{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T10:33:12Z","timestamp":1771929192941,"version":"3.50.1"},"reference-count":234,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,2,4]],"date-time":"2026-02-04T00:00:00Z","timestamp":1770163200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>Modern biology often relies on the analysis of entire sets of molecules (omics). A subset of omics uses nucleic acid sequencing to reconstruct genomes and profile gene expression. Novel findings and existing data are contextualized by databases, which have been growing exponentially due to falling sequencing costs and increased computing access. The increasing accessibility of omics has led to rapid adoption and widespread self-training via open-access tools. In this training environment new users (many of whom are students also applying computing for the first time) are confronted with Terabytes of sequence data and an ocean of topic-specific computing guides (often directed at high-level users). This flood of information creates an initial barrier of confusion and frustration, where it is challenging to identify the overarching goals of omics analyses through the details of computing. We believe this confusion is understandable but not pre-destined, as omics is\u2013at its core\u2013simple. This simplicity comes from its modular nature, where any analysis requires familiarity with only a few consistent steps. Here, we identify core elements of all omics analyses\u2013data products, tools, and workflows\u2013using microbiology applications to ground the discussion. This structure is informed by first-hand experience training early-stage omics users, where covering omics theory provides a foundation for practical implementation.<\/jats:p>","DOI":"10.3389\/fbinf.2025.1721028","type":"journal-article","created":{"date-parts":[[2026,2,4]],"date-time":"2026-02-04T06:36:50Z","timestamp":1770187010000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Essential nucleic acid omics: a theoretical foundation for early-stage users"],"prefix":"10.3389","volume":"5","author":[{"given":"Andrew J.","family":"Maritan","sequence":"first","affiliation":[{"name":"Montana State University, Department of Microbiology & Cell Biology","place":["Bozeman, MT, United States"]},{"name":"Max Planck Institute for Marine Microbiology","place":["Bremen, Germany"]}]},{"given":"Frank J.","family":"Stewart","sequence":"additional","affiliation":[{"name":"Montana State University, Department of Microbiology & Cell Biology","place":["Bozeman, MT, United States"]},{"name":"Georgia Institute of Technology, School of Biological Sciences, Center for Microbial Dynamics and Infection","place":["Atlanta, GA, United States"]}]}],"member":"1965","published-online":{"date-parts":[[2026,2,4]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"1651","DOI":"10.1126\/science.2047873","article-title":"Complementary DNA sequencing: expressed sequence tags and human genome project","volume":"252","author":"Adams","year":"1991","journal-title":"Science"},{"key":"B3","doi-asserted-by":"publisher","first-page":"8195","DOI":"10.1038\/s41467-023-44082-5","article-title":"Is protein BLAST a thing of the past?","volume":"14","author":"Al-Fatlawi","year":"2023","journal-title":"Nat. Commun."},{"key":"B4","doi-asserted-by":"publisher","first-page":"381","DOI":"10.1126\/science.65.1686.381","article-title":"The limitations of taxonomy","volume":"65","author":"Aldrich","year":"1927","journal-title":"Science"},{"key":"B5","doi-asserted-by":"publisher","first-page":"1144","DOI":"10.1038\/nmeth.3103","article-title":"Binning metagenomic contigs by coverage and composition","volume":"11","author":"Alneberg","year":"2014","journal-title":"Nat. Methods"},{"key":"B239","doi-asserted-by":"publisher","first-page":"13219","DOI":"10.1038\/ncomms13219","article-title":"Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system","volume":"7","author":"Anantharaman","year":"2016","journal-title":"Nat. Commun."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1093\/bioinformatics\/btv688","article-title":"hybrid SPA des: an algorithm for hybrid assembly of short and long reads","volume":"32","author":"Antipov","year":"2016","journal-title":"Bioinformatics"},{"key":"B7","doi-asserted-by":"publisher","first-page":"2251","DOI":"10.1093\/bioinformatics\/btz859","article-title":"KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold","volume":"36","author":"Aramaki","year":"2020","journal-title":"Bioinformatics"},{"key":"B8","doi-asserted-by":"publisher","first-page":"btaf147","DOI":"10.1093\/bioinformatics\/btaf147","article-title":"CoverM: read alignment statistics for metagenomics","volume":"41","author":"Aroney","year":"2025","journal-title":"Bioinformatics"},{"key":"B9","doi-asserted-by":"publisher","first-page":"2500","DOI":"10.1038\/s41467-020-16366-7","article-title":"Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0","volume":"11","author":"Asnicar","year":"2020","journal-title":"Nat. Commun."},{"key":"B10","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1084\/jem.79.2.137","article-title":"Studies on the chemical nature of the substance inducing transformation of pneumococcal types","volume":"79","author":"Avery","year":"1944","journal-title":"J. Exp. Med."},{"key":"B11","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1093\/bib\/bbz020","article-title":"New approaches for metagenome assembly with short reads","volume":"21","author":"Ayling","year":"2020","journal-title":"Brief. Bioinform."},{"key":"B12","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1186\/1471-2164-7-246","article-title":"Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach","volume":"7","author":"Bainbridge","year":"2006","journal-title":"BMC Genomics"},{"key":"B13","doi-asserted-by":"publisher","first-page":"516","DOI":"10.1046\/j.1462-2920.2000.00133.x","article-title":"Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage","volume":"2","author":"B\u00e9j\u00e0","year":"2000","journal-title":"Environ. Microbiol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s43705-023-00315-8","article-title":"Net-spinning caddisflies create denitrifier-enriched niches in the stream microbiome","volume":"3","author":"Bertagnolli","year":"2023","journal-title":"ISME Commun."},{"key":"B15","doi-asserted-by":"publisher","first-page":"9938","DOI":"10.1073\/pnas.1501615112","article-title":"Phytoplankton\u2013bacterial interactions mediate micronutrient colimitation at the coastal antarctic sea ice edge","volume":"112","author":"Bertrand","year":"2015","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B16","doi-asserted-by":"publisher","first-page":"e2407886121","DOI":"10.1073\/pnas.2407886121","article-title":"Protecting scientific integrity in an age of generative AI","volume":"121","author":"Blau","year":"2024","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B17","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1186\/s42523-024-00341-4","article-title":"Microscale sampling of the coral gastrovascular cavity reveals a gut-like microbial community","volume":"6","author":"Bollati","year":"2024","journal-title":"Anim. Microbiome"},{"key":"B18","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"e00012","DOI":"10.1128\/mBio.00012-11","article-title":"Directed culturing of microorganisms using metatranscriptomics","volume":"2","author":"Bomar","year":"2011","journal-title":"mBio"},{"key":"B20","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1038\/nbt.3893","article-title":"Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea","volume":"35","author":"Bowers","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"B21","unstructured":"L50 vs N50: that\u2019s another fine mess that bioinformatics got us into\n          \n          \n            \n              Bradnam\n              K.