostic features in gut microbiome data. The study also demonstrated the potential of MetaProClust-MS1 in clinical settings and large-scale metaproteomic screening.
Article
Microbiology
Zhongzhi Sun, Wenju Wang, Leyuan Li, Xu Zhang, Zhibin Ning, Janice Mayne, Krystal Walker, Alain Stintzi, Daniel Figeysa
Summary: The composition and function of the human gut microbiome are closely related to human health. Sugar substitute sweeteners, as commonly used food additives, have potential impacts on the functionality of the microbiome. This study systematically investigated the responses of the human gut microbiome to commonly used sugar substitute sweeteners and revealed the associations between sweetener properties and metaproteomic responses of individual microbiomes.
MICROBIOLOGY SPECTRUM
(2022)
Review
Nutrition & Dietetics
Kendra Hodgkinson, Faiha El Abbar, Peter Dobranowski, Juliana Manoogian, James Butcher, Daniel Figeys, David Mack, Alain Stintzi
Summary: Butyrate, produced by gut microbiota through fermentation of dietary fiber, serves as a key energy source for colonocytes. It has important roles in gastrointestinal health, impacting both host and microbial functions. Maintaining optimal butyrate levels improves gastrointestinal health by supporting colonocyte function, decreasing inflammation, maintaining the gut barrier, and promoting a healthy microbiome. However, increasing butyrate levels in humans and reversing negative outcomes have yielded mixed results, despite its protective actions in intestinal diseases.
CLINICAL NUTRITION
(2023)
Article
Biochemical Research Methods
Kai Cheng, Zhibin Ning, Leyuan Li, Xu Zhang, Joeselle M. Serrana, Janice Mayne, Daniel Figeys
Summary: The studies of microbial communities have become increasingly important in various fields, and metaproteomics is a powerful tool for interpreting the roles of community members. However, analyzing metaproteomic data sets at the genome resolution is still challenging. In this study, a specially designed tool called MetaLab-MAG was developed for characterizing microbiomes from metagenome-assembled genome databases.
JOURNAL OF PROTEOME RESEARCH
(2022)
Article
Biochemical Research Methods
Marybeth Creskey, Leyuan Li, Zhibin Ning, Emily E. F. Fekete, Janice Mayne, Krystal Walker, Anna Ampaw, Robert Ben, Xu Zhang, Daniel Figeys
Summary: This study demonstrates that the TMT labeling procedures can be simplified by using pre-aliquoted dry TMT reagents, which achieve high labeling efficiency in both microbiome and mammalian cell line samples. The workflow was successfully applied to analyze 97 samples and consistently revealed microbiome responses. This study supports the use of pre-aliquoted, dried, and stored TMT reagents for robust quantitative proteomics and metaproteomics in high throughput applications.
Article
Multidisciplinary Sciences
Leyuan Li, Tong Wang, Zhibin Ning, Xu Zhang, James Butcher, Joeselle M. M. Serrana, Caitlin M. A. Simopoulos, Janice Mayne, Alain Stintzi, David R. R. Mack, Yang-Yu Liu, Daniel Figeys
Summary: Functional redundancy is a crucial ecosystem property in which different species contribute to the ecosystem in similar ways through redundant functions. This study quantifies the proteome-level functional redundancy (FRp) in the human gut microbiome using metaproteomics. The research reveals high proteome-level functional redundancy and nestedness in the human gut proteomic content networks. The findings show that proteomic content networks' nested topology and small functional distances between taxa contribute to high FRp. FRp outperforms diversity indices in detecting significant microbiome responses to various environmental factors.
NATURE COMMUNICATIONS
(2023)
Article
Gastroenterology & Hepatology
Emily Ef Fekete, Daniel Figeys, Xu Zhang
Summary: Mounting evidence suggests that the gut microbiome plays a causative or correlative role in various diseases, such as gastrointestinal diseases, metabolic diseases, neurological disorders, and cancers. Therefore, there have been efforts to develop and apply therapies that target the gut microbiota for disease treatment and wellness maintenance. This review summarizes the current development of gut microbiota-directed therapeutics, emphasizes the importance of advanced -omics approaches for evaluating microbiota-type therapies, and discusses the clinical and regulatory challenges. It also explores the development and potential application of ex vivo microbiome assays and in vitro intestinal cellular models. Overall, this review provides a comprehensive view of the promises and challenges in the emerging field of microbiome-directed human healthcare.
Article
Biochemical Research Methods
Kai Cheng, Zhibin Ning, Leyuan Li, Xu Zhang, Joeselle M. Serrana, Janice Mayne, Daniel Figeys
Summary: The research on microbial communities has gained attention in agriculture, environment, and human health. Metaproteomics has become a powerful tool to understand the roles of microbes through analyzing their expressed proteins. However, analyzing metaproteomic data at genome resolution is challenging due to the lack of efficient bioinformatics tools. Here, we introduce MetaLab-MAG, a specialized tool for microbiome characterization from metagenome-assembled genomes databases. MetaLab-MAG performs well compared to directly searching the gene catalog protein database, allowing quantification of genome-level microbiota compositions and supporting different quantification strategies. It overcomes the obstacles in metaproteomic data analysis and provides comprehensive information from microbiomes to researchers.
JOURNAL OF PROTEOME RESEARCH
(2023)
Article
Biochemistry & Molecular Biology
Zhongzhi Sun, Zhibin Ning, Kai Cheng, Haonan Duan, Qing Wu, Janice Mayne, Daniel Figeys
Summary: Metaproteomics studies functional changes in the human gut microbiome and peptide identification is a crucial step in this research. However, the large search space complicates peptide identification methods. This study constructed MetaPep, a core peptide database, and demonstrated its importance for human gut metaproteomics research.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)