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).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Biller, S. J. et al. Marine microbial metagenomes sampled across space and time. Sci. Data 5, 180176 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Paoli, L. et al. Biosynthetic potential of the global ocean microbiome. Nature 607, 111–118 (2022).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Cavicchioli, R. et al. Scientists’ warning to humanity: microorganisms and climate change. Nat. Rev. Microbiol. 17, 569–586 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Azam, F. et al. The ecological role of water-column microbes in the sea. Mar. Ecol. Prog. Ser. 10, 257–263 (1983).

Article 
ADS 

Google Scholar
 

Field, C. B., Behrenfeld, M. J., Randerson, J. T. & Falkowski, P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science 281, 237–240 (1998).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Roberts, C. M. et al. Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295, 1280–1284 (2002).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

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).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Sunagawa, S. et al. Tara Oceans: towards global ocean ecosystems biology. Nat. Rev. Microbiol. 18, 428–445 (2020).

Article 
CAS 
PubMed 

Google Scholar
 

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

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Gaïa, M. et al. Mirusviruses link herpesviruses to giant viruses. Nature 616, 783–789 (2023).

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016).

Article 
CAS 
PubMed 

Google Scholar
 

Gregory, A. C. et al. Marine DNA viral macro- and microdiversity from pole to pole. Cell 177, 1109–1123.e14 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 

Google Scholar
 

Planes, S. et al. The Tara Pacific expedition—a pan-ecosystemic approach of the “-omics” complexity of coral reef holobionts across the Pacific Ocean. PLoS Biol. 17, e3000483 (2019).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
PubMed 
PubMed Central 

Google Scholar
 

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, 823–826 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
PubMed 
PubMed Central 

Google Scholar
 

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, 165–171 (2003).

Article 
CAS 
PubMed 

Google Scholar
 

Olm, M. R. et al. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat. Biotechnol. 39, 727–736 (2021).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Nayfach, S. et al. A genomic catalog of Earth’s microbiomes. Nat. Biotechnol. 39, 499–509 (2021).

Article 
CAS 
PubMed 

Google Scholar
 

Pachiadaki, M. G. et al. Charting the complexity of the marine microbiome through single-cell genomics. Cell 179, 1623–1635.e11 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Sowell, S. M. et al. Transport functions dominate the SAR11 metaproteome at low-nutrient extremes in the Sargasso Sea. ISME J. 3, 93–105 (2009).

Article 
CAS 
PubMed 

Google Scholar
 

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–phosphorus lyase pathway for phosphonate degradation. Environ. Microbiol. 21, 2402–2414 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Moreno-Vivián, C., Cabello, P., Martínez-Luque, M., Blasco, R. & Castillo, F. Prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases. J. Bacteriol. 181, 6573–6584 (1999).

Article 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Great Barrier Reef Marine Park Authority. Great Barrier Reef Marine Park Zoning Plan 2003 (Australian Government, 2004).

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

Article 
PubMed 
PubMed Central 

Google Scholar
 

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


Google Scholar
 

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).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Roda-Garcia, J. J., Haro-Moreno, J. M., Rodriguez-Valera, F., Almagro-Moreno, S. & López-Pérez, M. Single-amplified genomes reveal most streamlined free-living marine bacteria. Environ. Microbiol. 25, 1136–1154 (2023).

Article 
CAS 
PubMed 

Google Scholar
 

Martinez-Gutierrez, C. A. & Aylward, F. O. Strong purifying selection is associated with genome streamlining in epipelagic Marinimicrobia. Genome Biol. Evol. 11, 2887–2894 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
PubMed 
PubMed Central 

Google Scholar
 

Giovannoni, S. J., Cameron Thrash, J. & Temperton, B. Implications of streamlining theory for microbial ecology. ISME J. 8, 1553–1565 (2014).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Roach, T. N. F. et al. Microbial bioenergetics of coral–algal interactions. PeerJ 5, e3423 (2017).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Haas, A. F. et al. Global microbialization of coral reefs. Nat Microbiol 1, 16042 (2016).