\n            \n          \n          \n          2015"},{"key":"B22","doi-asserted-by":"publisher","first-page":"576","DOI":"10.1038\/190576a0","article-title":"An unstable intermediate carrying information from genes to ribosomes for protein synthesis","volume":"190","author":"Brenner","year":"1961","journal-title":"Nature"},{"key":"B23","volume-title":"Milestones in microbiology: 1546 to 1940","author":"Brock","year":"1999"},{"key":"B24","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"Buchfink","year":"2015","journal-title":"Nat. Methods"},{"key":"B25","doi-asserted-by":"publisher","first-page":"4091","DOI":"10.1021\/acsnano.3c01544","article-title":"Best practices for using AI when writing scientific manuscripts: caution, care, and consideration: creative science depends on it","volume":"17","author":"Buriak","year":"2023","journal-title":"ACS Nano"},{"key":"B26","doi-asserted-by":"publisher","first-page":"e0258693","DOI":"10.1371\/journal.pone.0258693","article-title":"Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy","volume":"16","author":"Bussi","year":"2021","journal-title":"PLOS ONE"},{"key":"B27","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinforma."},{"key":"B28","doi-asserted-by":"publisher","first-page":"45","DOI":"10.37441\/cejer\/2022\/4\/2\/11379","article-title":"Fair data: history and present context","volume":"4","author":"Carballo-Garc\u00eda","year":"2022","journal-title":"Central Eur. J. Educ. Res."},{"key":"B29","doi-asserted-by":"publisher","first-page":"18022","DOI":"10.1038\/s41598-017-18364-0","article-title":"Nanopore DNA sequencing and genome assembly on the international space station","volume":"7","author":"Castro-Wallace","year":"2017","journal-title":"Sci. Rep."},{"key":"B30","doi-asserted-by":"publisher","first-page":"5315","DOI":"10.1093\/bioinformatics\/btac672","article-title":"GTDB-Tk v2: memory friendly classification with the genome taxonomy database","volume":"38","author":"Chaumeil","year":"2022","journal-title":"Bioinformatics"},{"key":"B31","doi-asserted-by":"publisher","first-page":"982111","DOI":"10.3389\/fbioe.2023.982111","article-title":"Methods to improve the accuracy of next-generation sequencing","volume":"11","author":"Cheng","year":"2023","journal-title":"Front. Bioeng. Biotechnol."},{"key":"B32","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1038\/s41592-023-01940-w","article-title":"CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning","volume":"20","author":"Chklovski","year":"2023","journal-title":"Nat. Methods"},{"key":"B33","doi-asserted-by":"publisher","first-page":"e2413032122","DOI":"10.1073\/pnas.2413032122","article-title":"Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil","volume":"122","author":"Chuckran","year":"2025","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B34","article-title":"A data-supported history of bioinformatics tools","author":"Cl\u00e9ment","year":"2018"},{"key":"B35","doi-asserted-by":"publisher","first-page":"e00804","DOI":"10.1128\/mSystems.00804-20","article-title":"DOE JGI metagenome workflow","volume":"6","author":"Clum","year":"2021","journal-title":"mSystems"},{"key":"B36","doi-asserted-by":"publisher","first-page":"310","DOI":"10.3389\/fgene.2020.00310","article-title":"A primer for microbiome time-series analysis","volume":"11","author":"Coenen","year":"2020","journal-title":"Front. Genet."},{"key":"B37","doi-asserted-by":"publisher","first-page":"7506","DOI":"10.1038\/s41467-024-51841-5","article-title":"Covariation of hot spring geochemistry with microbial genomic diversity, function, and evolution","volume":"15","author":"Colman","year":"2024","journal-title":"Nat. Commun."},{"key":"B38","doi-asserted-by":"publisher","first-page":"1222","DOI":"10.1038\/s41396-021-01149-9","article-title":"Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations","volume":"16","author":"Conrad","year":"2022","journal-title":"ISME J."},{"key":"B39","first-page":"138","article-title":"On protein synthesis","volume":"12","author":"Crick","year":"1958","journal-title":"Symp. Soc. Exp. Biol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1126\/science.1096806","article-title":"The rise of the rhizosolenid diatoms","volume":"304","author":"Damst\u00e9","year":"2004","journal-title":"Science"},{"key":"B41","doi-asserted-by":"publisher","first-page":"obad036","DOI":"10.1093\/iob\/obad036","article-title":"Understanding organisms using ecological observatory networks. Integr. Org","volume":"5","author":"Dantzer","year":"2023","journal-title":"Biol"},{"key":"B42","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1186\/s40168-018-0605-2","article-title":"Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data","volume":"6","author":"Davis","year":"2018","journal-title":"Microbiome"},{"key":"B43","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1038\/s41564-018-0202-y","article-title":"Recognizing the reagent microbiome","volume":"3","author":"De Goffau","year":"2018","journal-title":"Nat. Microbiol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1139\/gen-2024-0068","article-title":"AVITI as an alternative to illumina for low-cost genome-wide genotyping","volume":"68","author":"De Ronne","year":"2025","journal-title":"Genome"},{"key":"B45","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1126\/science.1120250","article-title":"Community genomics among stratified microbial assemblages in the ocean\u2019s interior","volume":"311","author":"DeLong","year":"2006","journal-title":"Science"},{"key":"B46","doi-asserted-by":"publisher","first-page":"e0133021","DOI":"10.1128\/msystems.01330-21","article-title":"Elevational constraints on the composition and genomic attributes of microbial communities in antarctic soils","volume":"7","author":"Dragone","year":"2022","journal-title":"mSystems"},{"key":"B47","doi-asserted-by":"publisher","first-page":"e00338","DOI":"10.1128\/jcm.00338-23","article-title":"Direct 16S\/18S rRNA gene PCR followed by sanger sequencing as a clinical diagnostic tool for detection of bacterial and fungal infections: a systematic review and meta-analysis","volume":"61","author":"Drevinek","year":"2023","journal-title":"J. Clin. Microbiol."},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2014.00034","article-title":"Classification of pmoA amplicon pyrosequences using BLAST and the lowest common ancestor method in MEGAN","volume":"5","author":"Dumont","year":"2014","journal-title":"Front. Microbiol."},{"key":"B49","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1038\/s41587-022-01632-4","article-title":"Illumina faces short-read rivals","volume":"41","author":"Eisenstein","year":"2023","journal-title":"Nat. Biotechnol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"958","DOI":"10.1016\/j.cels.2021.08.009","article-title":"Minimizer-space de Bruijn graphs: whole-genome assembly of long reads in minutes on a personal computer","volume":"12","author":"Ekim","year":"2021","journal-title":"Cell Syst."},{"key":"B51","doi-asserted-by":"publisher","first-page":"992","DOI":"10.1038\/s41586-023-06186-2","article-title":"Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes","volume":"618","author":"Eme","year":"2023","journal-title":"Nature"},{"key":"B52","doi-asserted-by":"publisher","first-page":"5151","DOI":"10.1016\/j.cell.2024.08.028","article-title":"Modern microbiology: embracing complexity through integration across scales","volume":"187","author":"Eren","year":"2024","journal-title":"Cell"},{"key":"B53","doi-asserted-by":"publisher","first-page":"e1319","DOI":"10.7717\/peerj.1319","article-title":"Anvi\u2019o: an advanced analysis and visualization platform for \u2018omics data","volume":"3","author":"Eren","year":"2015","journal-title":"PeerJ"},{"key":"B54","doi-asserted-by":"publisher","first-page":"434","DOI":"10.1126\/science.aac7745","article-title":"Methane metabolism in the archaeal phylum bathyarchaeota revealed by genome-centric metagenomics","volume":"350","author":"Evans","year":"2015","journal-title":"Science"},{"key":"B55","doi-asserted-by":"publisher","first-page":"1570","DOI":"10.1038\/s41564-025-02035-2","article-title":"Guidelines for preventing and reporting contamination in low-biomass microbiome studies","volume":"10","author":"Fierer","year":"2025","journal-title":"Nat. Microbiol."