HiFi-Metagenomics-Publications.md

HiFi Metagenomics Publications

(Updated 04/26)

Pre-prints

• Agrawal AA, Bader CD, Garcia R, Muller R, and OV Kalinina. 2026. LoReMINE: Long Read-based Microbial genome mining pipeline. bioRxiv, https://doi.org/10.64898/2026.02.02.703231

• Al-Ghalith GA, Ryon KA, Henriksen JR, Danko DC, Farthing B, Marengo M, Church GM, Peixoto RS, Patel CJ, Knights D, and BT Tierny. 2025. XTree enables memory-efficient, accurate short and long sequence alignment to millions of genomes across the tree of life. bioRxiv, https://doi.org/10.64898/2025.12.22.696015

• Audemard J, Creusot N, Leloup J, Duval C, Halary S, Mary L, Eon M, Forjonel T, Mouffok M, Puppo R, Belmonte E, Gautier V, Got J, Lefebvre M, Markov GV, Muller C, Marie B, Diémé B, and C Frioux. 2026. Integrating metagenome-scale metabolic modelling and metabolomics to identify biochemical interactions in Microcystis phycospheres. bioRxiv, https://doi.org/10.64898/2026.03.18.712574

• Belliardo C, Maurice N, Pere A, Mondy S, Franc A, Bailly-Bechet M, Lemaitre C, Vicedomini R, Frigerio J-M, Salin F, Belmonte E, Sherman DJ, Abad P, Frioux C, and EGJ Danchin. 2025. Accurate MAG reconstruction from complex soil microbiome through combined short- and HiFi long-reads metagenomics. bioRxiv, https://doi.org/10.1101/2025.09.12.675765

• Bushnell B, Schulz F, and JC Villada. 2025. Rapid terabase-scale simulation of realistic metagenomes for experimental design and pathogen detection with RandomReadsMG. bioRxiv, https://doi.org/10.1101/2025.07.18.665570

• Bushnell B, and JC Villada. 2026. Deployable high-fidelity metagenome binning at scale with QuickBin. bioRxiv, https://doi.org/10.64898/2026.01.08.698506

• Byl P, Schvarcz CR, Thomy J, Li Q, Williams CB, LaButti K, Schulz F, Edwards KF, and GF Steward. 2026. Evidence for the acquisition of a proteorhodopsin-like rhodopsin by a chrysophyte-infecting giant virus. bioRxiv, https://doi.org/10.1101/2025.06.17.660233

• Cameron ES, Tremblay BJM, Yahr R, Blaxter ML, and RD Finn. 2026. Transposable element diversification and the evolution of Peltigerales lichen symbionts. bioRxiv, https://doi.org/10.64898/2026.02.14.705750

• Cerk K, Duncan A, Shrestha N, Baker D, Kukreja M, Ahn-Jarvis J, James R, Quince C, and F Hildebrand. 2025. Optimizing storage, high-molecular weight DNA extraction and genome reconstructions from human faecal samples. bioRxiv, https://doi.org/10.1101/2025.08.27.672560

• Costeira R, Wong EE, and JT Bell. 2026. methbiome: reference-based DNA methylation profiling of long-read metagenomic data. bioRxiv, https://doi.org/10.64898/2026.03.28.714822

• Deng Z-L, Safaei N, and AC McHardy. 2025. Metax: A coverage-informed probabilistic framework for accurate cross-domain taxon profiling. bioRxiv, https://doi.org/10.64898/2025.12.04.692287

• Diaz-Rua R, Drautz-Moses DI, Zhao X, Perumal S, Esau L, Angelov A, Putra A, Driguez P, Cheung MS, and E Palescandolo. 2025. Comparative metagenomic assessment of short- and long-read sequencing technologies reveals unknown microbial information in a complex environmental sample. bioRxiv, https://doi.org/10.64898/2025.12.22.696079

• Enuh BM, Myers KS, Ackman P, Weiland T, Beach N, Young M, Donohue TJ, and DR Noguera. 2025. Metagenomes and metagenome-assembled genomes from microbial communities in a biological nutrient removal plant operated at Los Angeles County Sanitation District (LACSD) with High and Low Dissolved Oxygen Conditions. bioRxiv, https://doi.org/10.1101/2025.11.10.687646

• Enuh BM, Myers KS, Bott C, Klaus S, McCullough K, McIntosh L, Beach N, Young M, Donohue TJ, and DR Noguera. 2025. Metagenomes and metagenome-assembled genomes from microbial communities in a biological nutrient removal plant operated at Hamptons Road Sanitation District (HRSD) with high and low dissolved oxygen conditions. bioRxiv, https://doi.org/10.1101/2025.11.10.687637

• Fan Y, Ni M, Aggarwala V, Mead EA, Ksiezarek M, Cao L, Kamm MA, Borody T, Paramsothy S, Kaakoush NO, Grinspan A, Faith JJ, and G Fang. 2024. LongTrack: long read metagenomics-based precise tracking of bacterial strains and their genomic changes after fecal microbiota transplantation. bioRxiv, https://doi.org/10.1101/2024.09.30.615906

• Faure R, Faure U, Truong T, Derzelle A, Lavenier D, Flot J-F, and C Quince. 2025. SNooPy: a statistical framework for long-read metagenomic variant calling. bioRxiv, https://doi.org/10.64898/2025.12.01.691549

• Faure R, Hilaire B, Flot J-F, and D Lavenier. 2025. Alice: fast and haplotype-aware assembly of high-fidelity reads based on MSR sketching. bioRxiv, https://doi.org/10.1101/2025.09.29.679204

• Filee J, Lopez-Villavicencio M, Debat V, Rignault G, Fourdin R, Salazar C, Silva-Brandao KL, Blandin P, Lucci Freitas AV, Pardo-Diaz C, and V Llaurens. 2025. Genome evolution and between-host transmission of Spiroplasma endosymbiont in wild communities of Morpho butterflies. bioRxiv, https://doi.org/10.1101/2024.02.22.581604

• Friedline S, McDaniel E, Scarborough M, Madill M, Waring K, Lin VS, Malmstrom RR, Goudeau D, Chrisler W, Dueholm MKD, Gorham LJ, Kombala CJ, Griggs LH, Olson HM, Lehmann SB, Munoz N, Trejo J, Tolic N, Pasa-Tolic L, Williams S, Lipton M, Hallam SJ, and RM Ziels. 2025. Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism. bioRxiv, https://doi.org/10.1101/2025.07.15.664484

• Gómez-Pérez D, Raguideau S, Warring S, James R, Hildebrand F, and C Quince. 2026. REMAG: recovery of eukaryotic genomes from metagenomic data using contrastive learning. bioRxiv, https://doi.org/10.64898/2026.03.05.709928

• Gonzalez-Ramirez I, Song MJ, and BD Mishler. 2025. The microbiome of Calasterella californica is shaped mostly by the genetics of the host thalli. bioRxiv, https://doi.org/10.1101/2025.01.23.634585

• Gu Z, Sharma P, Wong L, and N Nagarajan. 2026. Skiver: alignment-free estimation of sequencing error rates and spectra using (k, v)-mer sketches. bioRxiv, https://doi.org/10.64898/2026.02.12.705514

• Guitor AK, Tuck OT, Firek B, Mostacci N, Jauhal A, Chen LX, Dziegiel AH, Baker S, Duong VT, Mather AE, Corander J, Kantele A, Shenhav L, Hilty M, Morowitz M, Sachdeva R, and JF Banfield. 2025. Megaplasmids associate with Escherichia coli and other Enterobacteriaceae. bioRxiv, https://doi.org/10.1101/2025.09.30.679422

• Guo J, Aroney S, Dominguez-Huerta G, Smith D, Vik D, Ansah CO, Pratama AA, Solonenko S, Tian F, Howard-Varona C, Zhong ZP, Fofana A, Smith G, Hodgkins SB, Cronin D, EMERGE Field Teams 2010-2019, EMERGE Coordinators, Woodcroft BJ, Tyson GW, Rich VI, Sullivan MB, Roux S, and SC Bagby. 2025. Mobile genetic elements that shape microbial diversity and functions in thawing permafrost soils. bioRxiv, https://doi.org/10.1101/2025.02.12.637893

• Gutiérrez-Preciado A, Struillou A, Liang L, Iniesto M, Deschamps P, Eme L, Zivanovic Y, López-García JM, Benzerara K, Moreira D,and P López-García. 2026. Redox distribution of Asgard archaea and co-occurring taxa in microbial mats from an early Proterozoic ecosystem analog. bioRxiv, https://doi.org/10.64898/2026.03.20.713109

• Hornett EA, Hayashi M, Nagamine K, Paterson S, Kageyama D, and GDD Hurst. 2025. Concerted genome expansion of heritable symbionts in an insect host. bioRxiv, https://doi.org/10.1101/2025.05.06.652349

• Jin J, Wang X, Zhang X, Mei J, Zheng W, Guo L, Sun H, Zhang L, Liu C, Ye W, and L Guo. 2025. Grapevine phyllosphere pan-metagenomics reveals pan-microbiome structure, diversity, and functional roles in downy mildew resistance. bioRxiv, https://doi.org/10.1101/2025.05.04.652149

• Klauer RR, Hansen DA, Schyns ZOG, Monteiro LO, Moore-Ott JA, Williams M, Tarr M, Singh J, Mhadeshwar A, Korley LTJ, Solomon KV, and MA Blenner. 2025. Biological polyethylene deconstruction initiated by oxidation from DyP peroxidases. bioRxiv, https://doi.org/10.1101/2025.02.27.640435

• Knight R, Din MO, Salido R, Wright G, Brennan C, Ambre M, Hansen L, Boyer T, Cao J, Oles R, Patel L, Weng Y, McDonald D, Bhute S, Solini G, Karthikeyan S, Humphrey G, DeHoff P, Kracilicek S, Levy J, Zeller M, Hecht G, Laurent L, Yeo G, Andersen K, and A Bartko. 2025. Versatile wastewater monitoring of pathogens and antimicrobial resistance enabled by metatranscriptomics and long-read metagenomics. Research Square, https://doi.org/10.21203/rs.3.rs-7492978/v1

• Kurokawa R, Maskawa R, Arakawa M, Masuoka H, Takayasu H, Yoshikawa Y, Raihan T, Shindo C, Kaida K, Takagi M, Tanokura M, De Vlaminck I, Takayasu L, Takayasu M, and W Suda. 2026. High-resolution temporal profiling reveals synchronized dynamics of the mouse gut microbiome. bioRxiv, https://doi.org/10.64898/2026.03.26.714232

• Kutuzova S, Lindez PP, Nielsen KN, Olsen NS, Riber L, Gobbi A, Junco LMF, Dougherty PE, Westergaard JC, Christensen S, Hansen LH, Nielsen M, Nissen JN, and S Rasmussen. 2024. Binning meets taxonomy: TaxVAMB improves metagenome binning using bi-modal variational autoencoder. bioRxiv, https://doi.org/10.1101/2024.10.25.620172