Article 
CAS 
PubMed 

Google Scholar
 

Dinsdale, E. A. & Rohwer, F. in Coral Reefs: An Ecosystem in Transition (eds Dubinsky, Z. & Stambler, N.) 231–240 (Springer, 2011).

Lauro, F. M. et al. The genomic basis of trophic strategy in marine bacteria. Proc. Natl Acad. Sci. USA 106, 15527–15533 (2009).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Suttle, C. A. Marine viruses — major players in the global ecosystem. Nat. Rev. Microbiol. 5, 801–812 (2007).

Article 
CAS 
PubMed 

Google Scholar
 

Camargo, A. P. et al. Identification of mobile genetic elements with geNomad. Nat. Biotechnol. 42, 1303–1312 (2023).

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
PubMed 
PubMed Central 

Google Scholar
 

Tian, F. et al. Prokaryotic-virus-encoded auxiliary metabolic genes throughout the global oceans. Microbiome 12, 159 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
PubMed 
PubMed Central 

Google Scholar
 

Du, S. et al. Genome sequences of the first Autographiviridae phages infecting marine Roseobacter. Microb. Genom. 10, 001240 (2024).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Pope, W. H. et al. Genome sequence, structural proteins, and capsid organization of the cyanophage Syn5: a “horned” bacteriophage of marine Synechococcus. J. Mol. Biol. 368, 966–981 (2007).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Zhao, Y. et al. Abundant SAR11 viruses in the ocean. Nature 494, 357–360 (2013).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

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

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Guerin, E. et al. Biology and taxonomy of CrAss-like bacteriophages, the most abundant virus in the human gut. Cell Host Microbe 24, 653–664.e6 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Shkoporov, A. N. et al. ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis. Nat. Commun. 9, 4781 (2018).

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Yutin, N. et al. Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut. Nat. Microbiol. 3, 38–46 (2017).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Edwards, R. A. et al. Global phylogeography and ancient evolution of the widespread human gut virus crAssphage. Nat. Microbiol. 4, 1727–1736 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bartlau, N. et al. Highly diverse flavobacterial phages isolated from North Sea spring blooms. ISME J. 16, 555–568 (2022).

Article 
CAS 
PubMed 

Google Scholar
 

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

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Li, W. K. W. Primary production of prochlorophytes, cyanobacteria, and eucaryotic ultraphytoplankton: measurements from flow cytometric sorting. Limnol. Oceanogr. 39, 169–175 (1994).

Article 
ADS 
CAS 

Google Scholar
 

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, 168–179 (2004).

Article 
ADS 
CAS 

Google Scholar
 

Simmons, M. P. et al. Abundance and biogeography of picoprasinophyte ecotypes and other phytoplankton in the Eastern North Pacific Ocean. Appl. Environ. Microbiol. 82, 1693–1705 (2016).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Derelle, E. et al. Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc. Natl Acad. Sci. USA 103, 11647–11652 (2006).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Palenik, B. et al. The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc. Natl Acad. Sci. USA 104, 7705–7710 (2007).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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, 1372–1385 (2017).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Fernández-Gómez, B. et al. Ecology of marine Bacteroidetes: a comparative genomics approach. ISME J. 7, 1026–1037 (2013).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Hudson, J. & Egan, S. Opportunistic diseases in marine eukaryotes: could Bacteroidota be the next threat to ocean life? Environ. Microbiol. 24, 4505–4518 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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, 1612–1625 (2016).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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, 2034–2043 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Kolmogorov, M. et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat. Methods 17, 1103–1110 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 27, 737–746 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Li, H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
PubMed 
PubMed Central 

Google Scholar
 

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, 605–607 (2016).

Article 
CAS 
PubMed 

Google Scholar
 

Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144–1146 (2014).

