参考文献

Borer, Benedict, Hannah Kleyer, and Dani Or. 2022. “Primary Carbon Sources and Self-Induced Metabolic Landscapes Shape Community Structure in Soil Bacterial Hotspots.” Soil Biology and Biochemistry 168 (May): 108620. https://doi.org/10.1016/j.soilbio.2022.108620.

Chen, Jin, Jose A. Gomez, Kai Höffner, Paul I. Barton, and Michael A. Henson. 2015. “Metabolic Modeling of Synthesis Gas Fermentation in Bubble Column Reactors.” Biotechnology for Biofuels 8 (1). https://doi.org/10.1186/s13068-015-0272-5.

Diener, Christian, Sean M. Gibbons, and Osbaldo Resendis-Antonio. 2020. “MICOM: Metagenome-Scale Modeling to Infer Metabolic Interactions in the Gut Microbiota.” mSystems 5 (1): 10.1128/msystems.00606–19. https://doi.org/10.1128/msystems.00606-19.

Eren, A. Murat, Evan Kiefl, Alon Shaiber, Iva Veseli, Samuel E. Miller, Matthew S. Schechter, Isaac Fink, et al. 2021. “Community-Led, Integrated, Reproducible Multi-Omics with Anvi’o.” Nature Microbiology 6 (1): 3–6. https://doi.org/10.1038/s41564-020-00834-3.

Harcombe, William R., William J. Riehl, Ilija Dukovski, Brian R. Granger, Alex Betts, Alex H. Lang, Gracia Bonilla, et al. 2014. “Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics.” Cell Reports 7 (4): 1104–15. https://doi.org/10.1016/j.celrep.2014.03.070.

Henson, Michael A. 2015. “Genome-scale modelling of microbial metabolism with temporal and spatial resolution.” Biochemical Society Transactions 43 (6): 1164–71. https://doi.org/10.1042/BST20150146.

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 (1): 7318. https://doi.org/10.1038/s41467-023-43000-z.

Nayfach, Stephen, Simon Roux, Rekha Seshadri, Daniel Udwary, Neha Varghese, Frederik Schulz, Dongying Wu, et al. 2021. “A Genomic Catalog of Earth’s Microbiomes.” Nature Biotechnology 39 (4): 499–509. https://doi.org/10.1038/s41587-020-0718-6.

Pacheco, Alan R., and Julia A. Vorholt. 2023. “Resolving Metabolic Interaction Mechanisms in Plant Microbiomes.” Current Opinion in Microbiology 74 (August): 102317. https://doi.org/10.1016/j.mib.2023.102317.

Parks, Donovan H., Maria Chuvochina, Pierre-Alain Chaumeil, Christian Rinke, Aaron J. Mussig, and Philip Hugenholtz. 2020. “A Complete Domain-to-Species Taxonomy for Bacteria and Archaea.” Nature Biotechnology 38 (9): 1079–86. https://doi.org/10.1038/s41587-020-0501-8.

Parks, Donovan H, Maria Chuvochina, Christian Rinke, Aaron J Mussig, Pierre-Alain Chaumeil, and Philip Hugenholtz. 2022. “GTDB: An Ongoing Census of Bacterial and Archaeal Diversity Through a Phylogenetically Consistent, Rank Normalized and Complete Genome-Based Taxonomy.” Nucleic Acids Research 50 (D1): D785–94. https://doi.org/10.1093/nar/gkab776.

Schmidt, Thomas S B, Anthony Fullam, Pamela Ferretti, Askarbek Orakov, Oleksandr M Maistrenko, Hans-Joachim Ruscheweyh, Ivica Letunic, et al. 2024. “SPIRE: A Searchable, Planetary-Scale mIcrobiome REsource.” Nucleic Acids Research 52 (D1): D777–83. https://doi.org/10.1093/nar/gkad943.

Scott, Helen, and Daniel Segrè. 2024. “Metabolic Flux Modeling in Marine Ecosystems.” Annual Review of Marine Science, September. https://doi.org/10.1146/annurev-marine-032123-033718.

Wickham, Hadley, Maximilian Girlich, and Edgar Ruiz. 2023. “Dbplyr: A ’Dplyr’ Back End for Databases.” https://CRAN.R-project.org/package=dbplyr.