• Lindez PP, Danielsen LS, Kovacic I, Avelli MP, Nesme J, Jensen LJ, Nissen JN, Sorensen SJ, and S Rasmussen. 2025. Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning. bioRxiv, https://doi.org/10.1101/2025.02.26.640269

• Lipovac J, Šikić M, Vicedomini R, and K Križanović. 2025. MADRe: Strain-Level Metagenomic Classification Through Assembly-Driven Database Reduction. bioRxiv, https://doi.org/10.1101/2025.05.12.653324

• Liu X, Guo X, Xue L, Lu Z, Wang J, Liu L, Chen Y, Peng Y, Han Y, Wu F, Cheng R, and X Dong. 2025. A global atlas of deep-sea cold seep viruses uncovers extensive genomic novelty, pervasive viral dark matter, and biotechnological potential. bioRxiv, https://doi.org/10.64898/2025.12.10.692286

• Lui LM, and TN Nielsen. 2026. General-purpose embeddings for long-read metagenomic sequences via β-VAE on multi-scale k-mer frequencies. bioRxiv, https://doi.org/10.64898/2026.03.19.713080

• Ma J, Kim N, Cha JH, Kim W, Kim CY, Lee Y-H, Kim HS, Han YD, Yong D, Han E, Yang S, Beck S, and I Lee. 2025. A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models. bioRxiv, https://doi.org/10.1101/2024.12.11.627901

• Mainguy J, Vienne M, Fourquet J, Darbot V, Noirot C, Castinel A, Combes S, Gaspin C, Milan D, Donnadieu C, Iampietro C, Bouchez O, Pascal G, and C Hoede. 2024. metaWGS, a comprehensive workflow to analyze metagenomic data using Illumina or PacBio HiFi reads. bioRxiv, https://doi.org/10.1101/2024.09.13.612854

• Markkanen M, Pezzutto D, Virta M, and A Karkman. 2025. Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts including clinically relevant species. bioRxiv, https://doi.org/10.1101/2025.01.22.634252

• Markkanen M, Putkuri H, Kiciatovas D, Mustonen V, Virta M, and A Karkman. 2026. Long-read metagenomics and methylation-based binning allow the description of the emerging high-risk antibiotic resistance genes and their hidden hosts in complex communities. medRxiv, https://doi.org/10.64898/2026.02.18.26346558

• Martayan I, Robidou L, Shibuya Y, and A Limasset. 2024. Hyper-k-mers: efficient streaming k-mers representation. bioRxiv, https://doi.org/10.1101/2024.11.06.620789

• Martinez-Garcia M, Martinez-Hernandez F, Gomez, ML, Vila-Nistal M, Roux S, and O Fornas. 2024. Limited consensus of marine viral diversity observed across techniques. Research Square, https://doi.org/10.21203/rs.3.rs-5482008/v1

• Merritt B, Ratcliff JD, Ta S, Osis G, Mauldin MR, and PM Thielen. 2025. TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection. bioRxiv, https://doi.org/10.1101/2025.07.16.664785

• Nguyen MH, and MC Schatz. 2026. Perseus: lineage-aware refinement of Kraken2 taxonomic classification for long read metagenomes. bioRxiv, https://doi.org/10.64898/2026.03.06.710148

• Ni M, Fan Y, Liu Y, Li Y, Qiao W, Davey LE, Zhang X-S, Ksiezarek M, Mead E, Touracheau A, Jiang W, Blaser MJ, Valdivia RH, and G Fang. 2025. Epigenetic phase variation in the gut microbiome enhances bacterial adaptation. bioRxiv, https://doi.org/10.1101/2025.01.11.632565

• Oladele P, Wickware CL, Trachsel J, Looft T, and TA Johnson. 2025. In-feed bacitracin methylene disalicylate alters microbiota function and increases antibiotic resistance in a dose-dependent manner. bioRxiv, https://doi.org/10.1101/2025.02.16.638580

• Peng Y, Ji B, Wang Y, and H Lu. 2025. Euktect: Enhanced Eukaryotic Sequence Detection and Classification in Metagenomes via the DNA Language Model. bioRxiv, https://doi.org/10.1101/2025.06.19.660294

• Pietroni C, Wang B, Bogri A, Langa J, Odriozola I, Horisberger Z, Contreras-Serrano M, Lauritsen JG, Gaun N, Toffano A, Bojesen AM, Thofner I, Drauch V, Sorensen SJ, Trivedi U, and A Alberdi. 2026. Micro-scale spatial metagenomics: revealing high-resolution spatial biogeography of gut microbiomes. bioRxiv, https://doi.org/10.1101/2025.09.30.679663

• Portik DM, Feng X, Benoit G, Nasko DJ, Auch B, Bryson SJ, Cano R, Carlin M, Damerum A, Farthing B, Grove JR, Islam M, Langford KW, Liachko I, Locken K, Mangelson H, Tang S, Zhang S, Quince C, and JE Wilkinson. 2024. Highly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods. bioRxiv, https://doi.org/10.1101/2024.05.10.593587

• Ryu B, Avalon N, Cuau M, Almaliti J, Din MO, Brennan C, Glukhov E, Knight R, Gerwick L, and W Gerwick. 2025. Cyanobacteria Join the Kahalalide Conversation: Genome and Metabolite Evidence for Structurally Related Peptides. ChemRxiv, https://doi.org/10.26434/chemrxiv-2025-dmqr1

• Sapoval N, Liu Y, Curry K, Kille B, Huang W, Kokroko N, Nute MG, Tyshaieva A, Dilthey AT, Molloy E, and TJ Treangan. 2024. Lightweight taxonomic profiling of long-read sequenced metagenomes with Lemur and Magnet. bioRxiv, https://doi.org/10.1101/2024.06.01.596961

• Shen C, Wedell E, Pop M, and T Warnow. 2025. TIPP-SD: A New Method for Species Detection in Microbiomes. bioRxiv, https://doi.org/10.1101/2025.08.27.672749

• Shi L-D, Kolody BC, Wang S, Valentin-Alvarado LE, Lei S, Sachdeva R, and JF Banfield. 2026. Jumbo circular extrachromosomal elements of methane-oxidizing archaea with variably extensive metabolic and defense gene repertoires. bioRxiv, https://doi.org/10.64898/2026.01.21.700959

• Sidhu C, Bartosik D, Kale V, Trautwein-Schult A, Becher D, Schweder T, Amann RI, and H Teeling. 2024. Resource partitioning in organosulfonate utilization by free-living heterotrophic bacteria during a North Sea microalgal bloom. bioRxiv, https://doi.org/10.1101/2024.12.10.627767

• Suarez-Moo P, Haro-Moreno JM, and F Rodriguez-Valera. 2024. Microdiversity in marine pelagic ammonia-oxidizing archaeal populations. bioRxiv, https://doi.org/10.1101/2024.04.23.590705

• Toth CRA, Molenda O, Nesbo C, Luo F, Devine CE, Chen X, Wu K, Xiao J, Guo S, Bawa N, Flick R, and EA Edwards. 2024. Identification of a cluster of benzene activation enzymes in a strictly anoxic methanogenic consortium. bioRxiv, https://doi.org/10.1101/2024.12.15.628547

• Tsuda Y, Tanizawa Y, Vu TMH, Nishimura Y, Shintani M, Abe H, Hasebe F, Kasuga I, Nagao M, and M Suzuki. 2026. VicMAG, an open-source tool for visualizing circular metagenome-assembled genomes highlighting bacterial virulence and antimicrobial resistance. bioRxiv, https://doi.org/10.64898/2026.03.31.714378

• Tucker SJ, Fuessel J, Freel KC, Kiefl E, Freel EB, Ramfelt O, Sullivan CES, Gajigan AP, Mochimaru H, de Souza MR, Quinn M, Ratum C, Tran LL, Sobczyk M, Miller SE, Trigodet F, Lolans K, Morrison HG, Fallon B, Huettel B, Pan T, Rappé MS, and AM Eren. 2025. A high-resolution diel survey of surface ocean metagenomes, metatranscriptomes, and transfer RNA transcripts. bioRxiv, https://doi.org/10.1101/2025.09.15.676277

• Visci G, Notario E, Defazio G, Caratozzolo MF, Fosso B, Marzano M, and G Pesole. 2026. Shotgun metagenomics: a deep insight into the composition and function of the complex microbial world. Research Square, https://doi.org/10.21203/rs.3.rs-7581938/v1

• Wang G, Zhao L, Shi Y, Qu F, Ding Y, Liu W, Liu C, Luo G, Li M, Bai X, Li L, Ho Y-P, and J Yu. 2023. High-throughput generic single-entity sequencing using droplet microfluidics. bioRxiv, https://doi.org/10.1101/2023.08.15.549386

• Wang S, Guitor AK, Valentin-Alvarado LE, Garner RE, Zhang P, Yan M, Shi L-D, Schoelmerich MC, Steininger HM, Portik DM, Zhang S, Wilkinson JE, Lynch S, Morowitz MJ, Hess M, Diamond S, Banfield JF, and R Sachdeva. 2026. Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains. bioRxiv, https://doi.org/10.64898/2026.03.27.714056

• Wang S, Qin Z, Yu H, Liu R, Ge Y, Dutta M, Vu L, and Y Du. 2025. METAHIT enables comprehensive and flexible genome-resolved microbiome analysis with metagenomic Hi-C. bioRxiv, https://doi.org/10.1101/2025.10.12.681839.