},{"key":"B56","doi-asserted-by":"publisher","first-page":"496","DOI":"10.1126\/science.7542800","article-title":"Whole-genome random sequencing and assembly of Haemophilus influenzae Rd","volume":"269","author":"Fleischmann","year":"1995","journal-title":"Science"},{"key":"B57","doi-asserted-by":"publisher","first-page":"1206","DOI":"10.1016\/j.cell.2024.01.039","article-title":"A cryptic plasmid is among the most numerous genetic elements in the human gut","volume":"187","author":"Fogarty","year":"2024","journal-title":"Cell"},{"key":"B58","article-title":"Zombie ideas in ecology","author":"Fox","year":"2011","journal-title":"Oikos Blog"},{"key":"B59","doi-asserted-by":"publisher","first-page":"3805","DOI":"10.1073\/pnas.0708897105","article-title":"Microbial community gene expression in ocean surface waters","volume":"105","author":"Frias-Lopez","year":"2008","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B60","doi-asserted-by":"publisher","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"B61","doi-asserted-by":"publisher","first-page":"1981","DOI":"10.1093\/bib\/bby063","article-title":"A brief history of bioinformatics","volume":"20","author":"Gauthier","year":"2019","journal-title":"Brief. Bioinform."},{"key":"B62","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1038\/345060a0","article-title":"Genetic diversity in Sargasso Sea bacterioplankton","volume":"345","author":"Giovannoni","year":"1990","journal-title":"Nature"},{"key":"B63","doi-asserted-by":"publisher","first-page":"2224","DOI":"10.3389\/fmicb.2017.02224","article-title":"Microbiome datasets are compositional: and this is not optional","volume":"8","author":"Gloor","year":"2017","journal-title":"Front. Microbiol."},{"key":"B64","doi-asserted-by":"publisher","first-page":"546","DOI":"10.1126\/science.274.5287.546","article-title":"Life with 6000 genes","volume":"274","author":"Goffeau","year":"1996","journal-title":"Science"},{"key":"B65","doi-asserted-by":"publisher","first-page":"e00744","DOI":"10.1128\/mBio.00744-13","article-title":"Protein domains of unknown function are essential in bacteria","volume":"5","author":"Goodacre","year":"2014","journal-title":"mBio"},{"key":"B66","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1099\/ijs.0.64483-0","article-title":"DNA\u2013DNA hybridization values and their relationship to whole-genome sequence similarities","volume":"57","author":"Goris","year":"2007","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"B67","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-seq data without a reference genome","volume":"29","author":"Grabherr","year":"2011","journal-title":"Nat. Biotechnol."},{"key":"B240","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1038\/s41586-021-03297-6","article-title":"Anaerobic endosymbiont generates energy for ciliate host by denitrification","volume":"591","author":"Graf","year":"2021","journal-title":"Nat."},{"key":"B68","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/190581a0","article-title":"Unstable ribonucleic acid revealed by pulse labelling of Escherichia coli","volume":"190","author":"Gros","year":"1961","journal-title":"Nature"},{"key":"B69","volume-title":"Practical computing for biologists","author":"Haddock","year":"2011"},{"key":"B70","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1093\/nar\/29.1.41","article-title":"TIGRFAMs: a protein family resource for the functional identification of proteins","volume":"29","author":"Haft","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"B71","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1007\/s00248-011-9824-9","article-title":"Environmental constraints underpin the distribution and phylogenetic diversity of nifH in the yellowstone geothermal complex","volume":"61","author":"Hamilton","year":"2011","journal-title":"Microb. Ecol."},{"key":"B72","doi-asserted-by":"publisher","first-page":"931","DOI":"10.1111\/geb.13675","article-title":"The biogeography of host\u2010associated bacterial microbiomes: revisiting classic biodiversity patterns","volume":"32","author":"H\u00e4rer","year":"2023","journal-title":"Glob. Ecol. Biogeogr."},{"key":"B73","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1038\/s41579-020-0323-1","article-title":"Next-generation physiology approaches to study microbiome function at single cell level","volume":"18","author":"Hatzenpichler","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"B74","doi-asserted-by":"publisher","first-page":"3373","DOI":"10.1038\/s41467-024-47155-1","article-title":"Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes","volume":"15","author":"Hauptfeld","year":"2024","journal-title":"Nat. Commun."},{"key":"B75","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1038\/s41587-025-02584-1","article-title":"An open letter to graduate students and other procrastinators: it\u2019s time to write","volume":"43","author":"Hazelett","year":"2025","journal-title":"Nat. Biotechnol."},{"key":"B76","doi-asserted-by":"publisher","first-page":"msae061","DOI":"10.1093\/molbev\/msae061","article-title":"The diverse evolutionary histories of domesticated metaviral capsid genes in mammals","volume":"41","author":"Henriques","year":"2024","journal-title":"Mol. Biol. Evol."},{"key":"B77","doi-asserted-by":"publisher","first-page":"1940","DOI":"10.1111\/j.1462-2920.2010.02198.x","article-title":"Spatial patterns and light\u2010driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean","volume":"12","author":"Hewson","year":"2010","journal-title":"Environ. Microbiol."},{"key":"B78","doi-asserted-by":"publisher","first-page":"e6978","DOI":"10.1371\/journal.pone.0006978","article-title":"Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes","volume":"4","author":"Hou","year":"2009","journal-title":"PloS One"},{"key":"B79","doi-asserted-by":"publisher","first-page":"16048","DOI":"10.1038\/nmicrobiol.2016.48","article-title":"A new view of the tree of life","volume":"1","author":"Hug","year":"2016","journal-title":"Nat. Microbiol."},{"key":"B80","doi-asserted-by":"publisher","first-page":"2384","DOI":"10.1038\/s41564-025-02116-2","article-title":"A roadmap for equitable reuse of public microbiome data","volume":"10","author":"Hug","year":"2025","journal-title":"Nat. Microbiol."},{"key":"B81","doi-asserted-by":"publisher","first-page":"4399","DOI":"10.1128\/AEM.67.10.4399-4406.2001","article-title":"Counting the uncountable: statistical approaches to estimating microbial diversity","volume":"67","author":"Hughes","year":"2001","journal-title":"Appl. Environ. Microbiol."},{"key":"B82","doi-asserted-by":"publisher","first-page":"2880","DOI":"10.1038\/s41467-024-46947-9","article-title":"Genomic language model predicts protein co-regulation and function","volume":"15","author":"Hwang","year":"2024","journal-title":"Nat. Commun."},{"key":"B83","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinforma."},{"key":"B84","doi-asserted-by":"publisher","first-page":"5114","DOI":"10.1038\/s41467-018-07641-9","article-title":"High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries","volume":"9","author":"Jain","year":"2018","journal-title":"Nat. Commun."