China 
Africa 
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Graphical Models in Genetics, Genomics, and Metagenomics
Published in Marloes Maathuis, Mathias Drton, Steffen Lauritzen, Martin Wainwright, Handbook of Graphical Models, 2018
Metagenomics is an emerging field that holds a great promise in biomedical research. Most of the published works are still at the level of establishing association between taxa composition and microbial gene abundances with various covariates or disease states. A major challenge is to go beyond association studies and elucidate causalities. Mathematical modeling of the human gut microbiome at a genome scale is a useful tool to decipher microbe-microbe, diet-microbe and microbe-host interactions [38]. Graphical models, especially causal graphical models, provide a natural and useful tool for elucidating such causal pathways. Parallel to advances in sequencing technologies, publicly available database of experimentally elucidated metabolic pathways from all domains of life, such as MetaCyc [8], is becoming more and more complete. Currently, MetaCyc contains more than 2400 pathways from 2788 different organisms, including those involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes and genes. This provides important resources for analysis of microbiome and metagenomic data. Figure 21.6 presents an example of such a metabolic network. How to incorporate the metabolic networks/pathways into analysis of metagenomic data is an important area for future research.
Metabolic modeling of synthetic microbial communities for bioremediation
Published in Critical Reviews in Environmental Science and Technology, 2023
Lvjing Wang, Xiaoyu Wang, Hao Wu, Haixia Wang, Yihan Wang, Zhenmei Lu
Currently, the genetic and genomic knowledge base (BiGG Models) (King et al., 2016) integrates 108 high-quality, manually curated GEMs with a set of specified identifiers, such as iAF1260 for Escherichia coli str. K-12 substr. MG1655, iNJ661 for Mycobacterium tuberculosis H37Rv, iMM904 for Saccharomyces cerevisiae S288C, and Recon3D for Homo sapiens. BioCyc is a collection of 20,005 pathways/genome databases for modeling eukaryotes and thousands of microbes that contain 470 databases of archaea, 19416 databases of bacteria, and 37 databases of eukaryotes. Only EcoCyc (Keseler et al., 2021) and MetaCyc are available to freely access, while the remaining databases of BioCyc, such as HumanCyc, BsubCyc, and YeastCyc, require a paid subscription. A total of 2777 GEMs in BioModels (Malik-Sheriff et al., 2020) have been developed, which contain 1053 manually curated and 1373 non-curated models. Until fairly recently, 818 GEMs of gut microbes and 1 human reconstruction were included in the Virtual Metabolic Human database (Noronha et al., 2019), and 41 plant models were reconstructed using the PlantSEED resource (Seaver et al., 2014) in the ModelSEED database (Henry et al., 2010). The draft reconstruction of GEMs requires manual refinement and curation, which might be a time-consuming procedure despite the abundance of automatic reconstruction and gap-filling programs.