• Wang Y, Zuo W, Huang J, Sun F, and Y Du. 2025. Benchmarking Alignment Strategies for Hi-C Reads in Metagenomic Hi-C Data. bioRxiv, https://doi.org/10.1101/2025.07.30.667754

• West-Roberts J, Valentin-Alvarado L, Mullen S, Sachdeva R, Smith J, Hug LA, Gregoire DS, Liu W, Lin T-Y, Husain G, Amano Y, Ly L, and JF Banfield. 2023. Giant genes are rare but implicated in cell wall degradation by predatory bacteria. bioRxiv, https://doi.org/10.1101/2023.11.21.568195

• Yamamura T, Takewaki D, Kiguchi Y, Masuoka H, Manu M, Raveney B, Narushima S, Kurokawa R, Ogata Y, Kimura Y, Sato N, Ozawa Y, Yagishita S, Araki T, Miyake S, Sato W, and W Suda. 2023. Horizontal gene transfer shapes pathogenic bacteria in multiple sclerosis. Research Square, https://dx.doi.org/10.21203/rs.3.rs-3716024/v1

• Zhang Y, Mead EA, Ni M, Ksiezarek M, Liu Y, Cao L, Chen H, Fan Y, Qiao W, Li Y, Zuluaga L, Deikus G, Sebra R, Brody R, Yong RL, Badani KK, Zhang X-S, and G Fang. 2026. Critical assessment of intratumor and low-biomass microbiome using long-read sequencing. bioRxiv, https://doi.org/10.64898/2026.02.02.703393

2026

• van Almsick V, Sobkowiak A, and V Schwierzeck. 2026. Long-read sequencing for bacterial plasmid analysis: a brief overview. FEMS Microbiology Letters, 373: fnag014. https://doi.org/10.1093/femsle/fnag014

• Beinart R, Breusing C, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership, and R O’Brien. 2026. The chromosomal genome sequence of Alviniconcha strummeri S.B.Johnson, Warén, Tunnicliffe, Van Dover, Wheat, T.F.Schultz & Vrijenhoek, 2014 (Provannidae) and its associated microbial metagenome sequences. Wellcome Open Research, 11: 101. https://doi.org/10.12688/wellcomeopenres.25894.1

• Cárdenas P, Busch K, Erpenbeck D, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2026. The chromosomal genome sequence of the sponge, Geodia parva Hansen, 1885 (Tetractinellida: Geodiidae) and its associated microbial metagenome sequences. Wellcome Open Research, 11: 132. https://doi.org/10.12688/wellcomeopenres.25960.1

• Cárdenas P, Busch K, Erpenbeck D, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2026. The chromosomal genome sequence of the demosponge, Geodia phlegraei (Sollas, 1880) (Tetractinellida: Geodiidae) and its associated microbial metagenome sequences. Wellcome Open Research, 11: 142. https://doi.org/10.12688/wellcomeopenres.25984.1

• Chen K, Luo S, Jiang C, Gu S, Yang F, Liu X, Wang S, Qu X, Zhang Q, Zhang P, Gong Y, Zeng H, Qiu D, Miao W, and J Xiong. 2026. HiMBar: A high-fidelity metagenomic barcoding approach for transkingdom species detection and interaction analysis in aquatic ecosystems. Molecular Ecology Resources, 26: e70092. https://doi.org/10.1111/1755-0998.70092

• Chin D, Campbell B, Petersen J, Lim SJ, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2026. The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences. Wellcome Open Research, 11: 131. https://doi.org/10.12688/wellcomeopenres.25920.1

• Chrismas N, Cunliffe M, Adkins P, Harley J, Marine Biological Association Genome Acquisition Lab, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective, Darwin Tree of Life Consortium. 2026. The chromosomal genome sequence of the Black Lichen, Lichina pygmaea (Lightf.) C.Agardh (Lichinales: Lichinaceae) and its associated microbial metagenome sequences. Wellcome Open Research, 11: 42. https://doi.org/10.12688/wellcomeopenres.25380.1

• Dawson MN, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2026. The chromosomal genome sequence of a scyphozoan jellyfish, Aurelia sp. 3 (Semaeostomeae: Ulmaridae) and its associated microbial metagenome sequences. Wellcome Open Research, 11: 143. https://doi.org/10.12688/wellcomeopenres.25906.1

• Della-Negra O, Servien R, Milferstedt K, Hamelin J, Klopp C, and C Hoede. 2026. Metagenome-assembled genomes from oxygenic photogranules obtained from photobioreactors treating synthetic wastewater. Microbiology Resource Announcements, e01310-25. https://doi.org/10.1128/mra.01310-25

• Dong Z, Sun MS, He YD, Zhou L, Xiang W, Li XY, Huang P, and JG Zeng. 2026. Fungal photobiont and microbiome genome composition in the Cladonia uncialis tripartite symbiosis. Scientific Data, https://doi.org/10.1038/s41597-026-06624-6.

• Eilertsen MH, Rimskaya-Korsakova N, Martín-Durán JM, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2026. The chromosome-level genome sequence of a bone-eating worm, Osedax fenrisi Eilertsen, Dahlgren & Rapp, 2020 (Sabellida: Siboglinidae) and its associated microbial metagenome sequences. Wellcome Open Research, 11: 150. https://doi.org/10.12688/wellcomeopenres.26048.1

• Enuh BM, Myers KS, Ackman P, Weiland T, Beach N, Young M, Donohue TJ, and DR Noguera. 2026. Metagenomes and metagenome-assembled genomes from a nutrient removal plant at Los Angeles County Sanitation Districts (LACSD) that transitioned from high to low dissolved oxygen. MIcrobiology Resource Announcements, e01494-25. https://doi.org/10.1128/mra.01494-25

• Guo Z, Xiao Y, Zhao J, Tang Z, Lin Y, and K Yang. 2026. MetaRanker: precise profiling of antibiotic resistome risk in metagenomes by integrating abundance and genetic co-occurrence. Environmental Microbiology, e02422-25. https://doi.org/10.1128/aem.02422-25

• Hirose E, Lopez JV, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2026. The genome sequence of the photosymbiotic ascidian, Trididemnum nubilum Kott, 1980 and its cyanobacterial symbionts. Wellcome Open Research, 11: 138. https://doi.org/10.12688/wellcomeopenres.25911.1

• Le B, Jia L, Pang T, Han S, Duan Y, and X-M Zhao. 2026. A review of computational approaches for metagenomics by long-read sequencing. Science China Life Sciences, https://doi.org/10.1007/s11427-025-3133-3

• Lindez PP, Danielsen LS, Kovacic I, Avelli MP, Nesme J, Jensen LJ, Andersen JN, Sorensen SJ, and S Rasmussen. 2026. Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning. Nature Biotechnology, https://doi.org/10.1038/s41587-026-03005-7

• McCormack GP, Sandoval K, Erpenbeck D, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2026. The chromosomal genome sequence of Haliclona indistincta (Bowerbank, 1866) (Haplosclerida: Chalinidae) and its associated microbial metagenome sequences. Wellcome Open Research, 11: 139. https://doi.org/10.12688/wellcomeopenres.25928.1

• Middlebrooks M, Lopez JV, Curtis N, Krug PJ, Pettingill J, Pruzinsky N, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2026. The chromosomal genome sequence of the lettuce sea slug, Elysia crispata (Mörch, 1863) (Plakobranchidae) and its associated microbial metagenome sequences. Wellcome Open Research, 11: 146. https://doi.org/10.12688/wellcomeopenres.25908.1

• Pérez T, Vacelet J, Erpenbeck D, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2026. The chromosomal genome sequence of the carnivorous sponge, Lycopodina hypogea (Vacelet & Boury-Esnault, 1996) (Poecilosclerida: Cladorhizidae) and its associated microbial metagenome sequences. Wellcome Open Research, 11: 130. https://doi.org/10.12688/wellcomeopenres.25959.1

• Schizas NV, García-Hernández JE, Lopez JV, Pruzinsky N, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2026. The chromosomal genome sequence of the common sea fan, Gorgonia ventalina (Linnaeus, 1758) (Malacalcyonacea: Gorgoniidae). Wellcome Open Research, 11: 14. https://doi.org/10.12688/wellcomeopenres.25430.1

• Shaw J, MG Marin, and H Li. 2026. High-resolution metagenome assembly for modern long reads with myloasm. Nature Biotechnology, https://doi.org/10.1038/s41587-026-03053-z

• Shi L-D, Penev PI, Nissley AJ, Nayak DD, Sachdeva R, Cate JHD, and JF Banfield. 2026. Circularization of 23S rRNA but not 16S rRNA within archaeal ribosomes. Genome Biology, in press. https://doi.org/10.1186/s13059-025-03903-0

• a Silva AK, de Paula CH, de Matos JP, Ribeiro DF, Cordeiro IF, de Carvalho Lemes CG, Sanchez AB, Garcia CCM, de Abreu VAC, Alves RM, de Medeiros Oliveira M, dos Anjos Almeida JV, Almeida NF, Varani AM, and LM Moreira. 2026. Comparative genomics of Sphingomonas from the cupuassu (Theobroma grandiflorum) phyllosphere reveals signatures of host adaptation and beneficial interactions. Symbiosis, https://doi.org/10.1007/s13199-026-01124-y

• Taboada S, Riesgo A, Busch K, Erpenbeck D, Hentschel U, Galià C, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2026. The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences. Wellcome Open Research, 11: 15. https://doi.org/10.12688/wellcomeopenres.25431.1

• Tian W, Petrova E, Sakai S, Nweze JE, Daebeler A, and R Angel. 2026. Cultivation and genomic characterization of novel methanogens from arid desert biocrust. ISME Communications 6: ycag013. https://doi.org/10.1093/ismeco/ycag013

• Trigodet F, Sachdeva R, Banfield JF, and AM Eren. 2026. Troubleshooting common errors in assemblies of long-read metagenomes. Nature Biotechnology, https://doi.org/10.1038/s41587-025-02971-8

• Wörheide G, Busch K, Schupp P, Erpenbeck D, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2026. The chromosomal genome sequence of the deep-sea glass sponge sponge, Bolosoma cyanae Tabachnick & Lévi, 2004 (Lyssacinosida: Euplectellidae) and its associated microbial metagenome sequences. Wellcome Open Research, 11: 24. https://doi.org/10.12688/wellcomeopenres.25437.1

• Yepes-Garcia J, and L Falquet. 2026. 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction. Microbial Ecology, e00844-25. https://doi.org/10.1128/msystems.00844-25

• Yoshioka Y, Ando C, Yamashita H, Kawamitsu M, Kawachi M, Tsunematsu Y, and E Shoguchi. 2026. A dataset for forty complete bacterial genome sequences in cultures of the toxic dinoflagellate Ostreopsis cf. ovata. Data in Brief, 65: 112499. https://doi.org/10.1016/j.dib.2026.112499

• Zentgraf J, Schmitz JE, and S Rahmann. 2026. Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index. Bioinformatics, 42: btaf632. https://doi.org/10.1093/bioinformatics/btaf632

• Zhang S, Li Q, Peng Y, Huo J, Ran T, Zhang X, Wang R, Jiao J, Jiang A, Luo G, Zhang Z, Qiu Q, Li Z, Mao S, Yu Z, Tan Z, Dong X, and M Wang. 2026. Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants. Journal of Advanced Research, in press. https://doi.org/10.1016/j.jare.2026.01.013

• Zhang W, Liu Y, Li G, Xu J, Chen E, Schonhuth A, and X Luo. 2026. Strain-level metagenomic profiling using pangenome graphs with PanTax. Genome Research 36: 405-420. https://www.genome.org/cgi/doi/10.1101/gr.280858.125

2025

• Arnau V, Ortiz-Maiques A, Valero-Tebar J, Mora-Quilis L, Kurmauskaite V, Dopazo LC, Domingo-Calap P, and M Dzunkova. 2025. CleanBar: a versatile demultiplexing tool for split-and-pool barcoding in single-cell omics. ISME Communications, 5: ycaf134. https://doi.org/10.1093/ismeco/ycaf134