},{"key":"B85","doi-asserted-by":"publisher","first-page":"giab060","DOI":"10.1093\/gigascience\/giab060","article-title":"ISA API: an open platform for interoperable life science experimental metadata","volume":"10","author":"Johnson","year":"2021","journal-title":"GigaScience"},{"key":"B86","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41586-021-03819-2","article-title":"Highly accurate protein structure prediction with AlphaFold","volume":"596","author":"Jumper","year":"2021","journal-title":"Nature"},{"key":"B87","doi-asserted-by":"publisher","first-page":"910","DOI":"10.1016\/s0140-6736(78)91629-x","article-title":"Antenatal diagnosis of sickle-cell anaemia by DNA analysis of amniotic-fluid cells","volume":"312","author":"Kan","year":"1978","journal-title":"Lancet"},{"key":"B88","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1038\/s41576-020-0233-0","article-title":"Phylogenetic tree building in the genomic age","volume":"21","author":"Kapli","year":"2020","journal-title":"Nat. Rev. Genet."},{"key":"B89","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1093\/sysbio\/syad036","article-title":"DNA sequences are as useful as protein sequences for inferring deep phylogenies","volume":"72","author":"Kapli","year":"2023","journal-title":"Syst. Biol."},{"key":"B90","doi-asserted-by":"publisher","first-page":"D62","DOI":"10.1093\/nar\/gkae1058","article-title":"The international nucleotide sequence database collaboration (INSDC): enhancing global participation","volume":"53","author":"Karsch-Mizrachi","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"B91","doi-asserted-by":"publisher","first-page":"100121","DOI":"10.1016\/j.jcoa.2024.100121","article-title":"Evolution and applications of next generation sequencing and its intricate relations with chromatographic and spectrometric techniques in modern day sciences","volume":"5","author":"Katara","year":"2024","journal-title":"J. Chromatogr. Open"},{"key":"B92","doi-asserted-by":"publisher","first-page":"D387","DOI":"10.1093\/nar\/gkab1053","article-title":"The sequence read archive: a decade more of explosive growth","volume":"50","author":"Katz","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"B93","doi-asserted-by":"publisher","first-page":"1691","DOI":"10.1038\/s41467-019-09419-z","article-title":"Diel population and functional synchrony of microbial communities on coral reefs","volume":"10","author":"Kelly","year":"2019","journal-title":"Nat. Commun."},{"key":"B94","doi-asserted-by":"publisher","first-page":"e00084","DOI":"10.1128\/msystems.00084-22","article-title":"Deciphering active prophages from metagenomes","volume":"7","author":"Kieft","year":"2022","journal-title":"mSystems"},{"key":"B95","doi-asserted-by":"publisher","first-page":"320","DOI":"10.3390\/v11040320","article-title":"Protein structure-guided hidden markov models (HMMs) as A powerful method in the detection of ancestral endogenous viral elements","volume":"11","author":"Kirsip","year":"2019","journal-title":"Viruses"},{"key":"B96","doi-asserted-by":"publisher","first-page":"767","DOI":"10.1038\/s41467-020-14542-3","article-title":"Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean","volume":"11","author":"Kitzinger","year":"2020","journal-title":"Nat. Commun."},{"key":"B97","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1525\/bio.2012.62.4.9","article-title":"Past, present, and future roles of long-term experiments in the LTER network","volume":"62","author":"Knapp","year":"2012","journal-title":"BioScience"},{"key":"B98","doi-asserted-by":"publisher","first-page":"1118","DOI":"10.1038\/s41586-024-07631-6","article-title":"Cultivation and visualization of a methanogen of the phylum thermoproteota","volume":"632","author":"Kohtz","year":"2024","journal-title":"Nature"},{"key":"B99","doi-asserted-by":"publisher","first-page":"1329","DOI":"10.1038\/s41396-018-0058-4","article-title":"Solar-panel and parasol strategies shape the proteorhodopsin distribution pattern in marine flavobacteriia","volume":"12","author":"Kumagai","year":"2018","journal-title":"ISME J."},{"key":"B100","doi-asserted-by":"publisher","first-page":"2386","DOI":"10.1038\/ismej.2015.48","article-title":"Single-cell genomics-based analysis of virus\u2013host interactions in marine surface bacterioplankton","volume":"9","author":"Labont\u00e9","year":"2015","journal-title":"ISME J."},{"key":"B101","doi-asserted-by":"publisher","first-page":"2570","DOI":"10.1016\/j.cub.2018.07.008","article-title":"Systematic revision of symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts","volume":"28","author":"LaJeunesse","year":"2018","journal-title":"Curr. Biol."},{"key":"B102","doi-asserted-by":"publisher","first-page":"860","DOI":"10.1038\/35057062","article-title":"Initial sequencing and analysis of the human genome","volume":"409","author":"Lander","year":"2001","journal-title":"Nature"},{"key":"B103","doi-asserted-by":"publisher","first-page":"1317","DOI":"10.1128\/JB.01184-10","article-title":"Plasmids with a chromosome-like role in rhizobia","volume":"193","author":"Landeta","year":"2011","journal-title":"J. Bacteriol."},{"key":"B104","doi-asserted-by":"publisher","first-page":"6955","DOI":"10.1073\/pnas.82.20.6955","article-title":"Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses","volume":"82","author":"Lane","year":"1985","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"B105","doi-asserted-by":"publisher","first-page":"lqaf105","DOI":"10.1093\/nargab\/lqaf105","article-title":"Targeted decontamination of sequencing data with CLEAN","volume":"7","author":"Lataretu","year":"2025","journal-title":"Nar. Genomics Bioinforma."},{"key":"B106","doi-asserted-by":"publisher","first-page":"D19","DOI":"10.1093\/nar\/gkq1019","article-title":"The sequence read archive","volume":"39","author":"Leinonen","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"B107","article-title":"Greening lab metabolic marker gene databases","author":"Leung","year":"2020"},{"key":"B108","doi-asserted-by":"publisher","first-page":"639","DOI":"10.1146\/annurev-micro-042924-095145","article-title":"Cyanophages: billions of years of coevolution with cyanobacteria","volume":"79","author":"Li","year":"2025","journal-title":"Annu. Rev. Microbiol."},{"key":"B109","doi-asserted-by":"publisher","first-page":"474","DOI":"10.1186\/s12859-017-1911-6","article-title":"Reference-guided de novo assembly approach improves genome reconstruction for related species","volume":"18","author":"Lischer","year":"2017","journal-title":"BMC Bioinforma."},{"key":"B110","doi-asserted-by":"publisher","first-page":"14139","DOI":"10.1038\/srep14139","article-title":"Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites","volume":"5","author":"Liu","year":"2015","journal-title":"Sci. Rep."},{"key":"B111","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1038\/s41422-024-01026-y","article-title":"The 1% gift to humanity: the human genome project II","volume":"34","author":"Liu","year":"2024","journal-title":"Cell Res."},{"key":"B112","doi-asserted-by":"publisher","first-page":"1272","DOI":"10.1126\/science.aaf4507","article-title":"Decoupling function and taxonomy in the global ocean microbiome","volume":"353","author":"Louca","year":"2016","journal-title":"Science"},{"key":"B113","doi-asserted-by":"publisher","first-page":"955","DOI":"10.1093\/nar\/25.5.955","article-title":"tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence","volume":"25","author":"Lowe","year":"1997","journal-title":"Nucleic Acids Res."},{"key":"B114","doi-asserted-by":"publisher","first-page":"1704","DOI":"10.1101\/gr.151803.112","article-title":"Meta-analyses of studies of the human microbiota","volume":"23","author":"Lozupone","year":"2013","journal-title":"Genome Res."