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bioRxiv · 10.64898/2025.12.22.696022

Modular metagenomic analysis of pan-domain symbioses with MAGUS

Al-Ghalith, G. A.·Ryon, K. A.·Santoro, E.·Barno, A.·Casartelli, M.·Villela, H.·Diana, S. C.·Henriksen, J. R.·Carpenter, G. E.·Quatrini, P.·Milazzo, M.·Patel, C. J.·Peixoto, R.·Tierney, B. T.
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Abstract

Metagenomic analysis of deeply sequenced, eukaryotic-dominant symbiotic communities can be difficult for many metagenomic workflows. Here, we present MAGUS, a bioinformatic toolkit that uses a suite of custom bioinformatic methods for iterative genome assembly and filtering of pan-domain communities, where eukaryotes, bacteria, viruses, and functionally annotated gene catalogs are resolved and analyzed over a series of interconnected, modular software components. We evaluated MAGUS using deeply sequenced (median depth: 579 million reads) ten samples of hard corals, soft corals, and hydrozoans, which comprise complex, eukaryote-dominated symbiotic communities. We successfully resolved phylogenetically comparable host (N = 10), algal (N = 6), bacterial (N = 55), and viral (N = 160,925) genomes, as well as a gene catalog comprising 15,369,684 non-redundant genes (7.6% functionally annotated). MAGUS is available on GitHub (https://github.com/two-frontiers-project/2FP_MAGUS/).

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Al-Ghalith, G. A., Ryon, K. A., Santoro, E., Barno, A., Casartelli, M., Villela, H., Diana, S. C., Henriksen, J. R., Carpenter, G. E., Quatrini, P., Milazzo, M., Patel, C. J., Peixoto, R., Tierney, B. T.. 2025-12-24. Modular metagenomic analysis of pan-domain symbioses with MAGUS. https://doi.org/10.64898/2025.12.22.696022

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