• Beinart R, Breusing C, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the Seven Luminaries Vent Mussel, Bathymodiolus septemdierum Hashimoto & Okutani, 1994, and its associated microbial metagenome sequences. Wellcome Open Research, 10: 470. https://doi.org/10.12688/wellcomeopenres.24799.1

• Berg M, Reiter T, Emerson J, Brown CT, and S Roux. 2025. Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations. NAR Genomics and Bioinformatics, 7: lqaf163. https://doi.org/10.1093/nargab/lqaf163

• Calayag A, Priest T, Oldenburg E, Muschiol J, Popa O, Wietz M, and DM Needham. 2025. Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations. Nature Communications, 16: 6427. https://doi.org/10.1038/s41467-025-61568-6

• Chen X, Yin X, Xu X, and T Zhang. 2025. Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo. Nature Communications, 16: 1744. https://doi.org/10.1038/s41467-025-57088-y

• Costa R, Gonçalves JMS, Grenier M, Pérez T, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the elephant ear sponge, Spongia lamella (Schulze, 1879), and its associated microbial metagenome sequences. Wellcome Open Research, 10: 463. https://doi.org/10.12688/wellcomeopenres.24744.1

• Cui Y, Yang Y, Li X, Wang J, Jin H, Liao H, Wang X, Shi K, Huang S, Zhou T, Loffler FE, and J Yan. 2025. Complete genome sequence of Dehalococcoides mccartyi strain NK, an acid-tolerant organohalide-respiring bacterium. Microbiology Resource Announcements, 14: e00633-25. https://doi.org/10.1128/mra.00633-25

• Defazio G, Tangaro MA, Pesole G, and B Fosso. 2025. kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes. Briefings in Bioinformatics, 26: bbae680. https://doi.org/10.1093/bib/bbae680

• Deng F, Han Y, Li M, Peng Y, Chai J, Yang G, Li Y, and J Zhao. 2025. HiFi based metagenomic assembly strategy provides accuracy near isolated genome resolution in MAG assembly. iMetaOmics, e70041. https://doi.org/10.1002/imo2.70041

• Duxbury SJN, Raguideau S, Cremin K, Richards L, Medvecky M, Rosko J, Coates M, Randall K, Chen J, Quince C, and OS Soyer. 2025. Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community. The ISME Journal, wraf126. https://doi.org/10.1093/ismejo/wraf126

• Florl L, Meyer A, and NA Bokulich. 2025. Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential. Applied and Environmental Microbiology, e00524-25. https://doi.org/10.1128/aem.00524-25

• Garcia-Munoz A, and R Pino-Bodas. 2025. Evaluating the Assembly Strategy of a Fungal Genome from Metagenomic Data: Solorina crocea (Peltigerales, Ascomycota) as a Case Study. Journal of Fungi, 11: 596. https://doi.org/10.3390/jof11080596

• Gautam P, Molina V, First M, Erill I, and KD Cusick. 2025. Determining the taxonomic and functional profile of marine bacterial copper systems involved in marine early copper surface colonization. Frontiers in Marine Science, 12: 1661535. https://doi.org/10.3389/fmars.2025.1661535

• Girard M, Vandamme L, Cazaux B, and A Limasset. 2025. OReO: optimizing read order for practical compression. Bioinformatics Advances, 5: vbaf128. https://doi.org/10.1093/bioadv/vbaf128

• de Goeij JM, Mueller B, Achlatis M, Campana S, Hudspith M, Kornder NA, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The scaffold-level genome sequence of an encrusting sponge, Halisarca caerulea Vacelet & Donadey, 1987, and its associated microbial metagenome sequences. Wellcome Open Research, 10: 344. https://doi.org/10.12688/wellcomeopenres.24281.1

• Goffredi SK, Appy R, Martín-Durán JM, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the marine leech, Branchellion lobata Moore, 1952 and its associated microbial metagenome sequences. Wellcome Open Research, 10: 304. https://doi.org/10.12688/wellcomeopenres.24186.1

• Gonzalez A, Fullaondo A, and A Odriozola. 2025. Why Are Long-Read Sequencing Methods Revolutionizing Microbiome Analysis? Microorganisms, 13: 1861. https://doi.org/10.3390/microorganisms13081861

• Han H, Wang Z, and S Zhu. 2025. Benchmarking metagenomic binning tools on real datasets across sequencing platforms and binning modes. Nature Communications, 16: 2865. https://doi.org/10.1038/s41467-025-57957-6

• Haro-Moreno JM, Lopez-Perez M, Molina-Pardines C, and F Rodriguez-Valera. 2025. Large diversity in the O-chain biosynthetic cluster within populations of Pelagibacterales. Environmental Microbiology, e03455-24. https://doi.org/10.1128/mbio.03455-24

• Haro-Moreno JM, Roda-Garcia JJ, Molina-Pardines C, and M Lopez-Perez. 2025. The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity. Environmental Microbiome, 20: 110. https://doi.org/10.1186/s40793-025-00773-8

• Hentschel U, Busch K, Rios P, Cristobo J, Xavier JR, Erpenbeck D, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory Team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the glass sponge Aphrocallistes beatrix Gray, 1858 and its associated microbial metagenome sequences. Wellcome Open Research, 10: 280. https://doi.org/10.12688/wellcomeopenres.24099.1

• Hirose E, Lopez JV, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the photosymbiotic ascidian, Trididemnum clinides Kott, 1977 and its associated microbial metagenome sequences. Wellcome Open Research, 10: 357. https://doi.org/10.12688/wellcomeopenres.24563.2

• Hubert J, Glowska-Patyniak E, Dowd SE, and PB Klimov. 2025. A novel Erwiniaceae gut symbiont modulates gene expression of the intracellular bacterium Cardinium in the stored product mite Tyrophagus putrescentiae. mSphere, e00879-24. https://doi.org/10.1128/msphere.00879-24

• Hubert J, Xiong Q, Glowska-Patyniak E, Furtek EV, and PB Klimov. 2025. Analysis of the tripartite interactions between two bacterial symbionts, a novel Solitalea-like bacterium (Bacteroidota) and Cardinium, and the stored product mite Tyrophagus putrescentiae based on gene expression data. Microbiology Spectrum, e00609-25. https://doi.org/10.1128/spectrum.00609-25

• Kathirithamby J, Crowley LM, University of Oxford and Wytham Woods Genome Acquisition Lab, Darwin Tree of Life Barcoding Collective, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics team, Tree of Life Core Informatics collective, Darwin Tree of Life Consortium. 2025. The genome sequence of Stylops aterrimus Newport, 1851 (Strepsiptera: Stylopidae). Wellcome Open Research, 10: 684. https://doi.org/10.12688/wellcomeopenres.25398.1

• Kim H, Ahn J, Kim J, and H-S Kang. 2025. Metagenomic insights and biosynthetic potential of Candidatus Entotheonella symbiont associated with Halichondria marine sponges. Enviromental Microbiology, 13: e0235524. https://doi.org/10.1128/spectrum.02355-24

• Koester F, Myers KS, Donohue TJ, and DR Noguera. 2025. Metagenome-assembled genomes from microbial communities producing lactic acid from dairy residues. Microbiology Resource Announcements, e00179-25. https://doi.org/10.1128/mra.00179-25

• Leys SP, Hentschel U, Easson CG, Stimson D, Lopez JV, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the fragile freshwater sponge, Eunapius fragilis (Leidy, 1851) and its associated microbial metagenome sequences. Wellcome Open Research, 10: 268. https://doi.org/10.12688/wellcomeopenres.24165.1

• Leys SP, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Erpenbeck D, Niu H, McKenna V, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosome-level genome sequences of the freshwater sponge, Spongilla lacustris (Linnaeus, 1759) and the chlorophyte cobiont Choricystis sp., and the associated microbial metagenome sequences. Wellcome Open Research, 10: 222. https://doi.org/10.12688/wellcomeopenres.23988.1

• Li X, Wang J, Jin H, Cui Y, Zhong H, Zhou T, and J Yan. 2025. Complete genome sequence of Dehalobacter sp. strain CP, an organohalide-respiring anaerobe from a chlorophenol-dechlorinating consortium. Genome Sequences, e00092-25. https://doi.org/10.1128/mra.00092-25

• Li Y, Gao Y, Liu X, Mao Y, Wang M, Qin Y, Zhang C, Chen Q, Ning K, Wang Z, and M Han. 2025. Quantifying antibiotic resistome risks across environmental niches: the L-ARRAP for long-read metagenomic profiling. Briefings in Bioinformatics, 26: bbaf535. https://doi.org/10.1093/bib/bbaf535

• Liu S, Rodriguez JS, Munteanu V, Ronkowski C, Sharma NK, Alser M, Andreace F, Blekhman R, Blaszczyk D, Chikhi R, Crandall KA, Della LK, Francis D, Frolova A, Gancz AS, Huntley NE, Jaiswal P, Kosciolek T, Labaj PP, Labaj W, Luan T, Mason C, Moustafa AM, Muralidharan HS, Mutlu O, Ghiasi NM, Rahnavard A, Sun F, Tian S, Tierney BT, Van Syoc E, Vicedomini R, Zackular JP, Zelikovsky A, Zielińska K, Ganda E, Davenport ER, Pop M, Koslicki D, and M Serghei. 2025. Analysis of metagenomic data. Nature Reviews Methods Primers, 5: 5. https://doi.org/10.1038/s43586-024-00376-6

• Liu X, Tang Y, Chen H, Liu J-X, and H-Z Sun. 2025. Rumen DNA virome and its relationship with feed efficiency in dairy cows. Microbiome, 13: 14. https://doi.org/10.1186/s40168-024-02019-0

• Lopez JV, Pomponi SA, Hentschel U, Erpenbeck D, Pruzinsky N, Fiore C, Mulheron R, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the giant barrel sponge, Xestospongia muta Schmidt 1870 and its associated microbial metagenome sequences. Wellcome Open Research, 10: 336. https://doi.org/10.12688/wellcomeopenres.24173.2

• Maldonado M, Pita L, Hentschel U, Erpenbeck D, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the sponge Crambe crambe (Schmidt, 1862) and its associated microbial metagenome sequences. Wellcome Open Research, 10: 275. https://doi.org/10.12688/wellcomeopenres.24154.1

• Maldonado M, Pita L, Erpenbeck D, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the sponge, Corticium candelabrum Schmidt, 1862 and its associated microbial metagenome sequences. Wellcome Open Research, 10: 535. https://doi.org/10.12688/wellcomeopenres.24923.1

• Mao Y, Shisler JL, and TH Nguyen. 2025. Enhanced detection for antibiotic resistance genes in wastewater using CRISPR-enriched metagenomic method. Water Research, 274: 123056. https://doi.org/10.1016/j.watres.2024.123056

