Hirose, Yujiro Zielinski, Daniel C. Poudel, Saugat Rychel, Kevin Baker, Jonathon L. Toya, Yoshihiro Yamaguchi, Masaya Heinken, Almut Thiele, Ines Kawabata, Shigetada
...
Published in
mSystems
Genome-scale models (GEMs) play a crucial role in investigating bacterial metabolism, predicting the effects of inhibiting specific metabolic genes and pathways, and aiding in the identification of potential drug targets. Here, we have developed the first GEM for the S. pyogenes highly virulent serotype, M1, which we name iYH543. The iYH543 achieve...
Casey, John Bennion, Brian D’haeseleer, Patrik Kimbrel, Jeffrey Marschmann, Gianna Navid, Ali
Published in
Frontiers in Systems Biology
Mechanistic, constraint-based models of microbial isolates or communities are a staple in the metabolic analysis toolbox, but predictions about microbe-microbe and microbe-environment interactions are only as good as the accuracy of transporter annotations. A number of hurdles stand in the way of comprehensive functional assignments for membrane tr...
Tueffers, Leif Batra, Aditi Zimmermann, Johannes Botelho, João Buchholz, Florian Liao, Junqi Mendoza Mejía, Nicolás Munder, Antje Klockgether, Jens Tüemmler, Burkhard
...
Published in
Microbiology Spectrum
New treatment strategies are urgently needed for high-risk pathogens such as the opportunistic and often multidrug-resistant pathogen Pseudomonas aeruginosa. Here, we characterize the major P. aeruginosa clone type (mPact) panel. It consists of 20 strains with different origins that cover the major clone types of the species as well as its genomic ...
Furtado, Kathleen L. Plott, Lucas Markovetz, Matthew Powers, Deborah Wang, Hao Hill, David B. Papin, Jason Allbritton, Nancy L. Tamayo, Rita
Published in
mSphere
Clostridioides difficile results in upward of 250,000 infections and 12,000 deaths annually in the United States. Community-acquired infections continue to rise, and recurrent disease is common, emphasizing a vital need to understand C. difficile pathogenesis. C. difficile undoubtedly interacts with colonic mucus, but the extent to which the pathog...
Paulay, Amandine Grimaud, Ghjuvan M. Caballero, Raphaël Laroche, Béatrice Leclerc, Marion Labarthe, Simon Maguin, Emmanuelle
Published in
mSystems
Microbial proteolysis is understudied despite the availability of dietary proteins for the gut microbiota. Here, the proteolytic potential of the gut symbiont Bacteroides caccae was analyzed for the first time using pan-genomics. This sketches a well-equipped bacteria for protein breakdown, capable of producing 156 different proteases with a broad ...
Liu, Danni Nagana Gowda, G A Jiang, Zhongli Alemdjrodo, Kangni Zhang, Min Zhang, Dabao Raftery, Daniel
Published in
Proceedings of the National Academy of Sciences of the United States of America
Blood metabolite levels are affected by numerous factors, including preanalytical factors such as collection methods and geographical sites. These perturbations have caused deleterious consequences for many metabolomics studies and represent a major challenge in the metabolomics field. It is important to understand these factors and develop models ...
Liu, Danni Nagana Gowda, G Jiang, Zhongli Alemdjrodo, Kangni Zhang, Min Zhang, Dabao Raftery, Daniel
Blood metabolite levels are affected by numerous factors, including preanalytical factors such as collection methods and geographical sites. These perturbations have caused deleterious consequences for many metabolomics studies and represent a major challenge in the metabolomics field. It is important to understand these factors and develop models ...
Thi Doan, Dieu Kremling, Andreas Morchain, Jérôme
Abstract Population heterogeneity is due to intrinsic and extrinsic noises; cell to cell variability is related to cell partitioning at division and external forcing by the environment. In this article, a Monte‐Carlo calculation of integral source terms is coupled to a compartment approach. The biological phase is represented by an ensemble of disc...
Han, Fang Li, Huiquan Lyu, Ermeng Zhang, Qianqian Gai, Haoyu Xu, Yunfang Bai, Xuemei He, Xueqian Khan, Abdul Qadir Li, Xiaolin
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Published in
Applied and Environmental Microbiology
The present study demonstrates, for the first time, that the BjaI/BjaR1 QS system of Bradyrhizobium diazoefficiens has a significant impact on its nodulation and nitrogen fixation capability in soybean by positively regulating NodD2 expression and bacterial nitrogen metabolism. Moreover, it provides novel insights into the importance of suppressing...
Sun, Xinli Xie, Jiyu Zheng, Daoyue Xia, Riyan Wang, Wei Xun, Weibing Huang, Qiwei Zhang, Ruifu Kovács, Ákos T. Xu, Zhihui
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Published in
mSystems
Co-occurrence network analysis is an effective tool for predicting complex networks of microbial interactions in the natural environment. Using isolates from a rhizosphere, we constructed multi-species biofilm communities and investigated co-occurrence patterns between microbial species in genome-scale metabolic models and in vitro experiments. Acc...
