Unveiling soil microbial diversity through ultra-deep short-read metagenomic sequencing and co-assembly

References

[1] Delmont, Tom O., Patrick Robe, Sébastien Cecillon, Ian M. Clark, Florentin Constancias, Pascal Simonet, Penny R. Hirsch, and Timothy M. Vogel. 2011. “Accessing the Soil Metagenome for Studies of Microbial Diversity.” Applied and Environmental Microbiology 77: 1315-1324. https://doi.org/10.1128/AEM.01526-10

[2] Torsvik, Vigdis, and Lise Øvreås. 2002. “Microbial Diversity and Function in Soil: From Genes to Ecosystems.” Current Opinion in Microbiology 5: 240-245. https://doi.org/10.1016/S1369-5274(02)00324-7

[3] Singh, Brajesh K., Zhen-Zhen Yan, Maxine Whittaker, Ronald Vargas, and Ahmed Abdelfattah. 2023. “Soil Microbiomes Must Be Explicitly Included in One Health Policy.” Nature Microbiology 8: 1367-1372. https://doi.org/10.1038/s41564-023-01386-y

[4] Crowther, T. W., J. van den Hoogen, J. Wan, M. A. Mayes, A. D. Keiser, L. Mo, C. Averill, and D. S. Maynard. 2019. “The Global Soil Community and Its Influence on Biogeochemistry.” Science 365: eaav0550. https://doi.org/10.1126/science.aav0550

[5] Geers, Aileen Ute, Yannick Buijs, Mikael Lenz Strube, Lone Gram, and Mikkel Bentzon-Tilia. 2022. “The Natural Product Biosynthesis Potential of the Microbiomes of Earth - Bioprospecting for Novel Anti-Microbial Agents in the Meta-Omics Era.” Computational and Structural Biotechnology Journal 20: 343-352. https://doi.org/10.1016/j.csbj.2021.12.024

[6] Lloyd, Karen G., Andrew D. Steen, Joshua Ladau, Junqi Yin, and Lonnie Crosby. 2018. “Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes.” mSystems 3: e00055-18. https://doi.org/10.1128/msystems.00055-18

[7] Anthony, Winston E., Steven D. Allison, Caitlin M. Broderick, Luciana Chavez Rodriguez, Alicia Clum, Hugh Cross, Emiley Eloe-Fadrosh, et al. 2024. “From Soil to Sequence: Filling the Critical Gap in Genome-Resolved Metagenomics Is Essential to the Future of Soil Microbial Ecology.” Environmental Microbiome 19: 56. https://doi.org/10.1186/s40793-024-00599-w

[8] Ma, Bin, Caiyu Lu, Yiling Wang, Jingwen Yu, Kankan Zhao, Ran Xue, Hao Ren, et al. 2023. “A Genomic Catalogue of Soil Microbiomes Boosts Mining of Biodiversity and Genetic Resources.” Nature Communications 14: 7318. https://doi.org/10.1038/s41467-023-43000-z

[9] Singleton, Cm, Tbn Jensen, F. Delogu, Ea Sørensen, Vr Jørgensen, Sm Karst, Y. Yang, et al 2024. “Microflora Danica: The Atlas of Danish Environmental Microbiomes.” bioRxiv, preprint: 2024.06.27.600767. https://doi.org/10.1101/2024.06.27.600767

[10] Blanco-Míguez, Aitor, Francesco Beghini, Fabio Cumbo, Lauren J. McIver, Kelsey N. Thompson, Moreno Zolfo, Paolo Manghi, et al. 2023. “Extending and Improving Metagenomic Taxonomic Profiling With Uncharacterized Species Using MetaPhlAn 4.” Nature Biotechnology 41: 1633-1644. https://doi.org/10.1038/s41587-023-01688-w

[11] Edwin, Niranjana Rose, Amy Heather Fitzpatrick, Fiona Brennan, Florence Abram, and Orla O'Sullivan. 2024. “An In-Depth Evaluation of Metagenomic Classifiers for Soil Microbiomes.” Environmental Microbiome 19: 19. https://doi.org/10.1186/s40793-024-00561-w

[12] Riley, Robert, Robert M. Bowers, Antonio Pedro Camargo, Ashley Campbell, Rob Egan, Emiley A. Eloe-Fadrosh, Brian Foster, et al. 2023. “Terabase-Scale Coassembly of a Tropical Soil Microbiome.” Microbiology Spectrum 11: e00200-23. https://doi.org/10.1128/spectrum.00200-23

[13] Pasolli, Edoardo, Francesco Asnicar, Serena Manara, Moreno Zolfo, Nicolai Karcher, Federica Armanini, Francesco Beghini, et al. 2019. “Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes From Metagenomes Spanning Age, Geography, and Lifestyle.” Cell 176: 649-662.e20. https://doi.org/10.1016/j.cell.2019.01.001

[14] Saheb Kashaf, Sara, Alexandre Almeida, Julia A. Segre, and Robert D. Finn. 2021. “Recovering Prokaryotic Genomes From Host-Associated, Short-Read Shotgun Metagenomic Sequencing Data.” Nature Protocols 16: 2520-2541. https://doi.org/10.1038/s41596-021-00508-2

[15] Mendes, Catarina Inês, Pedro Vila-Cerqueira, Yair Motro, Jacob Moran-Gilad, João André Carriço, and Mário Ramirez. 2023. “LMAS: Evaluating Metagenomic Short De Novo Assembly Methods Through Defined Communities.” GigaScience 12: giac122. https://doi.org/10.1093/gigascience/giac122

[16] Aroney, Samuel T. N., Rhys J. P. Newell, Gene W. Tyson, and Ben J. Woodcroft. 2024. “Bin Chicken: Targeted Metagenomic Coassembly for The Efficient Recovery of Novel Genomes.” bioRxiv. https://doi.org/10.1101/2024.11.24.625082

[17] Truong, Duy Tin, Adrian Tett, Edoardo Pasolli, Curtis Huttenhower, and Nicola Segata. 2017. “Microbial Strain-Level Population Structure and Genetic Diversity From Metagenomes.” Genome Research 27: 626-638. https://doi.org/10.1101/gr.216242.116

[18] Liu, Meng, Nuohan Xu, Bingfeng Chen, Zhenyan Zhang, Xinyu Chen, Yuke Zhu, Wenjie Hong, et al. 2024. “Effects of Different Assembly Strategies on Gene Annotation in Activated Sludge.” Environmental Research 252: 119116. https://doi.org/10.1016/j.envres.2024.119116

[19] Orellana, Luis H., Karen Krüger, Chandni Sidhu, and Rudolf Amann. 2023. “Comparing Genomes Recovered From Time-Series Metagenomes Using Long- and Short-Read Sequencing Technologies.” Microbiome 11: 105. https://doi.org/10.1186/s40168-023-01557-3

[20] Zhang, Zhi-Feng, Li-Rui Liu, Yue-Ping Pan, Jie Pan, and Meng Li. 2023. “Long-Read Assembled Metagenomic Approaches Improve Our Understanding on Metabolic Potentials of Microbial Community in Mangrove Sediments.” Microbiome 11: 188. https://doi.org/10.1186/s40168-023-01630-x

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