• Marangon E, Ramsby BD, Luter HM, Bell SC, Laffy P, Webster NS, Hentschel U, Fiore C, Oatley G, Thomas T, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the sponge Cliona cf. orientalis Thiele (1900) and its associated microbial metagenome sequences. Wellcome Open Research, 10: 342. https://doi.org/10.12688/wellcomeopenres.24304.1

• Markkanen M, Pezzutto D, Virta M, and A Karkman. 2025. Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts. Microbiology Spectrum, e00857-25. https://doi.org/10.1128/spectrum.00857-25

• Maurice N, Lemaitre C, Vicedomini R, and C Frioux. 2025. Mapler: a pipeline for assessing assembly quality in taxonomically rich metagenomes sequenced with HiFi reads. Bioinformatics, 41: bta334. https://doi.org/10.1093/bioinformatics/btaf334

• Minich JJ, Allsing N, Din MO, Tisza MJ, Maleta K, McDonald D, Hartwick N, Mamerto A, Brennan C, Hansen L, Shaffer J, Murray ER, Duong T, Knight R, Stephenson K, Manary MJ, and TP Michael. 2025. Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition. Cell, https://doi.org/10.1016/j.cell.2025.08.020

• Mokoena MI, Nkuna R, and TS Matambo. 2025. Metagenomic and proxy monitoring of surfactant degradation by microbial consortia from oil-contaminated soil. Applied Microbiology, 6: 3. https://doi.org/10.3390/applmicrobiol6010003

• Molina-Pardines C, Haro-Moreno JM, Rodriguez-Valera F, and M Lopez-Perez. 2025. Extensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations. Microbiome, 13: 41. https://doi.org/10.1186/s40168-025-02037-6

• Nooij S, Plomp N, Sanders IMJG, Schout L, van der Meulen AE, Terveer EM, Norman JM, Karcher N, Larralde MF, Vossen RHAM, Kloet SL, Faber KN, Harmsen HJM, Zeller GF, Kuijper EJ, Smits WK, and QR Ducarmon. 2025. Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status. Nature Communications, 16: 1182. https://doi.org/10.1038/s41467-025-56449-x

• Ochiai KK, Toyoda A, Itoh T, Goshima G, and K Uesaka. 2025. High-quality metagenome-assembled genomes of bacteria associated with long-term cultivated giant coenocytic green alga Bryopsis. Microbiology Resource Announcements, e00722-25. https://doi.org/10.1128/mra.00722-25

• Oehler JB, Burns K, Warner J, and U Schmitz. 2025. Long-read sequencing for the rapid response to infectious diseases outbreaks. Current Clinical Microbiology Reports, 12: 10. https://doi.org/10.1007/s40588-025-00247-y

• Papamentzelopoulou M, Vrioni G, and V Pitiriga. 2025. Comparative evaluation of sequencing technologies for detecting antimicrobial resistance in bloodstream infections. Antibiotics, 14: 1257. https://doi.org/10.3390/antibiotics14121257

• Passos GS, Pellegrinetti TA, and MF Fiore. 2025. Metagenome-assembled bacterial genomes from long accurate reads associated with Capilliphycus salinus ALCB114379. Microbiology Resource Announcements, e00807-24. https://doi.org/10.1128/mra.00807-24

• Pita L, Hentschel U, Steindler L, Maldonado M, Riesgo A, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of Aplysina aerophoba (Nardo, 1833) and its associated microbial metagenome sequences. Wellcome Open Research, 10: 250. https://doi.org/10.12688/wellcomeopenres.24098.1

• Pita L, Maldonado M, Erpenbeck D, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the Maltese sponge, Agelas oroides (Schmidt, 1864), and its associated microbial metagenome sequences. Wellcome Open Research, 10: 464. https://doi.org/10.12688/wellcomeopenres.24745.1

• Pita L, Maldonado M, Koutsouveli V, Riesgo A, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the kidney sponge, Chondrosia reniformis Nardo, 1847, and its associated microbial metagenome sequences. Wellcome Open Research, 10: 283. https://doi.org/10.12688/wellcomeopenres.24166.1

• Pitt KA, Diaz PE, Dawson MN, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of blue blubber, Catostylus mosaicus (Quoy & Gaimard, 1824) and its associated microbial metagenome sequences. Wellcome Open Research, 10: 481. https://doi.org/10.12688/wellcomeopenres.24798.1

• Priest T, Oldenburg E, Popa O, Dede B, Metfies K, von Appen W-J, Torres-Valdes S, Bienhold C, Fuchs BM, Amann R, Boetius A, and M Wietz. 2025. Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome. Nature Communications, 16: 1326. https://doi.org/10.1038/s41467-025-56203-3

• Riesgo A, Renard E, Schenkelaars Q, Borchiellini C, Pita L, Maldonado M, Erpenbeck D, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the sponge, Oscarella lobularis (Schmidt, 1862) (Porifera, Homoscleromorpha) and its associated microbial metagenome sequences. Wellcome Open Research, 10: 340. https://doi.org/10.12688/wellcomeopenres.24187.1

• Rodriguez-Ramos J, Sadler N, Zegeye EK, Farris Y, Purvine S, Couvillion S, Nelson WC, and KS Hofmockel. 2025. Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation. mSystems, e01616-24. https://doi.org/10.1128/msystems.01616-24

• Sanchez G, Simakov O, Nyholm S, Nishiguchi M, McFall-Ngai M, Lami R, Heath-Heckman E, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the bigfin reef squid, Sepioteuthis lessoniana d'Orbigny, 1826 and its associated microbial metagenome sequences. Wellcome Open Research, 10: 351. https://doi.org/10.12688/wellcomeopenres.24553.1

• Sakurai R, Fukuda Y, and C Tada. 2025. Culture-independent discovery of a novel thermotolerant lipase and its producer from mesophilic anaerobic digestion sludge. Applied Microbiology and Biotechnology, 109: 283. https://doi.org/10.1007/s00253-025-13674-0

• Shaw J, Boucher C, Yu YW, Noyes N, and H Li. 2025. devider: long-read reconstruction of many diverse haplotypes. Genome Research, gr.280510.125. https://doi.org/10.1101/gr.280510.125

• de Silva AB, Polson SW, Schvarcz CR, Steward GF, and KF Edwards. 2025. Genomic diversity and global distribution of four new prasinoviruses from the tropical north Pacific. Microbiology Spectrum, 13: e02583-24. https://doi.org/10.1128/spectrum.02583-24

• Sibalekile A, Araya T, Hernandez JC, and E Kotze. 2025. Glyphosate-microbial interactions: metagenomic insights and future directions. Frontiers in Microbiology, 16: 1570235. https://doi.org/10.3389/fmicb.2025.1570235

• Smith DDN, Subasinghe RM, Kehoe C, and DS Gregoire. 2025. Multi-omics provides functional insights and underscores practical challenges in assessing the composition and performance of a nitrifying microbial consortium. Applied and Environmental Microbiology, e01984-25. https://doi.org/10.1128/aem.01984-25

• Song MJ, Li F-W, Freund F, Tribble CM, Toffelmier E, Miller C, Shaffer HB, and CJ Rothfels. 2025. The nitrogen-fixing fern Azolla has a complex microbiome characterized by varying degrees of cophylogenetic signal. American Journal of Botany, 112: e70010. https://doi.org/10.1002/ajb2.70010

• Song X, Chen G, Zheng L, Shen J, Xue C, Y Chang. 2025. Microbiota Involved in the Degradation of Tremella fuciformis Polysaccharide and Microbial Enzymatic Potential Revealed by Microbiome and Metagenome. Microorganisms, 13: 263. https://doi.org/10.3390/microorganisms13020263

• Steindler L, Canché MAD, Ilan M, Bar-Shalom R, Lopez JV, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the marine sponge Diacarnus erythraeanus Kelly-Borges & Vacelet, 1995, and its associated microbial metagenome sequences. Wellcome Open Research, 10: 466. https://doi.org/10.12688/wellcomeopenres.24763.1

• Steindler L, Maldonado M, Pita L, Riesgo A, Erpenbeck D, Hentschel U, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the stone sponge Petrosia ficiformis (Poiret, 1789) and its associated microbial metagenome sequences. Wellcome Open Research, 10: 450. https://doi.org/10.12688/wellcomeopenres.24743.1

• Tashyreva D, Faktorová D, Stříbrná E, Horák A, Lukeš J, Archibald JM, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The genome sequences of the diplonemid protist Diplonema japonicum YPF1604 and its bacterial endosymbionts Ca. Cytomitobacter primus and Ca. Nesciobacter abundans. Wellcome Open Research, 10: 193. https://doi.org/10.12688/wellcomeopenres.23917.1

• Viver T, Knittel K, Amann R, and LH Orellana. 2025. Comparative metagenomics indicates metabolic niche differentiation of benthic and planktonic Woeseiaceae. Environmental Microbiome, 20: 74. https://doi.org/10.1186/s40793-025-00732-3

• Wang B, Jia P, Gao S, Zhao H, Zheng G, Xu L, and K Ye. 2025. Long and accurate: how HiFi sequencing is transforming genomics. Genomics, Proteomics & Bioinformatics, qzaf003. https://doi.org/10.1093/gpbjnl/qzaf003

• Wilkins L, Yuen B, Petersen J, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of Mound Coral, Porites lutea Milne Edwards & Haime, 1851 and its associated microbial metagenome sequences. Wellcome Open Research, 10: 382. https://doi.org/10.12688/wellcomeopenres.24400.1

• Wilkins L, Yuen B, Petersen J, Oatley G, Sinclair E, Aunin E, Gettle N, Santos C, Paulini M, Niu H, McKenna V, O’Brien R, Wellcome Sanger Institute Tree of Life Management: Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations, Wellcome Sanger Institute Tree of Life Core Informatics Team, EBI Aquatic Symbiosis Genomics Data Portal Team, Aquatic Symbiosis Genomics Project Leadership. 2025. The chromosomal genome sequence of the mollusc, Ctena decussata (O.G.Costa, 1829) and its bacterial endosymbiont Candidatus Thiodiazotropha sp. CDECU1 (Chromatiales). Wellcome Open Research, 10: 435. https://doi.org/10.12688/wellcomeopenres.24738.1

• Wilkinson JE and DM Portik. 2025. Highly accurate long-read PacBio HiFi sequencing for microbiome and metagenomic applications. In M Rivera & J Izard (Eds.), Metagenomics for Microbiology (2nd ed., pp 163-190). Elsevier. https://doi.org/10.1016/B978-0-443-22376-1.00006-4

• Yang Y, Du W, Li Y, Lei J, and W Pan. 2025. Recent advances and challenges in de novo genome assembly. Genomic Communications, 2: e104. https://doi.org/10.48130/gcomm-0025-0015