Article 
CAS 
PubMed 

Google Scholar
 

Nissen, J. N. et al. Improved metagenome binning and assembly using deep variational autoencoders. Nat. Biotechnol. 39, 555–560 (2021).

Article 
CAS 
PubMed 

Google Scholar
 

Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol. 3, 836–843 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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, 1043–1055 (2015).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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, 1203–1212 (2023).

Article 
CAS 
PubMed 

Google Scholar
 

Chaumeil, P. A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk v2: memory friendly classification with the genome taxonomy database. Bioinformatics 38, 5315–5316 (2022).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Aroney, S. T. N. et al. CoverM: read alignment statistics for metagenomics. Bioinformatics 41, btaf147 (2025).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

R Core Team. R: A Language and Environment for Statistical Computing http://www.R-project.org/ (R Foundation for Statistical Computing, 2024).

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

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

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Nickols, W. A. et al. MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery. Nat. Methods 23, 554–564 (2026).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
ADS 

Google Scholar
 

Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).

Article 
CAS 
PubMed 

Google Scholar
 

Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Aramaki, T. et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Rohart, F., Eslami, A., Matigian, N., Bougeard, S. & Lê Cao, K.-A. MINT: a multivariate integrative method to identify reproducible molecular signatures across independent experiments and platforms. BMC Bioinform. 18, 128 (2017).

Article 

Google Scholar
 

Lê Cao, K.-A., Boitard, S. & Besse, P. Sparse PLS discriminant analysis: biologically relevant feature selection and graphical displays for multiclass problems. BMC Bioinform. 12, 253 (2011).

Article 

Google Scholar
 

Rohart, F., Gautier, B., Singh, A. & Lê Cao, K.-A. mixOmics: An R package for ‘omics feature selection and multiple data integration. PLoS Comput. Biol. 13, e1005752 (2017).

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Lê Cao, K.-A., Martin, P. G., Robert-Granié, C. & Besse, P. Sparse canonical methods for biological data integration: application to a cross-platform study. BMC Bioinform. 10, 34 (2009).

Article 

Google Scholar
 

Lê Cao, K.-A., Rossouw, D., Robert-Granié, C. & Besse, P. A sparse PLS for variable selection when integrating omics data. Stat. Appl. Genet. Mol. Biol. 7, 35 (2008).

Article 
MathSciNet 
PubMed 

Google Scholar
 

Antipov, D., Raiko, M., Lapidus, A. & Pevzner, P. A. MetaviralSPAdes: assembly of viruses from metagenomic data. Bioinformatics 36, 4126–4129 (2020).

Article 
CAS 
PubMed 

Google Scholar
 

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).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

Article 
PubMed 
PubMed Central 

Google Scholar
 

Ren, J. et al. Identifying viruses from metagenomic data using deep learning. Quant. Biol. 8, 64–77 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Nayfach, S. et al. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat. Biotechnol. 39, 578–585 (2021).

Article 
CAS 
PubMed 

Google Scholar
 

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. 22, 349 (2021).

Article 
CAS 

Google Scholar
 

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, 830–847 (2024).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Eren, A. M. et al. Community-led, integrated, reproducible multi-omics with anvi’o. Nat. Microbiol. 6, 3–6 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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

PubMed 
PubMed Central 

Google Scholar
 

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, 569–580 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Darling, A. C. E., Mau, B., Blattner, F. R. & Perna, N. T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394–1403 (2004).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bouras, G. et al. Pharokka: a fast scalable bacteriophage annotation tool. Bioinformatics 39, btac776 (2023).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Nishimura, Y. et al. ViPTree: the viral proteomic tree server. Bioinformatics 33, 2379–2380 (2017).

Article 
CAS 
PubMed 

Google Scholar
 

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–W82 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

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).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Robbins, S. et al. Great Barrier Reef Microbial Genomes Database (GBR-MGD). Zenodo https://doi.org/10.5281/zenodo.20503966 (2026).