},{"key":"B115","doi-asserted-by":"publisher","first-page":"642422","DOI":"10.3389\/fmicb.2021.642422","article-title":"Mechanism across scales: a holistic modeling framework integrating laboratory and field studies for microbial ecology","volume":"12","author":"Lui","year":"2021","journal-title":"Front. Microbiol."},{"key":"B116","doi-asserted-by":"publisher","first-page":"877","DOI":"10.1016\/j.cell.2023.01.002","article-title":"Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states","volume":"186","author":"Ma","year":"2023","journal-title":"Cell"},{"key":"B117","doi-asserted-by":"publisher","first-page":"mgen000436","DOI":"10.1099\/mgen.0.000436","article-title":"Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic islands","volume":"6","author":"Maguire","year":"2020","journal-title":"Microb. Genomics"},{"key":"B118","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1093\/gbe\/evx015","article-title":"Phylogenetic diversity of NTT nucleotide transport proteins in free-living and parasitic bacteria and eukaryotes","volume":"9","author":"Major","year":"2017","journal-title":"Genome Biol. Evol."},{"key":"B119","volume-title":"Zooming in and out on coral reef microbiomes: molecular patterns over space and time","author":"Maritan","year":"2025"},{"key":"B120","doi-asserted-by":"publisher","first-page":"wraf088","DOI":"10.1093\/ismejo\/wraf088","article-title":"Sea cucumber grazing linked to enrichment of anaerobic microbial metabolisms in coral reef sediments","volume":"19","author":"Maritan","year":"2025","journal-title":"ISME J."},{"key":"B121","doi-asserted-by":"publisher","first-page":"fnaa031","DOI":"10.1093\/femsle\/fnaa031","article-title":"Mapping metabolic activity at single cell resolution in intact volcanic fumarole sediment","volume":"367","author":"Marlow","year":"2020","journal-title":"FEMS Microbiol. Lett."},{"key":"B122","doi-asserted-by":"publisher","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet.J."},{"key":"B123","doi-asserted-by":"publisher","first-page":"5514","DOI":"10.1093\/molbev\/msab254","article-title":"Phylogenetic signal, congruence, and uncertainty across bacteria and archaea","volume":"38","author":"Martinez-Gutierrez","year":"2021","journal-title":"Mol. Biol. Evol."},{"key":"B124","doi-asserted-by":"publisher","first-page":"giad067","DOI":"10.1093\/gigascience\/giad067","article-title":"ARA: a flexible pipeline for automated exploration of NCBI SRA datasets","volume":"12","author":"Maurya","year":"2022","journal-title":"GigaScience"},{"key":"B125","doi-asserted-by":"publisher","first-page":"1545","DOI":"10.1038\/ismej.2017.37","article-title":"Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents","volume":"11","author":"Meier","year":"2017","journal-title":"ISME J."},{"key":"B126","doi-asserted-by":"publisher","first-page":"e02593-20","DOI":"10.1128\/AEM.02593-20","article-title":"The reliability of metagenome-assembled genomes (MAGs) in representing natural populations: insights from comparing MAGs against isolate genomes derived from the same fecal sample","volume":"87","author":"Meziti","year":"2021","journal-title":"Appl. Environ. Microbiol."},{"key":"B127","doi-asserted-by":"publisher","first-page":"19537","DOI":"10.1038\/s41598-019-55984-0","article-title":"Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype","volume":"9","author":"Mihel\u010di\u0107","year":"2019","journal-title":"Sci. Rep."},{"key":"B128","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1093\/bioinformatics\/btv697","article-title":"MetaQUAST: evaluation of metagenome assemblies","volume":"32","author":"Mikheenko","year":"2016","journal-title":"Bioinformatics"},{"key":"B129","doi-asserted-by":"crossref","DOI":"10.1201\/9780429258770","volume-title":"Cell biology by the numbers","author":"Milo","year":"2015"},{"key":"B130","doi-asserted-by":"publisher","first-page":"3029","DOI":"10.1093\/bioinformatics\/btab184","article-title":"Fast and sensitive taxonomic assignment to metagenomic contigs","volume":"37","author":"Mirdita","year":"2021","journal-title":"Bioinformatics"},{"key":"B131","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1038\/s43705-022-00204-6","article-title":"Unexpected absence of ribosomal protein genes from metagenome-assembled genomes","volume":"2","author":"Mise","year":"2022","journal-title":"ISME Commun."},{"key":"B132","doi-asserted-by":"publisher","first-page":"1526","DOI":"10.1038\/s41564-024-01704-y","article-title":"Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts","volume":"9","author":"Mitchell","year":"2024","journal-title":"Nat. Microbiol."},{"key":"B133","doi-asserted-by":"publisher","first-page":"1429","DOI":"10.1007\/s11831-020-09422-4","article-title":"A systematic review of hidden markov models and their applications","volume":"28","author":"Mor","year":"2021","journal-title":"Arch. Comput. Methods Eng."},{"key":"B134","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1038\/ismej.2012.94","article-title":"Sizing up metatranscriptomics","volume":"7","author":"Moran","year":"2013","journal-title":"ISME J."},{"key":"B135","doi-asserted-by":"publisher","first-page":"218","DOI":"10.1038\/s41559-021-01606-w","article-title":"Complex marine microbial communities partition metabolism of scarce resources over the diel cycle","volume":"6","author":"Muratore","year":"2022","journal-title":"Nat. Ecol. Evol."},{"key":"B136","doi-asserted-by":"publisher","first-page":"987","DOI":"10.1038\/s41564-020-0733-x","article-title":"Roadmap for naming uncultivated archaea and bacteria","volume":"5","author":"Murray","year":"2020","journal-title":"Nat. Microbiol."},{"key":"B137","doi-asserted-by":"publisher","first-page":"1344","DOI":"10.1126\/science.1158441","article-title":"The transcriptional landscape of the yeast genome defined by RNA sequencing","volume":"320","author":"Nagalakshmi","year":"2008","journal-title":"Science"},{"key":"B139","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/s41587-020-0718-6","article-title":"A genomic catalog of Earth\u2019s microbiomes","volume":"39","author":"Nayfach","year":"2021","journal-title":"Nat. Biotechnol."},{"key":"B140","doi-asserted-by":"publisher","first-page":"e10119","DOI":"10.7717\/peerj.10119","article-title":"Biases in genome reconstruction from metagenomic data","volume":"8","author":"Nelson","year":"2020","journal-title":"PeerJ"},{"key":"B141","doi-asserted-by":"publisher","first-page":"e1000424","DOI":"10.1371\/journal.pcbi.1000424","article-title":"A quick guide to organizing computational biology projects","volume":"5","author":"Noble","year":"2009","journal-title":"PLOS Comput. Biol."},{"key":"B142","doi-asserted-by":"publisher","first-page":"813","DOI":"10.1038\/s41396-023-01390-4","article-title":"Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression","volume":"17","author":"Nowinski","year":"2023","journal-title":"ISME J."},{"key":"B143","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1126\/science.abj6987","article-title":"The complete sequence of a human genome","volume":"376","author":"Nurk","year":"2022","journal-title":"Science"},{"key":"B144","doi-asserted-by":"publisher","first-page":"2864","DOI":"10.1038\/ismej.2017.126","article-title":"dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication","volume":"11","author":"Olm","year":"2017","journal-title":"ISME J."},{"key":"B145","doi-asserted-by":"publisher","first-page":"e2025322118","DOI":"10.1073\/pnas.2025322118","article-title":"Multiple energy sources and metabolic strategies sustain microbial diversity in antarctic desert soils","volume":"118","author":"Ortiz","year":"2021","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B146","doi-asserted-by":"publisher","first-page":"nwad022","DOI":"10.1093\/nsr\/nwad022","article-title":"Taxonomic species recognition should be consistent","volume":"9","author":"O\u2019Brien","year":"2022","journal-title":"Natl. Sci. Rev."