• Zaidi SSeA, Golyaev V, Mehta D, and H Vanderschuren. 2025. Full-Length Sequencing of Circular DNA Viruses Using CIDER-Seq. In: Zerbini FM, Fiallo-Olivé E, Navas-Castillo J (eds) Geminiviruses. Methods in Molecular Biology, vol 2912. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-4454-6_17

• Zhai Z, Che X, Shen W, Zhang Z, Li Y, and J Pan. 2025. HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data. Nucleic Acids Research, gkaf1152. https://doi.org/10.1093/nar/gkaf1152

• Zhang T, Jiang M, Li H, Gao Y, Yousuf S, Yu K, Yi X, Wang J, Yang L, and Y-X Liu. 2025. Computational Tools and Resources for Long-read Metagenomic Sequencing Using Nanopore and PacBio. Genomics, Proteomics & Bioinformatics, qzaf075. https://doi.org/10.1093/gpbjnl/qzaf075

• Zhao D, Salas-Leiva DE, Williams SK, Dunn KA, Shao JD, and AJ Roger. 2025. Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data. mBio, e00699-25. https://doi.org/10.1128/mbio.00699-25

2024

• Agustinho DP, Fu Y, Menon VK, Metcalf GA, Treangan TJ, and FJ Sedlazeck. 2024. Unveiling microbial diversity: harnessing long-read sequencing technology. Nature Methods, 21: 954-966. https://doi.org/10.1038/s41592-024-02262-1

• Aldeguer-Riquelme B, Conrad RE, Anton J, Rossello-Mora R, and KT Konstantinidis. 2024. A natural ANI gap that can define intra-species units of bacteriophages and other viruses. mBio, 8: e01536-24. https://doi.org/10.1128/mbio.01536-24

• Benoit G, Raguideau S, James R, Phillippy AM, Chikhi R, and C Quince. 2024. High-quality metagenome assembly from long accurate reads with metaMDBG. Nature Biotechnology, 42: 1378–1383. https://doi.org/10.1038/s41587-023-01983-6

• Bulka O, and EA Edwards. 2024. Metagenomic sequences from anaerobic chloroform and dichloromethane degrading microbial communities. Microbiology Resource Announcements, e00391-24. https://doi.org/10.1128/mra.00391-24

• Bulka O, and EA Edwards. 2024. Two distinct Dehalobacter metagenome-assembled genomes from anaerobic chloroform and dichloromethane degrading consortia. Microbiology Resource Announcements, e00803-24. https://doi.org/10.1128/mra.00803-24

• Bulka O, and EA Edwards. 2024. Metagenome from ACT-3/CF: an anaerobic chloroform-degrading microbial community. Microbiology Resource Announcements, 13: e00674-24. https://doi.org/10.1128/mra.00674-24

• Bulka O, Picott K, Mahadevan R, and EA Edwards. 2024. From mec cassette to rdhA: a key Dehalobacter genomic neighborhood in a chloroform and dichloromethane-transforming microbial consortium. Applied and Environmental Microbiology, 90: e0073224. https://doi.org/10.1128/aem.00732-24

• Chen J, Sun C, Dong Y, Jin M, Lai S, Jia L, Zhao X, Wang H, Gao NL, Bork P, Liu Z, Chen W-H, and X-M Zhao. 2024. Efficient recovery of complete gut phage genomes by combined short- and long-sequencing. Advanced Science, 2305818. https://doi.org/10.1002/advs.202305818

• Chen X, Yin X, Shi X, Yan W, Yang Y, Liu L, and T Zhang. 2024. Melon: metagenomic long-read-based taxonomic identification and quantification using marker genes. Genome Biology, 25: 226. https://doi.org/10.1186/s13059-024-03363-y

• Cook R, Brown N, Rihtman B, Michniewski S, Redgwell T, Clokie M, Stekel DJ, Chen Y, Scanlan DJ, Hobman JL, Nelson A, Jones MA, Smith D, and A Millard. 2024. The long and short of it: benchmarking viromics using Illumina, Nanopore, and PacBio sequencing technologies. Microbial Genomics, 10: 001198. https://doi.org/10.1099/mgen.0.001198

• Dong W, Fan X, Guo Y, Wang S, Jia S, Lv N, Yuan T, Pan Y, Xue Y, Chen X, Xiong Q, Yang R, Zhao W, and B Zhu. 2024. An expanded database and analytical toolkit for identifying bacterial virulence factors and their associations with chronic diseases. Nature Communications, 15: 8084. https://doi.org/10.1038/s41467-024-51864-y

• Eisenhofer R, Nesme J, Santos-Bay L, Koziol A, Sorenson SJ, Alberdi A, and O Aizpurua. 2024. A comparison of short-read, HiFi long-read and hybrid strategies for genome-resolved metagenomics. Microbiology Spectrum, 12: e03590-23. https://doi.org/10.1128/spectrum.03590-23

• Feng X, and H Li. 2024. Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies. Genome Biology, 25: 92. https://doi.org/10.1186/s13059-024-03234-6

• Funnicelli MIG, de Carvalho LAL, Teheran-Sierra LG, Dibelli SC, de Macedo Lemos EG, and DG Pinheiro. 2024. Unveiling genomic features linked to traits of plant growth-promoting bacterial communities from sugarcane. Science of the Total Environment, 947: 174577. https://doi.org/10.1016/j.scitotenv.2024.174577

• Glendinning L, Wu Z, Vervelde L, Watson M, and A Balic. 2024. Infectious bronchitis virus vaccination, but not the presence of XCRI, is correlated with large differences in chicken caecal microbiota. Microbial Genomics, 10: 001289. https://doi.org/10.1099/mgen.0.001289

• Han Y, He J, Li M, Peng Y, Jiang H, Zhao J, Li Y, and F Deng. 2024. Unlocking the potential of metagenomics with the PacBio high-fidelity sequencing technology. Microorganisms, 12: 2482. https://doi.org/10.3390/microorganisms12122482

• Hui X, Yang J, Sun J, Liu F, and W Pan. 2024. MCSS: microbial community simulator based on structure. Frontiers in Microbiology, 15: 1358257. https://doi.org/10.3389/fmicb.2024.1358257

• Kazantseva E, Donmez A, Frolova M, Pop M, and M Kolmogorov. 2024. Strainy: phasing and assembly of strain haplotypes from long-read metagenome sequencing. Nature Methods, https://doi.org/10.1038/s41592-024-02424-1

• Kutuzova S, Nielsen M, Piera P, Nissen JN, and S Rasmussen. 2024. Taxometer: improving taxonomic classification of metagenomic contigs. Nature Communications, 15: 8357. https://doi.org/10.1038/s41467-024-52771-y

• Lai S, Wang H, Bork P, Chen W-H, and X-M Zhao. 2024. Long-read sequencing reveals extensive gut phageome structural variations driven by genetic exchange with bacterial hosts. Science Advances, 10: eadn3316. https://doi.org/10.1126/sciadv.adn3316

• Manning VA, Moore PA, and KM Trippe. 2024. Metagenome-assembled genomes of an acid-tolerant nitrifying bacterial community isolated from a bioreactor used in ammonium scrubbers at animal-rearing facilities. Microbiology Resource Announcements, e00386-24. https://doi.org/10.1128/mra.00386-24

• Maric J, Krizanovic K, Riondet S, Nagarajan N, and M Sikic. 2024. Comparative analysis of metagenomic classifiers for long-read sequencing datasets. BMC Bioinformatics, 25: 15. https://doi.org/10.1186/s12859-024-05634-8

• Masuda S, Gan P, Kiguchi Y, Anda M, Sasaki K, Shibata A, Iwasaki W, Suda W, and K Shirasu. 2024. Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing. Communications Biology, 7: 357. https://doi.org/10.1038/s42003-024-05998-w

• Myeong NR, Choe Y-H, Shin SC, Kim J, Sul WJ, and M Kim. 2024. Genomic profiling of Antarctic geothermal microbiomes using long-read, Hi-C, and single-cell techniques. Scientific Data, 11: 1023. https://doi.org/10.1038/s41597-024-03875-z

• Nesbo CL, Yang MI, Sharan AA, Meyer T, and EA Edwards. 2024. Metagenomes and metagenome assembled genomes from anaerobic digesters at three Canadian pulp and paper mills. Microbiology Resource Announcements, e00561-24. https://doi.org/10.1128/mra.00561-24

• Peres de Silva R, Suphavilai C, and N Nagrajan. 2024. MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes. BMC Bioinformatics, 25: 153. https://doi.org/10.1186/s12859-024-05760-3

• Richy E, Dobbler PT, Tlaskal V, Lopez-Mondejar R, Baldrian P, and M Kyselkova. 2024. PacBio HiFi sequencing sheds light on key bacteria contributing to deadwood decomposition processes. Environmental Microbiome, 19: 99. https://doi.org/10.1186/s40793-024-00639-5

• Saini JS, Adler A, Cardona L, Rodilla Ramirez PN, Pei R, and C Holliger. 2024. Microbial genome collection of aerobic granular sludge cultivated in sequencing batch reactors using different carbon source mixtures. Microbiology Resource Announcements, 13: e00102-24. https://doi.org/10.1128/mra.00102-24

• Sakurai R, Fukuda Y, and C Tada. 2024. Circular metagenome-assembled genome of Candidatus Patescibacteria recovered from anaerobic digestion sludge. Microbiology Resource Announcements, 13: e00083-24. https://doi.org/10.1128/mra.00083-24

• Shaw J, and YW Yu. 2024. Rapid species-level metagenome profiling and containment estimation with sylph. Nature Biotechnology, https://doi.org/10.1038/s41587-024-02412-y

• Shaw J, Gounot J-S, Chen H, Nagarajan N, and YW Yu. 2024. Floria: fast and accurate strain haplotyping in metagenomes. Bioinformatics, 40: i30-i38. https://doi.org/10.1093/bioinformatics/btae252

• Silva-Solar S, Viver T, Wang Y, Orellana LH, Knittel K, and R Amann. 2024. Acidimicrobiia, the actinomycetota of coastal marine sediments: abundance, taxonomy and genomic potential. Systematic and Applied Microbiology, 47: 126555. https://doi.org/10.1016/j.syapm.2024.126555

• Stewart RD, Myers KS, Amstadt C, Seib M, McMahon KD, and DR Noguera. 2024. Refinement of the “Candidatus Accumulibacter” genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration. mSystems, 9: e01188-23. https://doi.org/10.1128/msystems.01188-23

• Suarez-Moo P, Haro-Moreno JM, and F Rodriguez-Valera. 2024. Microdiversity in marine pelagic ammonia-oxidizing archaeal populations in a Mediterranean long-read metagenome. Environmental Microbiology, 26: e16684. https://doi.org/10.1111/1462-2920.16684

