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The biosynthetic capabilities of microbes underlie their growth and interactions, playing a prominent role in microbial community structure. For large, diverse microbial communities, prediction of these capabilities is limited by uncertainty about metabolic functions and environmental conditions. To address this challenge, we propose a probabilistic method, inspired by percolation theory, to computationally quantify how robustly a genome-derived metabolic network produces a given set of metabolites under an ensemble of variable environments. We used this method to compile an atlas of predicted biosynthetic capabilities for 97 metabolites across 456 human oral microbes. This atlas captures taxonomically-related trends in biomass composition, and makes it possible to estimate inter-microbial metabolic distances that correlate with microbial co-occurrences. We also found a distinct cluster of fastidious/uncultivated taxa, including several (TM7) species, characterized by their abundant metabolic deficiencies. By embracing uncertainty, our approach can be broadly applied to understanding metabolic interactions in complex microbial ecosystems.
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Mixed networks of conducting and non-conducting nanoparticles show promise in a range of applications where fast charge transport is important. While the dependence of network conductivity on the cond...
Metabolic reprogramming is a hallmark of cancer. The main aim of this work is to integrate a genome-scale metabolic description of tumor cells into a tumor growth model that accounts for the spatiotem...
Metabolic brain network, which is based on functional correlation patterns of F-fluorodeoxyglucose (FDG) positron emission tomography (PET) images, has been widely applied in both basic and clinical n...
Carbohydrates are dietary nutrients that have an influence on cells physiology, cell reproductive capacity and, consequently, the lifespan of organisms. They are used in cellular processes after conve...
The discontinuous jump in the bulk modulus B at the jamming transition is a consequence of the formation of a critical contact network of spheres that resists compression. We introduce lattice models ...
The current study will test the central hypothesis that Glycine supplementation in humans improves Lipid profile and therefore reduces the risk of Atherosclerosis. Secondary outcomes inclu...
This is an prospective open label pilot study conducted over 32 weeks. A total of 25 eligible participants who are infected with HCV and HIV will be recruited from 2 Canadian HIV Trials N...
Eventration corresponds to the dehiscence of the abdominal wall, with passage of peritoneum and / or intra-abdominal viscera, through an acquired orifice of the abdominal wall. It is secon...
This Protocol is intended to facilitate development and testing of new cardiovascular MRI software capabilities by UC Davis Research Faculty, as well as to facilitate the evaluation of new...
This is a prospective, observational study aiming at improving the understanding of the pathophysiology of metabolic disease. As inflammation has been recognized as a key characteristic of...
Measurement of cells' substrate utilization and biosynthetic output for modeling of METABOLIC NETWORKS.
Methods and techniques used to genetically modify cells' biosynthetic product output and develop conditions for growing the cells as BIOREACTORS.
Methods and techniques used to modify or select cells and develop conditions for growing cells for biosynthetic production of molecules (METABOLIC ENGINEERING), for generation of tissue structures and organs in vitro (TISSUE ENGINEERING), or for other BIOENGINEERING research objectives.
A diverse group of metabolic diseases characterized by errors in the biosynthetic pathway of HEME in the LIVER, the BONE MARROW, or both. They are classified by the deficiency of specific enzymes, the tissue site of enzyme defect, or the clinical features that include neurological (acute) or cutaneous (skin lesions). Porphyrias can be hereditary or acquired as a result of toxicity to the hepatic or erythropoietic marrow tissues.
The circulation of the BLOOD through the MICROVASCULAR NETWORK.
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...