},{"key":"B147","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.tig.2014.12.002","article-title":"Accounting for uncertainty in DNA sequencing data","volume":"31","author":"O\u2019Rawe","year":"2015","journal-title":"Trends Genet."},{"key":"B148","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1126\/science.276.5313.734","article-title":"A molecular view of microbial diversity and the biosphere","volume":"276","author":"Pace","year":"1997","journal-title":"Science"},{"key":"B149","doi-asserted-by":"publisher","first-page":"100412","DOI":"10.1016\/j.cpb.2024.100412","article-title":"Using next-generation sequencing approach for discovery and characterization of plant molecular markers","volume":"40","author":"Panahi","year":"2024","journal-title":"Curr. Plant Biol."},{"key":"B150","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1101\/gr.186072.114","article-title":"CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes","volume":"25","author":"Parks","year":"2015","journal-title":"Genome Res."},{"key":"B151","doi-asserted-by":"publisher","first-page":"1533","DOI":"10.1038\/s41564-017-0012-7","article-title":"Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life","volume":"2","author":"Parks","year":"2017","journal-title":"Nat. Microbiol."},{"key":"B152","doi-asserted-by":"publisher","first-page":"996","DOI":"10.1038\/nbt.4229","article-title":"A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life","volume":"36","author":"Parks","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"B153","doi-asserted-by":"publisher","first-page":"1079","DOI":"10.1038\/s41587-020-0501-8","article-title":"A complete domain-to-species taxonomy for bacteria and archaea","volume":"38","author":"Parks","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"B154","doi-asserted-by":"publisher","first-page":"2416","DOI":"10.1038\/s41591-025-03693-9","article-title":"Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer","volume":"31","author":"Piccinno","year":"2025","journal-title":"Nat. Med."},{"key":"B155","doi-asserted-by":"publisher","first-page":"2877","DOI":"10.1038\/s41564-024-01808-5","article-title":"An intranuclear bacterial parasite of deep-sea mussels expresses apoptosis inhibitors acquired from its host","volume":"9","author":"Porras","year":"2024","journal-title":"Nat. Microbiol."},{"key":"B156","doi-asserted-by":"publisher","first-page":"1326","DOI":"10.1038\/s41467-025-56203-3","article-title":"Seasonal recurrence and modular assembly of an arctic pelagic marine microbiome","volume":"16","author":"Priest","year":"2025","journal-title":"Nat. Commun."},{"key":"B157","doi-asserted-by":"publisher","first-page":"e102","DOI":"10.1002\/cpbi.102","article-title":"Using SPAdes de novo Assembler","volume":"70","author":"Prjibelski","year":"2020","journal-title":"Curr. Protoc. Bioinforma."},{"key":"B158","doi-asserted-by":"publisher","first-page":"3342","DOI":"10.1128\/AEM.71.6.3342-3347.2005","article-title":"Genomic DNA amplification from a single bacterium","volume":"71","author":"Raghunathan","year":"2005","journal-title":"Appl. Environ. Microbiol."},{"key":"B159","doi-asserted-by":"publisher","first-page":"wrae195","DOI":"10.1093\/ismejo\/wrae195","article-title":"Leveraging genomic information to predict environmental preferences of bacteria","volume":"18","author":"Ramoneda","year":"2024","journal-title":"ISME J."},{"key":"B160","doi-asserted-by":"publisher","first-page":"e191","DOI":"10.1093\/nar\/gkq747","article-title":"FragGeneScan: predicting genes in short and error-prone reads","volume":"38","author":"Rho","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"B161","doi-asserted-by":"publisher","first-page":"wraf117","DOI":"10.1093\/ismejo\/wraf117","article-title":"Chemosynthesis enhances net primary production and nutrient cycling in a hypersaline microbial mat","volume":"19","author":"Ricci","year":"2025","journal-title":"ISME J."},{"key":"B162","doi-asserted-by":"publisher","first-page":"e00200-23","DOI":"10.1128\/spectrum.00200-23","article-title":"Terabase-scale coassembly of a tropical soil microbiome","volume":"11","author":"Riley","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"B163","doi-asserted-by":"publisher","first-page":"431","DOI":"10.1038\/nature12352","article-title":"Insights into the phylogeny and coding potential of microbial dark matter","volume":"499","author":"Rinke","year":"2013","journal-title":"Nature"},{"key":"B164","doi-asserted-by":"publisher","DOI":"10.1101\/2025.07.18.665519","article-title":"The MicrobeAtlas database: global trends and insights into","author":"Rodrigues","year":"2025","journal-title":"Earth\u2019s Microbial Ecosystems"},{"key":"B165","doi-asserted-by":"publisher","first-page":"629","DOI":"10.1093\/bioinformatics\/btt584","article-title":"Nonpareil: a redundancy-based approach to assess the level of coverage in metagenomic datasets","volume":"30","author":"Rodriguez-R","year":"2014","journal-title":"Bioinformatics"},{"key":"B166","doi-asserted-by":"publisher","first-page":"e00039","DOI":"10.1128\/mSystems.00039-18","article-title":"Nonpareil 3: fast estimation of metagenomic coverage and sequence diversity","volume":"3","author":"Rodriguez-R","year":"2018","journal-title":"mSystems"},{"key":"B168","doi-asserted-by":"publisher","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: a versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"B169","doi-asserted-by":"publisher","first-page":"2541","DOI":"10.1128\/AEM.66.6.2541-2547.2000","article-title":"Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms","volume":"66","author":"Rondon","year":"2000","journal-title":"Appl. Environ. Microbiol."},{"key":"B170","doi-asserted-by":"publisher","first-page":"fiae132","DOI":"10.1093\/femsec\/fiae132","article-title":"Widespread occurrence of dissolved oxygen anomalies, aerobic microbes, and oxygen-producing metabolic pathways in apparently anoxic environments","volume":"100","author":"Ruff","year":"2024","journal-title":"FEMS Microbiol. Ecol."},{"key":"B171","doi-asserted-by":"publisher","first-page":"1350","DOI":"10.1126\/science.2999980","article-title":"Enzymatic amplification of \u03b2-Globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia","volume":"230","author":"Saiki","year":"1985","journal-title":"Science"},{"key":"B172","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1038\/265687a0","article-title":"Nucleotide sequence of bacteriophage \u03c6X174 DNA","volume":"265","author":"Sanger","year":"","journal-title":"Nature"},{"key":"B173","doi-asserted-by":"publisher","first-page":"5463","DOI":"10.1073\/pnas.74.12.5463","article-title":"DNA sequencing with chain-terminating inhibitors","volume":"74","author":"Sanger","year":"","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B174","doi-asserted-by":"publisher","first-page":"997","DOI":"10.3390\/biology12070997","article-title":"Next-generation sequencing technology: current trends and advancements","volume":"12","author":"Satam","year":"2023","journal-title":"Biology"},{"key":"B175","doi-asserted-by":"publisher","first-page":"D33","DOI":"10.1093\/nar\/gkad1044","article-title":"Database resources of the national center for biotechnology information","volume":"52","author":"Sayers","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"B176","doi-asserted-by":"publisher","first-page":"D56","DOI":"10.1093\/nar\/gkae1114","article-title":"GenBank 2025 update","volume":"53","author":"Sayers","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"B177","doi-asserted-by":"publisher","first-page":"467","DOI":"10.1126\/science.270.5235.467","article-title":"Quantitative monitoring of gene expression patterns with a complementary DNA microarray","volume":"270","author":"Schena","year":"1995","journal-title":"Science"},{"key":"B178","volume-title":"Writing science: how to write papers that get cited and proposals that get funded","author":"Schimel","year":"2012"},{"key":"B179","doi-asserted-by":"publisher","first-page":"e02343-19","DOI":"10.1128\/AEM.02343-19","article-title":"Reintroducing mothur: 10 years later","volume":"86","author":"Schloss","year":"2020","journal-title":"Appl. Environ. Microbiol."