• Takewaki D, Kiguchi Y, Masuoka H, Manu MS, Raveney BJE, Narushima S, Kurokawa R, Ogata Y, Kimura Y, Sato N, Ozawa Y, Yagishita S, Araki T, Miyake S, Sato W, Suda W, and T Yamamura. 2024. Tyzzerella nexilis strains enriched in mobile genetic elements are involved in progressive multiple sclerosis. Cell Reports, 114785. https://doi.org/10.1016/j.celrep.2024.114785

• Tejada JN, Walters WA, Wang Y, Kordahi M, Chassaing B, Pickard J, Nunez G, Ley R, and AT Gewirtz. 2024. Prevention and cure of murine C. difficile infection by a Lachnospiraceae strain. Gut Microbes, 16: 2392872. https://doi.org/10.1080/19490976.2024.2392872

• Valentin-Alvarado LE, Shi L-D, Appler KE, Crits-Christoph A, De Anda V, Adler BA, Cui ML, Ly L, Leao P, Roberts RJ, Sachdeva R, Baker BJ, Savage DF, and JF Banfield. 2024. Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements. Genome Research, 34: 1-15. https://doi.org/10.1101/gr.279480.124

• Valentin-Alvarado LE, Appler KE, De Anda V, Schoelmerich MC, West-Roberts J, Kivenson V, Crits-Christoph A, Ly L, Sachdeva R, Greening C, Savage DF, Baker BJ, and JF Banfield. 2024. Asgard archaea modulate potential methanogenesis substrates in wetland soil. Nature Communications, 15: 6384. https://doi.org/10.1038/s41467-024-49872-z

• Wang F-Q, Bartosik D, Sidhu C, Siebers R, Lu D-C, Trautwein-Schult A, Becher D, Huettel B, Rick J, Kirstein IV, Wiltshire KH, Schweder T, Fuchs BM, Bengtsson MM, Teeling H, and RI Amann. 2025. Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides. Microbiome, 12: 32. https://doi.org/10.1186/s40168-024-01757-5

• Wang Y-C, Mao Y, Fu H-M, Wang J, Weng X, Liu Z-H, Xu X-W, Yan P, Fang F, Guo J-S, Shen Y, and Y-P Chen. 2024. New insights into functional divergence and adaptive evolution of uncultured bacteria in anammox community by complete genome-centric analysis. Science of the Total Environment, 924: 171530. https://doi.org/10.1016/j.scitotenv.2024.171530

• Wang H, Sun C, Li Y, Chen J, Zhao X-M, and W-H Chen. 2024. Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners. Microbiome, 12: 260. https://doi.org/10.1186/s40168-024-01981-z

• Xiao JZ, Nesbo CL, Molenda O, Toth CRA, and EA Edwards. 2024. Metagenomic and genomic sequences from a nitrate-reducing benzene-degrading enrichment culture. Microbiology Resource Announcements, e00294-24. https://doi.org/10.1128/mra.00294-24

• Yadav A, and S Subramanian. 2024. HiFiBGC: an ensemble approach for improved biosynthetic gene cluster detection in PacBio HiFi-read metagenomes. BMC Genomics, 15: 1096. https://doi.org/10.1186/s12864-024-10950-7

• Yu W, Luo H, Yang J, Zhang S, Jiang H, Zhao X, Hui X, Sun D, Li L, Wei X-Q, Lonardi S, and W Pan. 2024. Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes. Genome Research, 34: 326-340. https://www.genome.org/cgi/doi/10.1101/gr.278232.123

2023

• Ahmad N, Ritz M, Calchera A, Otte J, Schmitt I, Brueck T, and N Mehlmer. 2023. Biosynthetic potential of Hypogymnia holobionts: Insights into secondary metabolite pathways. Journal of Fungi, 9: 546. https://doi.org/10.3390/jof9050546

• Chen X, Molenda O, Brown CT, Toth CRA, Guo S, Luo F, Howe J, Nesbo CL, He C, Montabana EA, Cate JHD, Banfield JF, and EA Edwards. 2023. “Candidatus Nealsonbacteria” are likely biomass recycling ectosymbionts of methanogenic Archaea in a stable benzene-degrading enrichment culture. Applied and Environmental Microbiology, 89: e00025-23. https://doi.org/10.1128/aem.00025-23

• Ding Y, Zhao L, Wang G, Shi Y, Guo G, Liu C, Chen Z, Coker OO, She J, and J Yu. 2023. PacBio sequencing of human fecal samples uncovers the DNA methylation landscape of 22 673 gut phages. Nucleic Acids Research, gkad977. https://doi.org/10.1093/nar/gkad977

• Haro-Moreno JM, Cabello-Yeves PJ, Garcillan-Barcia MP, Zakharenko A, Zemskaya TI, and F Rodrigue-Valera. 2023. A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics. Environmental Microbiome, 18: 12. https://doi.org/10.1186%2Fs40793-023-00473-1

• Jang YJ, Kang J-S, and EH Bae. 2023. Metagenome-assembled genomes of the GU0601 sample (the Han River, South Korea). Microbiology Resource Announcements, 12: e00688-23. https://doi.org/10.1128/MRA.00688-23

• Jia L, Wu Y, Dong Y, Chen J, Chen W-H, and X-M Zhao. 2023. A survey on computational strategies for genome-resolved gut metagenomics. Briefings in Bioinformatics, 2023, 1-13. https://doi.org/10.1093/bib/bbad162

• Jiang F, Li Q, Wang S, Shen T, Wang H, Wang A, Xu D, Yuan L, Lei L, Chen R, Yang B, Deng Y, and W Fan. 2023. Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by Pacific Biosciences high-fidelity sequencing. Frontiers in Microbiology, 13: 1095497. https://doi.org/10.3389/fmicb.2022.1095497

• Merges D, Dal Grande F, Valim H, Singh G, and I Schmitt. 2023. Gene abundance linked to climate zone: parallel evolution of gene content along elevation gradients in lichenized fungi. Frontiers in Microbiology, 14: 1097787. https://doi.org/10.3389/fmicb.2023.1097787

• Nesbo CL, Fitamo TM, Lee H, and EA Edwards. 2023. Metagenomes and metagenome-assembled genomes from a sequentially fed anaerobic digester treating solid organic municipal waste. Microbiology Resource Announcements, 13: e00919-23. https://doi.org/10.1128/mra.00919-23

• Nielsen TK, Forero-Junco LM, Kot W, Moineau S, Hansen LH, and L Riber. 2023. Detection of nucleotide modifications in bacteria and bacteriophages: strengths and limitations of current technologies and software. Molecular Ecology, 32: 1236-1247. https://doi.org/10.1111/mec.16679

• Orellana LH, Kruger K, Sidhu C, and R Amann. 2023. Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies. Microbiome, 11: 105. https://doi.org/10.1186/s40168-023-01557-3

• Priest T, von Appen W-J, Oldenburg E, Popa O, Torres-Valdes S, Bienhold C, Metfies K, Boulton W, Mock T, Fuchs BM, Amann R, Boetius A, and M Wietz. 2023. Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities. The ISME Journal, https://doi.org/10.1038/s41396-023-01461-6

• Priest T, Vidal-Melgosa S, Hehemann J-H, Amann R, and BM Fuchs. 2023. Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic. ISME Communications, 3: 130. https://doi.org/10.1038/s43705-023-00324-7

• Rodriguez Ruiz A, and AR Van Dam. 2023. Metagenomic binning of PacBio HiFi data prior to assembly reveals a complete genome of Cosmopolites sordidus (Germar) (Coleopterea: Curculionidae, Dryophthorinae) the most damaging arthropod pest of bananas and plantains. PeerJ 11: e16276. https://doi.org/10.7717/peerj.16276

• Saak CC, Pierce EC, Dinh CB, Portik D, Hall R, Ashby M, and RJ Dutton. 2023. Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities. mSystems, 8:e00701-22. https://doi.org/10.1128/msystems.00701-22

• Schaerer L, Putman L, Bigcraft I, Byrne E, Kulas D, Zolghadr A, Aloba S, Ong R, Shonnard D, and S Techtmann. 2023. Coexistence of specialist and generalist species within mixed plastic derivative-utilizing microbial communities. Microbiome, 11: 224. https://doi.org/10.1186/s40168-023-01645-4

• Sidhu C, Kirstein IV, Meunier CL, Rick J, Fofonova V, Wiltshire KH, Steinke N, Vidal-Melgosa S, Hehemann J-H, Huettel B, Schweder T, Fuchs BM, Amann RI, and H Teeling. 2023. Dissolved storage glycans shaped the community composition of abundant bacterioplankton clades during a North Sea spring phytoplankton bloom. Microbiome, 11: 77. https://doi.org/10.1186/s40168-023-01517-x

• Sun C, Chen J, Jin M, Zhao X, Li Y, Dong Y, Gao N, Liu Z, Bork P, Zhao X-M, and W-H Chen. 2023. Long-read sequencing reveals extensive DNA methylations in human gut pangenome contributed by prevalently phage-encoded methyltransferases. Advanced Science, 10: 2302159. https://doi.org/10.1002/advs.202302159

• Tao Y, Xun F, Zhao C, Mao Z, Li B, Xing P, and QL Wu. 2023. Improved assembly of metagenome-assembled genomes and viruses in Tibetan saline lake sediment by HiFi metagenomic sequencing. Microbiology Spectrum, 11: e03328-22. https://doi.org/10.1128/spectrum.03328-22

• Toth CRA, Molenda O, Nesbo C, Luo F, Devine C, Guo S, Chen X, EA Edwards. 2023. Metagenomic and genomic sequences from a methanogenic benzene-degrading consortium. Microbiology Resource Announcements, 12: e01342-22. https://doi.org/10.1128/mra.01342-22

• Zhang Z, Yang C, Veldsman WP, Fang X, and L Zhang. 2023. Benchmarking genome assembly methods on metagenomic sequencing data. Briefings in Bioinformatics, 24: 1-17. https://doi.org/10.1093/bib/bbad087

• Zhang Z-F, Liu L-R, Pan Y-P, Pan J, and M Li. 2023. Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments. Microbiome, 11: 188. https://doi.org/10.1186/s40168-023-01630-x

2022

• Adler A, Poirier S, Pagni M, Maillard J, and C Holliger. 2022. Disentangle genus microdiversity within a complex microbial community by using a multi-distance long-read binning method: example of Candidatus Accumulibacter. Environmental Microbiology, 24: 2136-2156. https://doi.org/10.1111/1462-2920.15947

• Antipov D, Rayko M, Kolmogorov M, and PA Pevzner. 2022. viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data. Genome Biology, 23: 57. https://doi.org/10.1186/s13059-021-02566-x

• Bickhart DM, Kolmogorov M, Tseng E, Portik DM, Korobeynikov A, Tolstoganov I, Uritskiy G, Liachko I, Sullivan ST, Shin SB, Zorea A, Andreu VP, Panke-Buisse K, Medema MH, Mizrahi I, Pevzner PA, and TPL Smith. 2022. Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities. Nature Biotechnology, 40: 711-719. https://doi.org/10.1038/s41587-021-01130-z

