MetaQUAST: evaluation of metagenome assemblies

Cited by (717)

Items 401–500 of 717

  1. Microbial metabolic potential of hydrothermal vent chimneys along the submarine ring of fire
    Laura Murray, Heather E. Fullerton, C.L. Moyer · 2024 · Frontiers in Microbiology
  2. 16S rRNA-based taxonomy profiling in the metagenomics era
    Giovanni Bacci, Lorenzo Casbarra, Matteo Ramazzotti · 2024 · Elsevier eBooks
  3. The influence of depth on the global deep-sea plasmidome
    Melany Calderón-Osorno, Dorian Rojas-Villalta, Franck Lejzerowicz, Jorge Cortés, María Arias-Andrés, Keilor Rojas-Jiménez · 2025 · Scientific Reports
  4. HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations
    Thomas K. F. Wong, Louis Ranjard, Yu Lin, Allen G. Rodrigo · 2018 · BMC Bioinformatics
  5. Trimming and Decontamination of Metagenomic Data can Significantly Impact Assembly and Binning Metrics, Phylogenomic and Functional Analysis
    Jason M. Whitham, Amy Michele Grunden · 2023 · Current Bioinformatics
  6. A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences
    Carlos D. Ordóñez, Carmen Mayoral-Campos, Conceição Egas, Modesto Redrejo‐Rodríguez · 2023 · NAR Genomics and Bioinformatics
  7. Substrate Specificity of Biofilms Proximate to Historic Shipwrecks
    Rachel L. Mugge, Rachel D. Moseley, Leila J. Hamdan · 2023 · Microorganisms
  8. A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions
    Bianca Rodrigues Jardim, Cherie Gambley, Lucy T. T. Tran‐Nguyen, Craig G. Webster, Monica A. Kehoe, Wycliff M. Kinoti, Samantha Bond, R. I. Davis, LYNNE M. JONES, Nandita Pathania et al. · 2024 · Microbial Genomics
  9. IMP: a pipeline for reproducible integrated metagenomic and metatranscriptomic analyses
    Shaman Narayanasamy, Yohan Jarosz, Emilie E. L. Muller, Cedric Christian Laczny, Malte Herold, Anne Kaysen, Anna Heintz‐Buschart, Nicolás Pinel, Patrick May, Paul Wilmes · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
  10. Nutrient parsimony shapes diversity and functionality in hyper-oligotrophic Antarctic soils
    Marc W. Van Goethem, Surendra Vikram, DAVID W. HOPKINS, Grant Hall, Stephan M Woodborne, Thomas J. Aspray, Ian D. Hogg, Don Arthur Cowan, Thulani Peter Makhalanyane · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  11. First genome assembly of the order Strepsiptera using PacBio HiFi reads reveals a miniature genome
    María Isabel Castaño, Xinhai Ye, Floria M. K. Uy · 2024 · Scientific Data
  12. A detailed guide to assessing genome assembly based on long-read sequencing data using Inspector
    Yan Ping Guo, Yuwei Song, Limin Jiang, Yu Chen, Michele Ceccarelli, Min Gao, Zechen Chong · 2025 · Nature Protocols
  13. An early microbial landscape: inspiring endeavor from the China Space Station Habitation Area Microbiome Program (CHAMP)
    Junxia Yuan, Jinlu Yang, Yue Sun, Yaqi Meng, Ziwei He, Wende Zhang, Lei Dang, Yan Xiang Song, Kanyan Xu, Na Lv et al. · 2025 · Science China Life Sciences
  14. Comparative analysis of three experimental methods for revealing human fecal microbial diversity
    Caiqing Yao, Yu Zhang, Lijun You, E Jingjing, Junguo Wang · 2025 · BMC Microbiology
  15. CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets
    Louis Kraft, Johannes Söding, Martin Steinegger, Annika Jochheim, Peter Wad Sackett, Antonio Fernàndez-Guerra, Gabriel Renaud · 2025 · Genome biology