},{"key":"B180","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome annotation","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B181","first-page":"227","article-title":"BUSCO: assessing genome assembly and annotation completeness","volume-title":"Gene prediction","author":"Seppey","year":"2019"},{"key":"B182","doi-asserted-by":"publisher","first-page":"1544","DOI":"10.1126\/science.311.5767.1544","article-title":"The race for the $1000 genome","volume":"311","author":"Service","year":"2006","journal-title":"Science"},{"key":"B183","doi-asserted-by":"publisher","first-page":"2128","DOI":"10.1038\/s41564-022-01266-x","article-title":"Standardized multi-omics of Earth\u2019s microbiomes reveals microbial and metabolite diversity","volume":"7","author":"Shaffer","year":"2022","journal-title":"Nat. Microbiol."},{"key":"B184","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1101\/gr.142315.112","article-title":"Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization","volume":"23","author":"Sharon","year":"2013","journal-title":"Genome Res."},{"key":"B185","doi-asserted-by":"publisher","first-page":"e191","DOI":"10.1002\/imt2.191","article-title":"SeqKit2: a Swiss army knife for sequence and alignment processing","volume":"3","author":"Shen","year":"2024","journal-title":"iMeta"},{"key":"B186","doi-asserted-by":"publisher","first-page":"fiae105","DOI":"10.1093\/femsec\/fiae105","article-title":"Wood\u2013ljungdahl pathway encoding anaerobes facilitate low-cost primary production in hypersaline sediments at Great Salt Lake, Utah","volume":"100","author":"Shoemaker","year":"2024","journal-title":"FEMS Microbiol. Ecol."},{"key":"B187","doi-asserted-by":"publisher","first-page":"e9954","DOI":"10.7717\/peerj.9954","article-title":"The reuse of public datasets in the life sciences: potential risks and rewards","volume":"8","author":"Sielemann","year":"2020","journal-title":"PeerJ"},{"key":"B188","doi-asserted-by":"publisher","first-page":"e00038-18","DOI":"10.1128\/msystems.00038-18","article-title":"Holistic assessment of rumen microbiome dynamics through quantitative metatranscriptomics reveals multifunctional redundancy during key steps of anaerobic feed degradation","volume":"3","author":"S\u00f6llinger","year":"2018","journal-title":"mSystems"},{"key":"B189","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1186\/s40168-018-0465-9","article-title":"Setting the pace: host rhythmic behaviour and gene expression patterns in the facultatively symbiotic cnidarian aiptasia are determined largely by symbiodinium","volume":"6","author":"Sorek","year":"2018","journal-title":"Microbiome"},{"key":"B190","doi-asserted-by":"publisher","first-page":"e5614","DOI":"10.7717\/peerj.5614","article-title":"Metabolic marker gene mining provides insight in global mcrA diversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of the Methanomassiliicoccales","volume":"6","author":"Speth","year":"2018","journal-title":"PeerJ"},{"key":"B191","doi-asserted-by":"publisher","first-page":"1162","DOI":"10.1038\/s41467-017-01265-1","article-title":"Generalist species drive microbial dispersion and evolution","volume":"8","author":"Sriswasdi","year":"2017","journal-title":"Nat. Commun."},{"key":"B192","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1126\/science.224.4647.409","article-title":"Analysis of hydrothermal vent-associated symbionts by ribosomal RNA sequences","volume":"224","author":"Stahl","year":"1984","journal-title":"Science"},{"key":"B193","doi-asserted-by":"publisher","first-page":"1331","DOI":"10.1007\/s10295-009-0642-8","article-title":"Universal species concept: pipe dream or a step toward unifying biology?","volume":"36","author":"Staley","year":"2009","journal-title":"J. Ind. Microbiol. Biotechnol."},{"key":"B194","doi-asserted-by":"publisher","first-page":"834","DOI":"10.1038\/s41576-023-00620-x","article-title":"Incongruence in the phylogenomics era","volume":"24","author":"Steenwyk","year":"2023","journal-title":"Nat. Rev. Genet."},{"key":"B195","doi-asserted-by":"publisher","first-page":"591","DOI":"10.1128\/jb.178.3.591-599.1996","article-title":"Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon","volume":"178","author":"Stein","year":"1996","journal-title":"J. Bacteriol."},{"key":"B196","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nbt.3988","article-title":"MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets","volume":"35","author":"Steinegger","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"B197","doi-asserted-by":"publisher","first-page":"1257","DOI":"10.1002\/lno.12074","article-title":"Aerobic and anaerobic methane oxidation in a seasonally anoxic basin","volume":"67","author":"Steinsd\u00f3ttir","year":"2022","journal-title":"Limnol. Oceanogr."},{"key":"B198","doi-asserted-by":"publisher","first-page":"e1002195","DOI":"10.1371\/journal.pbio.1002195","article-title":"Big data: astronomical or genomical?","volume":"13","author":"Stephens","year":"2015","journal-title":"PLOS Biol."},{"key":"B199","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1111\/j.1462-2920.2010.02400.x","article-title":"Microbial metatranscriptomics in a permanent marine oxygen minimum zone","volume":"14","author":"Stewart","year":"2012","journal-title":"Environ. Microbiol."},{"key":"B200","doi-asserted-by":"publisher","first-page":"428","DOI":"10.1038\/s41579-020-0364-5","article-title":"Tara oceans: towards global ocean ecosystems biology","volume":"18","author":"Sunagawa","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"B202","doi-asserted-by":"publisher","first-page":"1788","DOI":"10.1038\/s41396-022-01229-4","article-title":"Linking transcriptional dynamics of CH4-cycling grassland soil microbiomes to seasonal gas fluxes","volume":"16","author":"T\u00e4umer","year":"2022","journal-title":"ISME J."},{"key":"B204","doi-asserted-by":"publisher","first-page":"D609","DOI":"10.1093\/nar\/gkae1010","article-title":"UniProt: the universal protein knowledgebase in 2025","volume":"53","author":"Bateman","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"B205","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/nature24621","article-title":"A communal catalogue reveals Earth\u2019s multiscale microbial diversity","volume":"551","author":"Thompson","year":"2017","journal-title":"Nature"},{"key":"B206","doi-asserted-by":"publisher","first-page":"1786","DOI":"10.1111\/1755-0998.13588","article-title":"High molecular weight DNA extraction strategies for long\u2010read sequencing of complex metagenomes","volume":"22","author":"Trigodet","year":"2022","journal-title":"Mol. Ecol. Resour."},{"key":"B207","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1038\/nature06776","article-title":"SAR11 marine bacteria require exogenous reduced sulphur for growth","volume":"452","author":"Tripp","year":"2008","journal-title":"Nature"},{"key":"B208","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1038\/s41586-024-07495-w","article-title":"Rhizobia\u2013diatom symbiosis fixes missing nitrogen in the ocean","volume":"630","author":"Tschitschko","year":"2024","journal-title":"Nature"},{"key":"B209","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1038\/nature19068","article-title":"SAR11 bacteria linked to ocean anoxia and nitrogen loss","volume":"536","author":"Tsementzi","year":"2016","journal-title":"Nature"},{"key":"B210","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1038\/nature02340","article-title":"Community structure and metabolism through reconstruction of microbial genomes from the environment","volume":"428","author":"Tyson","year":"2004","journal-title":"Nature"},{"key":"B211","doi-asserted-by":"publisher","first-page":"514","DOI":"10.1038\/s41564-023-01579-5","article-title":"Double-stranded RNA sequencing reveals distinct riboviruses associated with thermoacidophilic bacteria from hot springs in Japan","volume":"9","author":"Urayama","year":"2024","journal-title":"Nat. Microbiol."