User:Biomolecula/AGORA2

AGORA2 (abbreviation of Assembly of Gut Organisms through Reconstruction and Analysis, version 2) is a software tool that allows predictive models to estimate de capacity of the gut microbiota to degradate or metabolize drugs. Specifically, it performs metabolic genome-scale reconstructions for more than 7,000 strains.

AGORA2 was developed in 2020 by a research group of the University of Galway (Irland) and has raised interest for its potential use in personalized medicine.

To perform the AGORA2 reconstructions, they first expanded the taxonomic coverage of AGORA1.03 with genomic sequences obtained from literature searches and databases, such as NCBI or PubSEED. The data collection also provided information of the physiological and biochemical characteristics of each strain, which allowed to perform strain-resolved reconstructions.

The data obtained was integrated through the semi-automatic program KBase, thus generating a first draft. These reconstructions were transferred to the VHM website to test the thermodynamic, biochemical and structural consistency of the metabolic reactions. The generated inconsistencies were manually analyzed and contrasted with bibliographic and PUBSEED data, which led to the substitution of more than 650 metabolic reactions.

The reconstructions obtained were subjected to a test bench to check their predictive capacity as metabolic models. If the reconstructions resulted in false predictions, the data curation and refinement process was repeated until a positive result was obtained.

Version history
In 2017, researchers from the University of Galway, published AGORA on the VMH website (Virtual Metabolic Human), a page that collects information on human and microbial metabolism. AGORA was developed as an alternative to semi-automated reconstruction tools such as CarveMe or gapseq, which don't provide strain-level information. Specifically, AGORA consisted of 773 reconstructions, covering 605 species and 14 phyla.

In 2019, it was expanded to 818 rebuilds, resulting in version AGORA1.03.

En 2020, taxonomic coverage was expanded resulting in AGORA2 with 7,302 reconstructions, comprising 1644 species and 24 phyla.


 * Heinken, A., Hertel, J., Acharya, G., Ravcheev, D. A., Nyga, M., Okpala, O. E., Hogan, M., Magnúsdóttir, S., Martinelli, F., Nap, B., Preciat, G., Edirisinghe, J. N., Henry, C. S., Fleming, R. M. T., & Thiele, I. (2023). Genome-scale metabolic reconstruction of 7,302 human microorganisms for personalized medicine. Nature biotechnology, 41(9), 1320–1331. https://doi.org/10.1038/s41587-022-01628-0
 * Heinken, A., Acharya, G., Ravcheev, D. A., Hertel, J., Nyga, M., Okpala, O., Hogan, M., Magnúsdóttir, S., Martinelli, F., Nap, B., Preciat, G., Edirisinghe, J. N., Henry, C. S., Fleming, R. M. T., & Thiele, I. (2020).AGORA2: Large scale reconstruction of the microbiome highlights wide-spread drug-metabolising capacities. bioRxiv. https://doi.org/10.1101/2020.11.09.37545