  16. Metagenomic and culture-based genomics reveal virulence and resistance risks in Manila clam microbiomes
    Yaling Wang, Linan He, Xing Hu, Yuhan Guan, Xiangnan Chen, Jiahui Du, Jiayan Chen, Chensheng Ma, Lianwei Ye · 2025 · Food Microbiology
  17. Host–microbiome mutualism drives urea carbon salvage and acetogenesis during hibernation
    Matthew D. Regan, Edna Chiang, Michael Grahn, Marco Tonelli, Fariba M. Assadi‐Porter, Garret Suen, Hannah V. Carey · 2026 · Proceedings of the National Academy of Sciences
  18. 2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction
    Jeferyd Yepes-García, Laurent Falquet · 2026 · mSystems
  19. Metagenomic Insights into the Microbial Composition and Functional Potential of Cocoa (Theobroma cacao L.) During Fermentation and Drying in Colombia
    Daniel López-Puentes, Zaida Zarely Ojeda Pérez, Diana Marcela Arias Moreno · 2026 · Microbial Ecology
  20. Diversity of bacteriocins in the microbiome of the Tucuruí Hydroelectric Power Plant water reservoir and three-dimensional structure prediction of a zoocin
    Sávio Souza Costa, A B Lago Leticia, Artur Silva, Diego Assis das Graças, Jerônimo Lameira, Rafael Azevedo Baraúna · 2022 · Genetics and Molecular Biology
  21. Metagenomic Analysis of Microbial Diversity in the Moroccan Coastal Water of the Gibraltar Strait
    Manal Chrairi, Saïd Barrijal, Antonio Castellano‐Hinojosa, Youssra Boumait, Chahrazade El Hamouti, Afaf Lamzouri, Hassan Ghazal, Rajaa Chahboune · 2024 · Water
  22. Sequential co-assembly reduces computational resources and errors in metagenome-assembled genomes
    Hannah M. Lynn, Jeffrey I. Gordon · 2025 · Cell Reports Methods
  23. Assessment of Antimicrobial Resistance Genes and Pathobiome Diversity in Domestic Wastewater of a Tropical Country
    Fernando Molina-Ospina, Bradd Mendoza-Guido, Andrea Quesada-González, Luz Chacón, Mary Luz Barrios-Hernández · 2025 · Water
  24. Metagenomic and metatranscriptomic exploration of Avicennia germinans L.: Endophytic microbiome of leaves and roots
    César Alejandro Lemos-Lucumí, Valentina Cárdenas‐Hernández, Nelson Toro‐Perea · 2025 · Microbiological Research
  25. A model, mixed-species urinary catheter biofilm derived from spinal cord injury patients
    Parisa Noorian, Kailey Hamann, M. Mozammel Hoque, Gustavo Espinoza-Vergara, Joyce To, Dominic Leo, Priyadarshini Chari, Gerard Weber, Obaydullah Marial, Julie Pryor et al. · 2025 · Biofilm
  26. Tamock: simulation of habitat-specific benchmark data in metagenomics
    Samuel M. Gerner, Alexandra Bettina Graf, Thomas Rattei · 2021 · BMC Bioinformatics
  27. Role of co-infections in modulating disease severities and clinical phenotypes
    Priti Devi, Aanchal Yadav, Sunita Kumari Yadav, Jyoti Soni, Pallawi Kumari, Aakarshan Raina, Rajesh Pandey · 2023 · Elsevier eBooks
  28. Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning
    Harrison Ho, Mansi Chovatia, Rob S Egan, Guifen He, Yuko Yoshinaga, Ivan Liachko, Ronan C. O’Malley, Zhong Wang · 2023 · PeerJ
  29. Metagenomic survey reveals global distribution and evolution of microbial sialic acid catabolism
    Yisong Li, Yeshun Fan, Xiaofang Ma, Ying Wang, Jie Liu · 2023 · Frontiers in Microbiology
  30. A targeted approach to enrich host-associated bacteria for metagenomic sequencing