• Fedarko MW, Kolmogorov M, and PA Pevzner. 2022. Analyzing rare mutations in metagenomes assembled using long and accurate reads. Genome Research, 32: 2119-2133. https://doi.org/10.1101%2Fgr.276917.122

• Feng X, Cheng H, Portik D, and H Li. 2022. Metagenome assembly of high-fidelity long reads with hifiasm-meta. Nature Methods, 19: 671–674. https://doi.org/10.1038/s41592-022-01478-3

• Fortney NW, Myers KS, Ingle AT, Walters KA, Scarborough MJ, Donohue TJ, and DR Noguera. 2022. Metagenomes and metagenome-assembled genomes from microbiomes metabolizing thin stillage from an ethanol biorefinery. Microbiology Resource Announcements, 11: e00290-22. https://doi.org/10.1128/mra.00290-22

• Gehrig JL, Portik DM, Driscoll MD, Jackson E, Chakraborty S, Gratalo D, Ashby M, and R Valladares. 2022. Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data. Microbial Genomics, 8: 000794. https://doi.org/10.1099/mgen.0.000794

• Ingle AT, Fortney NW, Myers KS, Walters KA, Scarborough MJ, Donohue TJ, and DR Noguera. 2022. Metagenome-assembled genomes from a microbiome grown in dairy manure hydrolysate. Microbiology Resource Announcements, 11: e00292-22. https://doi.org/10.1128/mra.00292-22

• Jin H, You L, Zhao F, Li S, Ma T, Kwok L-Y, Xu H, and Z Sun. 2022. Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome. Gut Microbiomes, 14: e 2021790. https://doi.org/10.1080/19490976.2021.2021790

• Kato S, Masuda S, Shibata A, Shirasu K, and M Ohkuma. 2022. Insights into ecological roles of uncultivated bacteria in Katase hot spring sediment from long-read metagenomics. Frontiers in Microbiology, 13: 1045931. https://doi.org/10.3389/fmicb.2022.1045931

• Kim CY, Ma J, and I Lee. 2022. HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota. Nature Communications, 13: 6367. https://doi.org/10.1038/s41467-022-34149-0

• Loureiro C, Galani A, Gavriilidou A, de Mars, MC, van der Oost J, Medema MH, and D Sipkema. 2022. Comparative metagenomic analysis of biosynthetic diversity across sponge microbiomes highlights metabolic novelty, conservation, and diversification. mSystems, 7: e00357-22. https://doi.org/10.1128/msystems.00357-22

• Luo X, Kang X, and A Schonhuth. 2022. Enhancing long-read-based strain-aware metagenome assembly. Frontiers in Genetics, 13: 868280. https://doi.org/10.3389/fgene.2022.868280

• Meslier V, Quinquis B, Da Silva K, Plaza Onate F, Pons N, Roume H, Podar M, and M Almeida. 2022. Benchmarking second and third-generation sequencing platforms for microbial metagenomics. Scientific Data, 9: 694. https://doi.org/10.1038/s41597-022-01762-z

• Noonan AJC, Qiu Y, Kieft B, Formby S, Liu T, Dofher K, Koch M, and SJ Hallam. 2022. Metagenome-assembled genomes for “Candidatus Phormidium sp. Strain AB48” and co-occurring microorganisms from an industrial photobioreactor environment. Microbiology Resource Announcements, e0044722. https://doi.org/10.1128/mra.00447-22

• Patin NV, and KD Goodwin. 2022. Long-read sequencing improves recovery of picoeukaryotic genomes and zooplankton marker genes from marine metagenomes. mSystems, 7: e00595-22. https://doi.org/10.1128/msystems.00595-22

• Petrone JR, Munoz-Beristain A, Glusberger PR, Russell JT, and EW Triplett. 2022. Unamplified, long-read metagenomic sequencing approach to close endosymbiotic genomes of low-biomass insect populations. Microorganisms, 10: 513. https://doi.org/10.3390/microorganisms10030513

• Plaza Onate F, Roume H, and M Almeida. 2022. Recovery of metagenome-assembled genomes from a human fecal sample with Pacific Biosciences high-fidelity sequencing. Microbiology Resource Announcements, 11: e0025022. https://doi.org/10.1128/mra.00250-22

• Portik DM, Brown CT, and NT Pierce-Ward. 2022. Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets. BMC Bioinformatics, 23: 541. https://doi.org/10.1186/s12859-022-05103-0

• Seong HJ, Roux S, Hwang CY, and WJ Sul. 2022. Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics. Microbiome, 10: 157. https://doi.org/10.1186/s40168-022-01340-w

• Sereika M, Kirkegaard RH, Karst SM, Michaelsen TY, Sorensen EA, Wollenberg RD, and M Albertsen. 2022. 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. Nature Methods, 19: 823-826. https://doi.org/10.1038/s41592-022-01539-7

• Slizovskiy IB, Oliva M, Settle JK, Zyskina LV, Prosperi M, Boucher C, and NR Noyes. 2022. Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes. Microbiome, 10: 185. https://doi.org/10.1186/s40168-022-01368-y

• Walters KA, Myers KS, Wang H, Fortney NW, Ingle AT, Scarborough MJ, Donohue TJ, and DR Noguera. 2022. Metagenomes and metagenome-assembled genomes from microbial communities fermenting ultrafiltered milk permeate. Microbiology Resource Announcements, 11: e00293-22. https://doi.org/10.1128/mra.00293-22

• Wickramarachchi A, and Y Lin. 2022. Binning long reads in metagenomics datasets using composition and coverage information. Algorithms for Molecular Biology, 17: 14. https://doi.org/10.1186/s13015-022-00221-z

• Wilbanks EG, Dore H, Ashby MH, Heiner C, Roberts RJ, and JA Eisen. 2022. Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity. The ISME Journal, 16: 1921-1931. https://doi.org/10.1038/s41396-022-01242-7

• Xu G, Zhang L, Liu X, Guan F, Xu Y, Yue H, Huang J-Q, Chen J, Wu N, and J Tian. 2022. Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome. BMC Genomics, 23: 37. https://doi.org/10.1186/s12864-021-08260-3

• Zaragoza-Solas A, Haro-Moreno JM, Rodriguez-Valera F, and M Lopez-Perez. 2022. Long-read metagenomics improves the recovery of viral diversity from complex natural marine samples. mSystems, 7, e0019222. https://doi.org/10.1128/msystems.00192-22

• Zhang Y, Jiang F, Yang B, Wang S, Wang H, Wang A, Xu D, and W Fan. 2022. Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads. GigaScience, 11: 1-12. https://doi.org/10.1093/gigascience/giac116

• Zhao L, Shi Y, Lau HC-H, Liu W, Luo G, Wang G, Liu C, Pan Y, Zhou Q, Ding Y, Sung JJ-Y, and J Yu. 2022. Uncovering 1058 novel human enteric DNA viruses through deep long-read third-generation sequencing and their clinical impact. Gastroenterology, 163: 699-711. https://doi.org/10.1053/j.gastro.2022.05.048

2021

• Haro-Moreno JM, Lopez-Perez M, and F Rodriguez-Valera. 2021. Enhanced recovery of microbial genes and genomes from a marine water column using long-read metagenomics. Frontiers in Microbiology, 12: 708782. https://doi.org/10.3389/fmicb.2021.708782

• Kiguchi Y, Nishijima S, Kumar N, Hattori M, and W Suda. 2021. Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads. DNA Research, 28: dsab019. https://doi.org/10.1093/dnares/dsab019

• Priest T, Orellana LH, Huettel B, Fuchs BM, and R Amann. 2021. Microbial metagenome-assembled genomes of the Fram Strait from short and long read sequencing platforms. PeerJ, 9: e11721. https://doi.org/10.7717/peerj.11721

• Tedersoo L, Albertsen M, Anslan S, and B Callahan. 2021. Perspectives and benefits of high-throughput long-read sequencing in microbial ecology. Applied and Environmental Microbiology, 87: e00626-21. https://doi.org/10.1128/AEM.00626-21

2020

• Holm JB, France MT, Ma B, McComb E, Robinson CK, Mehta A, Tallon LJ, Brotman RM, and J Ravel. 2020. Comparative metagenome-assembled genome analysis of "Candidatus Lachnocurva vaginae", formerly known as bacterial vaginosis-associated bacterium-1 (BVAB1). Frontiers in Cellular and Infection Microbiology, 10: 117. https://doi.org/10.3389/fcimb.2020.00117

• Xie H, Yang C, Sun Y, Igarashi Y, Jin T, and F Luo. 2020. PacBio Long Reads Improve Metagenomic Assemblies, Gene Catalogs, and Genome Binning. Frontiers in Genetics, 11: 516269. https://doi.org/10.3389/fgene.2020.516269

2019

• Bickhart DM, Watson M, Koren S, Panke-Buisse K, Cersosimo LM, Press MO, Van Tassell CP, Van Kessel JAS, Haley BJ, Kim SW, Heiner C, Suen G, Bakshy K, Liachko I, Sullivan ST, Myer PR, Ghurye J, Pop M, Weimer PJ, Phillippy AM, and TPL Smith. 2019. Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation. Genome Biology, 20, 153. https://doi.org/10.1186/s13059-019-1760-x

• Sevim V, Lee J, Egan R, Clum A, Hundley H, Lee J, Everroad RC, Detweiler AM, Bebout BM, Pett-Ridge J, Goker M, Murray AE, Lindemann SR, Klenk H-P, O'Malley R, Zane M, Cheng J-F, Copeland A, Daum C, Singer E and T Woyke. 2019. Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio, and Illumina technologies. Scientific Data, 6: 285. https://doi.org/10.1038/s41597-019-0287-z

• Suzuki Y, Nishijima S, Furuta Y, Yoshimura J, Suda W, Oshima K, Hattori M, and S Morishita. 2019. Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut. Microbiome, 7: 119. https://doi.org/10.1186/s40168-019-0737-z

2018

• Liu Y-R, Johs A, Bi L, Lu X, Hu H-W, Sun D, He J-Z, and B Gu. 2018. Unraveling microbial communities associated with methylmercury production in paddy soils. Environmental Science and Technology, 52: 13110-13118. https://doi.org/10.1021/acs.est.8b03052

2017

• Driscoll CB, Otten TG, Brown NM, and TW Dreher. 2017. Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture. Standards in Genomic Sciences, 12: 9. https://doi.org/10.1186/s40793-017-0224-8

2016

• Frank JA, Pan Y, Tooming-Klunderud A, Eijsink VGH, McHardy AC, Nederbragt AJ, and PB Pope. 2016. Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data. Scientific Reports, 6: 25373. https://doi.org/10.1038%2Fsrep25373