{"id":780232,"date":"2026-07-23T17:24:14","date_gmt":"2026-07-23T17:24:14","guid":{"rendered":"https:\/\/www.newsbeep.com\/us\/780232\/"},"modified":"2026-07-23T17:24:14","modified_gmt":"2026-07-23T17:24:14","slug":"the-planktonic-microbiome-of-the-great-barrier-reef","status":"publish","type":"post","link":"https:\/\/www.newsbeep.com\/us\/780232\/","title":{"rendered":"The planktonic microbiome of the Great Barrier Reef"},"content":{"rendered":"

Tully, B. J., Graham, E. D. & Heidelberg, J. F. The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans. Sci. Data 5, 170203 (2018).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Tully, B. J., Sachdeva, R., Graham, E. D. & Heidelberg, J. F. 290 metagenome-assembled genomes from the Mediterranean Sea: a resource for marine microbiology. PeerJ 5, e3558 (2017).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Biller, S. J. et al. Marine microbial metagenomes sampled across space and time. Sci. Data 5, 180176 (2018).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Paoli, L. et al. Biosynthetic potential of the global ocean microbiome. Nature 607, 111\u2013118 (2022).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Nishimura, Y. & Yoshizawa, S. The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments. Sci. Data 9, 305 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Cavicchioli, R. et al. Scientists\u2019 warning to humanity: microorganisms and climate change. Nat. Rev. Microbiol. 17, 569\u2013586 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Azam, F. et al. The ecological role of water-column microbes in the sea. Mar. Ecol. Prog. Ser. 10, 257\u2013263 (1983).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Field, C. B., Behrenfeld, M. J., Randerson, J. T. & Falkowski, P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281, 237\u2013240 (1998).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Roberts, C. M. et al. Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295, 1280\u20131284 (2002).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Haro-Moreno, J. M. et al. Fine metagenomic profile of the Mediterranean stratified and mixed water columns revealed by assembly and recruitment. Microbiome 6, 128 (2018).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sunagawa, S. et al. Tara Oceans: towards global ocean ecosystems biology. Nat. Rev. Microbiol. 18, 428\u2013445 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Delmont, T. O. et al. Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean. Cell Genom. 2, 100123 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ga\u00efa, M. et al. Mirusviruses link herpesviruses to giant viruses. Nature 616, 783\u2013789 (2023).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689\u2013693 (2016).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Gregory, A. C. et al. Marine DNA viral macro- and microdiversity from pole to pole. Cell 177, 1109\u20131123.e14 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Duncan, A. et al. Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans. Microbiome 10, 67 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Alexander, H. et al. Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton. mBio 14, e01676-23 (2023).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Laiolo, E. et al. Metagenomic probing toward an atlas of the taxonomic and metabolic foundations of the global ocean genome. Front. Sci. 1, 1038696 (2024).<\/p>\n

Article<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Planes, S. et al. The Tara Pacific expedition\u2014a pan-ecosystemic approach of the \u201c-omics\u201d complexity of coral reef holobionts across the Pacific Ocean. PLoS Biol. 17, e3000483 (2019).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Lombard, F. et al. Open science resources from the Tara Pacific expedition across coral reef and surface ocean ecosystems. Sci. Data 10, 324 (2023).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sereika, M. et al. Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing. Nat. Methods 19, 823\u2013826 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Delmont, T. O. et al. Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade. eLife 8, e46497 (2019).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Huber, H., Hohn, M. J., Stetter, K. O. & Rachel, R. The phylum Nanoarchaeota: present knowledge and future perspectives of a unique form of life. Res. Microbiol. 154, 165\u2013171 (2003).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Olm, M. R. et al. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat. Biotechnol. 39, 727\u2013736 (2021).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Browne, P. D. et al. GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms. GigaScience 9, giaa008 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Nayfach, S. et al. A genomic catalog of Earth\u2019s microbiomes. Nat. Biotechnol. 39, 499\u2013509 (2021).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Pachiadaki, M. G. et al. Charting the complexity of the marine microbiome through single-cell genomics. Cell 179, 1623\u20131635.e11 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sowell, S. M. et al. Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J. 3, 93\u2013105 (2009).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sosa, O. A., Repeta, D. J., DeLong, E. F., Ashkezari, M. D. & Karl, D. M. Phosphate-limited ocean regions select for bacterial populations enriched in the carbon\u2013phosphorus lyase pathway for phosphonate degradation. Environ. Microbiol. 21, 2402\u20132414 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Moreno-Vivi\u00e1n, C., Cabello, P., Mart\u00ednez-Luque, M., Blasco, R. & Castillo, F. Prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases. J. Bacteriol. 181, 6573\u20136584 (1999).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Benedetti-Cecchi, L. et al. Marine protected areas promote stability of reef fish communities under climate warming. Nat. Commun. 15, 1822 (2024).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Great Barrier Reef Marine Park Authority. Great Barrier Reef Marine Park Zoning Plan 2003 (Australian Government, 2004).<\/p>\n