},{"key":"B212","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1186\/s40168-018-0541-1","article-title":"MetaWRAP\u2014a flexible pipeline for genome-resolved metagenomic data analysis","volume":"6","author":"Uritskiy","year":"2018","journal-title":"Microbiome"},{"key":"B213","doi-asserted-by":"publisher","first-page":"484","DOI":"10.1126\/science.270.5235.484","article-title":"Serial analysis of gene expression","volume":"270","author":"Velculescu","year":"1995","journal-title":"Science"},{"key":"B214","doi-asserted-by":"publisher","first-page":"243","DOI":"10.1016\/S0092-8674(00)81845-0","article-title":"Characterization of the yeast transcriptome","volume":"88","author":"Velculescu","year":"1997","journal-title":"Cell"},{"key":"B215","doi-asserted-by":"publisher","first-page":"1304","DOI":"10.1126\/science.1058040","article-title":"The sequence of the human genome","volume":"291","author":"Venter","year":"2001","journal-title":"Science"},{"key":"B216","doi-asserted-by":"publisher","first-page":"1178","DOI":"10.1038\/s41396-020-00842-5","article-title":"Distinct ecotypes within a natural haloarchaeal population enable adaptation to changing environmental conditions without causing population sweeps","volume":"15","author":"Viver","year":"2021","journal-title":"ISME J."},{"key":"B217","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1038\/171737a0","article-title":"Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid","volume":"171","author":"Watson","year":"1953","journal-title":"Nature"},{"key":"B218","doi-asserted-by":"publisher","first-page":"bbae229","DOI":"10.1093\/bib\/bbae229","article-title":"AnnoView enables large-scale analysis, comparison, and visualization of microbial gene neighborhoods","volume":"25","author":"Wei","year":"2024","journal-title":"Brief. Bioinform."},{"key":"B219","volume-title":"R for data science","author":"Wickham","year":"2023"},{"key":"B220","doi-asserted-by":"publisher","first-page":"1921","DOI":"10.1038\/s41396-022-01242-7","article-title":"Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity","volume":"16","author":"Wilbanks","year":"2022","journal-title":"ISME J."},{"key":"B221","doi-asserted-by":"publisher","first-page":"160018","DOI":"10.1038\/sdata.2016.18","article-title":"The FAIR guiding principles for scientific data management and stewardship","volume":"3","author":"Wilkinson","year":"2016","journal-title":"Sci. Data"},{"key":"B223","doi-asserted-by":"publisher","first-page":"5088","DOI":"10.1073\/pnas.74.11.5088","article-title":"Phylogenetic structure of the prokaryotic domain: the primary kingdoms","volume":"74","author":"Woese","year":"1977","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B224","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-025-02738-1","article-title":"Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and sandpiper","author":"Woodcroft","year":"2025","journal-title":"Nat. Biotechnol."},{"key":"B225","doi-asserted-by":"publisher","first-page":"e5299","DOI":"10.1371\/journal.pone.0005299","article-title":"Assembling the marine metagenome, one cell at a time","volume":"4","author":"Woyke","year":"2009","journal-title":"PLoS ONE"},{"key":"B226","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1038\/s41467-024-47371-9","article-title":"Accurately clustering biological sequences in linear time by relatedness sorting","volume":"15","author":"Wright","year":"2024","journal-title":"Nat. Commun."},{"key":"B227","doi-asserted-by":"publisher","first-page":"bbae122","DOI":"10.1093\/bib\/bbae122","article-title":"FAIR header reference genome: a TRUSTworthy standard","volume":"25","author":"Wright","year":"2024","journal-title":"Brief. Bioinform."},{"key":"B228","doi-asserted-by":"publisher","first-page":"12115","DOI":"10.1038\/ncomms12115","article-title":"Genomics-informed isolation and characterization of a symbiotic nanoarchaeota system from a terrestrial geothermal environment","volume":"7","author":"Wurch","year":"2016","journal-title":"Nat. Commun."},{"key":"B229","doi-asserted-by":"publisher","first-page":"1107","DOI":"10.1093\/molbev\/msk019","article-title":"Average gene length is highly conserved in prokaryotes and eukaryotes and diverges only between the two kingdoms","volume":"23","author":"Xu","year":"2006","journal-title":"Mol. Biol. Evol."},{"key":"B230","doi-asserted-by":"publisher","first-page":"4443","DOI":"10.1073\/pnas.82.13.4443","article-title":"Mitochondrial origins","volume":"82","author":"Yang","year":"1985","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B231","doi-asserted-by":"publisher","first-page":"6301","DOI":"10.1016\/j.csbj.2021.11.028","article-title":"A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data","volume":"19","author":"Yang","year":"2021","journal-title":"Comput. Struct. Biotechnol. J."},{"key":"B232","doi-asserted-by":"publisher","first-page":"e16","DOI":"10.1371\/journal.pbio.0050016","article-title":"The sorcerer II global ocean sampling expedition: expanding the universe of protein families","volume":"5","author":"Yooseph","year":"2007","journal-title":"PLoS Biol."},{"key":"B233","doi-asserted-by":"publisher","first-page":"ycae030","DOI":"10.1093\/ismeco\/ycae030","article-title":"Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia","volume":"4","author":"Yu","year":"2024","journal-title":"ISME Commun."},{"key":"B234","doi-asserted-by":"publisher","first-page":"1044","DOI":"10.1038\/s41467-021-21350-w","article-title":"Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features","volume":"12","author":"Yutin","year":"2021","journal-title":"Nat. Commun."},{"key":"B235","doi-asserted-by":"publisher","first-page":"919903","DOI":"10.3389\/fcimb.2022.919903","article-title":"Comparison analysis of different DNA extraction methods on suitability for long-read metagenomic nanopore sequencing","volume":"12","author":"Zhang","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B236","doi-asserted-by":"publisher","first-page":"1857","DOI":"10.1038\/s41467-024-46109-x","article-title":"Viral potential to modulate microbial methane metabolism varies by habitat","volume":"15","author":"Zhong","year":"2024","journal-title":"Nat. Commun."},{"key":"B237","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s40168-021-01213-8","article-title":"METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks","volume":"10","author":"Zhou","year":"2022","journal-title":"Microbiome"},{"key":"B238","doi-asserted-by":"publisher","first-page":"9472","DOI":"10.1038\/s41467-024-53753-w","article-title":"The biogeography of soil microbiome potential growth rates","volume":"15","author":"Zhou","year":"2024","journal-title":"Nat. Commun."}],"container-title":["Frontiers in Bioinformatics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2025.1721028\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,2,24]],"date-time":"2026-02-24T09:52:43Z","timestamp":1771926763000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2025.1721028\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2,4]]},"references-count":234,"alternative-id":["10.3389\/fbinf.2025.1721028"],"URL":"https:\/\/doi.org\/10.3389\/fbinf.2025.1721028","relation":{},"ISSN":["2673-7647"],"issn-type":[{"value":"2673-7647","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2,4]]},"article-number":"1721028"}}