Terzin, M. et al. The road forward to incorporate seawater microbes in predictive reef monitoring. Environ. Microbiome 19, 5 (2024).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Apprill, A. & Salerno, J. L. Reef water microorganisms as diagnostic indicators for coral reef ecosystem management and sustainability. Cell Rep. Sustain. 2, 100403 (2025).<\/p>\n


\n Google Scholar<\/a>\u00a0\n <\/p>\n

Viklund, J., Martijn, J., Ettema, T. J. G. & Andersson, S. G. E. Comparative and phylogenomic evidence that the Alphaproteobacterium HIMB59 is not a member of the oceanic SAR11 clade. PLoS ONE 8, e78858 (2013).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Roda-Garcia, J. J., Haro-Moreno, J. M., Rodriguez-Valera, F., Almagro-Moreno, S. & L\u00f3pez-P\u00e9rez, M. Single-amplified genomes reveal most streamlined free-living marine bacteria. Environ. Microbiol. 25, 1136\u20131154 (2023).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Martinez-Gutierrez, C. A. & Aylward, F. O. Strong purifying selection is associated with genome streamlining in epipelagic Marinimicrobia. Genome Biol. Evol. 11, 2887\u20132894 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Grote, J. et al. Streamlining and core genome conservation among highly divergent members of the SAR11 clade. mBio 3, e00252-12 (2012).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Giovannoni, S. J., Cameron Thrash, J. & Temperton, B. Implications of streamlining theory for microbial ecology. ISME J. 8, 1553\u20131565 (2014).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Roach, T. N. F. et al. Microbial bioenergetics of coral\u2013algal interactions. PeerJ 5, e3423 (2017).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Haas, A. F. et al. Global microbialization of coral reefs. Nat Microbiol 1, 16042 (2016).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Dinsdale, E. A. & Rohwer, F. in Coral Reefs: An Ecosystem in Transition (eds Dubinsky, Z. & Stambler, N.) 231\u2013240 (Springer, 2011).<\/p>\n

Lauro, F. M. et al. The genomic basis of trophic strategy in marine bacteria. Proc. Natl Acad. Sci. USA 106, 15527\u201315533 (2009).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Turner, D. et al. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee. Arch. Virol. 168, 74 (2023).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Suttle, C. A. Marine viruses \u2014 major players in the global ecosystem. Nat. Rev. Microbiol. 5, 801\u2013812 (2007).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Camargo, A. P. et al. Identification of mobile genetic elements with geNomad. Nat. Biotechnol. 42, 1303\u20131312 (2023).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Guo, J. et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9, 37 (2021).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Tian, F. et al. Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans. Microbiome 12, 159 (2024).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wang, T. et al. Characterization and genomic analysis of an oceanic cyanophage infecting marine Synechococcus reveal a novel genus. Front. Microbiol. 14, 1231279 (2023).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Du, S. et al. Genome sequences of the first Autographiviridae phages infecting marine Roseobacter. Microb. Genom. 10, 001240 (2024).<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sullivan, M. B., Coleman, M. L., Weigele, P., Rohwer, F. & Chisholm, S. W. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS Biol. 3, e144 (2005).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Pope, W. H. et al. Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a \u201chorned\u201d bacteriophage of marine Synechococcus. J. Mol. Biol. 368, 966\u2013981 (2007).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Zhao, Y. et al. Abundant SAR11 viruses in the ocean. Nature 494, 357\u2013360 (2013).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Dutilh, B. E. et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun. 5, 4498 (2014).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Guerin, E. et al. Biology and taxonomy of CrAss-like bacteriophages, the most abundant virus in the human gut. Cell Host Microbe 24, 653\u2013664.e6 (2018).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Shkoporov, A. N. et al. \u03a6CrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis. Nat. Commun. 9, 4781 (2018).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yutin, N. et al. Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut. Nat. Microbiol. 3, 38\u201346 (2017).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Edwards, R. A. et al. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat. Microbiol. 4, 1727\u20131736 (2019).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yutin, N. et al. Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features. Nat. Commun. 12, 1044 (2021).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Papudeshi, B. et al. Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2. Microb. Genom. 9, 001100 (2023).<\/p>\n

CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Bartlau, N. et al. Highly diverse flavobacterial phages isolated from North Sea spring blooms. ISME J. 16, 555\u2013568 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Piedade, G. J. et al. Seasonal dynamics and diversity of Antarctic marine viruses reveal a novel viral seascape. Nat. Commun. 15, 9192 (2024).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Li, W. K. W. Primary production of prochlorophytes, cyanobacteria, and eucaryotic ultraphytoplankton: measurements from flow cytometric sorting. Limnol. Oceanogr. 39, 169\u2013175 (1994).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Worden, A. Z., Nolan, J. K. & Palenik, B. Assessing the dynamics and ecology of marine picophytoplankton: the importance of the eukaryotic component. Limnol. Oceanogr. 49, 168\u2013179 (2004).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Simmons, M. P. et al. Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the Eastern North Pacific Ocean. Appl. Environ. Microbiol. 82, 1693\u20131705 (2016).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Derelle, E. et al. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc. Natl Acad. Sci. USA 103, 11647\u201311652 (2006).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Moreau, H. et al. Gene functionalities and genome structure in Bathycoccus prasinos reflect cellular specializations at the base of the green lineage. Genome Biol. 13, R74 (2012).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Palenik, B. et al. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc. Natl Acad. Sci. USA 104, 7705\u20137710 (2007).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Joli, N., Monier, A., Logares, R. & Lovejoy, C. Seasonal patterns in Arctic prasinophytes and inferred ecology of Bathycoccus unveiled in an Arctic winter metagenome. ISME J. 11, 1372\u20131385 (2017).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Fern\u00e1ndez-G\u00f3mez, B. et al. Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J. 7, 1026\u20131037 (2013).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Hudson, J. & Egan, S. Opportunistic diseases in marine eukaryotes: could Bacteroidota be the next threat to ocean life?\u00a0Environ. Microbiol. 24, 4505\u20134518 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Nayfach, S., Rodriguez-Mueller, B., Garud, N. & Pollard, K. S. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res. 26, 1612\u20131625 (2016).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kazantseva, E., Donmez, A., Frolova, M., Pop, M. & Kolmogorov, M. Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing. Nat. Methods 21, 2034\u20132043 (2024).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ma, B. et al. A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources. Nat. Commun. 14, 7318 (2023).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Gilbert, J. A. et al. Safeguarding microbial biodiversity: microbial conservation specialist group within the species survival commission of the International Union for Conservation of Nature. ISME J. 19, wraf239 (2025).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Terzin, M. et al. Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef. Microbiome 13, 11 (2025).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kolmogorov, M. et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat. Methods 17, 1103\u20131110 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Vaser, R., Sovi\u0107, I., Nagarajan, N. & \u0160iki\u0107, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737\u2013746 (2017).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824\u2013834 (2017).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094\u20133100 (2018).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kang, D. D., Froula, J., Egan, R. & Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165 (2015).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Wu, Y.-W., Simmons, B. A. & Singer, S. W. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics 32, 605\u2013607 (2016).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144\u20131146 (2014).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Nissen, J. N. et al. Improved metagenome binning and assembly using deep variational autoencoders. Nat. Biotechnol. 39, 555\u2013560 (2021).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol. 3, 836\u2013843 (2018).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043\u20131055 (2015).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Chklovski, A., Parks, D. H., Woodcroft, B. J. & Tyson, G. W. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat. Methods 20, 1203\u20131212 (2023).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Chaumeil, P. A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 38, 5315\u20135316 (2022).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Lynch, T. P. et al. IMOS National Reference Stations: a continental-wide physical, chemical and biological coastal observing system. PLoS ONE 9, e113652 (2014).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Aroney, S. T. N. et al. CoverM: read alignment statistics for metagenomics. Bioinformatics 41, btaf147 (2025).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

R Core Team. R: A Language and Environment for Statistical Computing http:\/\/www.R-project.org\/<\/a> (R Foundation for Statistical Computing, 2024).<\/p>\n

Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.6-8 https:\/\/CRAN.R-project.org\/package=vegan<\/a> (2024).<\/p>\n

McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Nickols, W. A. et al. MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery. Nat. Methods 23, 554\u2013564 (2026).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Larralde, M. Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. J. Open Source Softw. 7, 4296 (2022).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Steinegger, M. & S\u00f6ding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026\u20131028 (2017).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Aramaki, T. et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251\u20132252 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Rohart, F., Eslami, A., Matigian, N., Bougeard, S. & L\u00ea Cao, K.-A. MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms. BMC Bioinform.\u00a018, 128 (2017).<\/p>\n

Article<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

L\u00ea Cao, K.-A., Boitard, S. & Besse, P. Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems. BMC Bioinform.\u00a012, 253 (2011).<\/p>\n

Article<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Rohart, F., Gautier, B., Singh, A. & L\u00ea Cao, K.-A. mixOmics: An R package for \u2018omics feature selection and multiple data integration. PLoS Comput. Biol. 13, e1005752 (2017).<\/p>\n

Article<\/a>\u00a0
\n ADS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

L\u00ea Cao, K.-A., Martin, P. G., Robert-Grani\u00e9, C. & Besse, P. Sparse canonical methods for biological data integration: application to a cross-platform study. BMC Bioinform.\u00a010, 34 (2009).<\/p>\n

Article<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

L\u00ea Cao, K.-A., Rossouw, D., Robert-Grani\u00e9, C. & Besse, P. A sparse PLS for variable selection when integrating omics data. Stat. Appl. Genet. Mol. Biol. 7, 35 (2008).<\/p>\n

Article<\/a>\u00a0
\n MathSciNet<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Antipov, D., Raiko, M., Lapidus, A. & Pevzner, P. A. MetaviralSPAdes: assembly of viruses from metagenomic data. Bioinformatics 36, 4126\u20134129 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Kieft, K., Zhou, Z. & Anantharaman, K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 8, 90 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Fang, Z. et al. PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning. GigaScience 8, giz066 (2019).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Ren, J. et al. Identifying viruses from metagenomic data using deep learning. Quant. Biol. 8, 64\u201377 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Nayfach, S. et al. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat. Biotechnol. 39, 578\u2013585 (2021).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Pradier, L., Tissot, T., Fiston-Lavier, A.-S. & Bedhomme, S. PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets. BMC Bioinform.\u00a022, 349 (2021).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Yu, M. K., Fogarty, E. C. & Eren, A. M. Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess. Nat. Microbiol. 9, 830\u2013847 (2024).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Eren, A. M. et al. Community-led, integrated, reproducible multi-omics with anvi\u2019o. Nat. Microbiol. 6, 3\u20136 (2021).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Pronk, L. J. U. & Medema, M. H. Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure. Microb. Genom. 8, mgen000823 (2022).<\/p>\n

PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

West, P. T., Probst, A. J., Grigoriev, I. V., Thomas, B. C. & Banfield, J. F. Genome-reconstruction for eukaryotes from complex natural microbial communities. Genome Res. 28, 569\u2013580 (2018).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Darling, A. C. E., Mau, B., Blattner, F. R. & Perna, N. T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394\u20131403 (2004).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Brown, M. R., Manuel Gonzalez De La Rosa, P. & Blaxter, M. tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets. Bioinformatics 41, btaf049 (2025).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Bouras, G. et al. Pharokka: a fast scalable bacteriophage annotation tool. Bioinformatics 39, btac776 (2023).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772\u2013780 (2013).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Capella-Guti\u00e9rrez, S., Silla-Mart\u00ednez, J. M. & Gabald\u00f3n, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972\u20131973 (2009).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530\u20131534 (2020).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Nishimura, Y. et al. ViPTree: the viral proteomic tree server. Bioinformatics 33, 2379\u20132380 (2017).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Letunic, I. & Bork, P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 52, W78\u2013W82 (2024).<\/p>\n

Article<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Roux, S. et al. iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria. PLoS Biol. 21, e3002083 (2023).<\/p>\n

Article<\/a>\u00a0
\n CAS<\/a>\u00a0
\n PubMed<\/a>\u00a0
\n PubMed Central<\/a>\u00a0
\n
\n Google Scholar<\/a>\u00a0\n <\/p>\n

Robbins, S. et al. Great Barrier Reef Microbial Genomes Database (GBR-MGD). Zenodo https:\/\/doi.org\/10.5281\/zenodo.20503966<\/a> (2026).<\/p>\n","protected":false},"excerpt":{"rendered":"Tully, B. J., Graham, E. D. & Heidelberg, J. F. The reconstruction of 2,631 draft metagenome-assembled genomes from…\n","protected":false},"author":2,"featured_media":780233,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[32],"tags":[1159,23165,14376,14377,1160,79,332339],"class_list":["post-780232","post","type-post","status-publish","format-standard","has-post-thumbnail","category-science","tag-humanities-and-social-sciences","tag-metagenomics","tag-microbial-ecology","tag-microbiome","tag-multidisciplinary","tag-science","tag-water-microbiology"],"_links":{"self":[{"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/posts\/780232","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/comments?post=780232"}],"version-history":[{"count":0,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/posts\/780232\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/media\/780233"}],"wp:attachment":[{"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/media?parent=780232"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/categories?post=780232"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.newsbeep.com\/us\/wp-json\/wp\/v2\/tags?post=780232"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}