    Ashley M. Dungan, Kshitij Tandon, Vanta J. Jameson, Cecilie Ravn Gøtze, Linda L. Blackall, Madeleine J. H. van Oppen · 2023 · FEMS Microbes
  31. Biodegradation of chloroethene compounds under microoxic conditions
    Abidemi Oluranti Ojo, Julio Castillo, Errol Duncan Cason, Ángel Valverde · 2023 · Biotechnology and Bioengineering
  32. NGS-Based Metagenomics Depicting Taxonomic and Functional Insights into North-Western Himalayan Hot Springs
    Shailja Rangra, Nitish Kumar Sharma, Prem Lata, Kiran Bala Sharma, Reena Kumari, Sudhir P. Singh, Savitri · 2024 · Indian Journal of Microbiology
  33. Computational Metagenomics: State-of-the-Art, Facts and Artifacts
    Harpreet Singh, Purnima Sharma, Rupinder Preet Kaur, Diksha Thakur, Pardeep Kaur · 2020 · Springer eBooks
  34. Oligotyping and Genome-Resolved Metagenomics Reveal Distinct Candidatus Accumulibacter Communities in Full-Scale Side-Stream versus Conventional Enhanced Biological Phosphorus Removal (EBPR) Configurations
    Varun N. Srinivasan, Guangyu Li, Dongqi Wang, Nicholas Brewster Tooker, Zihan Dai, Annalisa Onnis‐Hayden, Ameet J. Pinto, April Z. Gu · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  35. Advantages and limits of metagenomic assembly and binning of a giant virus
    Frederik Schulz, Julien Andréani, Rania Francis, Jacques Yaacoub Bou Khalil, Janey Lee, Bernard La Scola, Tanja Woyke · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  36. Computational Methods for Chromosome-Scale Haplotype Reconstruction
    Shilpa Garg · 2021 · Preprints.org
  37. Urea nitrogen recycling via gut symbionts increases in hibernators over the winter fast
    Matthew D. Regan, Edna Chiang, Yunxi Liu, Marco Tonelli, Kristen M. Verdoorn, Sadie R. Gugel, Garret Suen, Hannah V. Carey, Fariba M. Assadi‐Porter · 2021 · bioRxiv (Cold Spring Harbor Laboratory)
  38. A multi omics approach unravels metagenomic and metabolic alterations of a probiotic in rainbow trout (Oncorhynchus mykiss)
    Jacob Agerbo Rasmussen, Kasper Rømer Villumsen, Madeleine Ernst, Martin Asser Hansen, Torunn Forberg, Shyam Gopalakrishnan, Marcus Thomas P. Gilbert, Anders Miki Bojesen, Karsten Kristiansen, Morten T. Limborg · 2021 · Research Square
  39. Direct DNA sequencing of ‘ Candidatus Liberibacter asiaticus’ from Diaphorina citri , the Asian citrus psyllid, and its implications for citrus greening disease management
    Steven Higgins, Marina Mann, Michelle Lynn Heck · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  40. Cross-kingdom metagenomic profiling of Lake Hillier reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations
    Maria A. Sierra, Krista A. Ryon, Braden T. Tierney, Jonathan Foox, Chandrima Bhattacharya, Evan E. Afshin, Daniel Butler, Stefan J. Green, W. Kelley Thomas, Jordan S. Ramsdell et al. · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  41. Deep sequencing-derived Metagenome Assembled Genomes from the gut microbiome of liver transplant patients
    Goutam Banerjee, Suraya Rahman Papri, Hai Huang, Sanjaya Kumar Satapathy, Pratik Banerjee · 2025 · Scientific Data
  42. 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
    Zhaoyu Zhai, Xiaohui Che, Wei Shen, Zishun Zhang, Yapeng Li, Jianbo Pan · 2025 · Nucleic Acids Research
  43. Preliminary characterization of Vibrio cholerae strains isolated from seafood samples marketed in Portugal
    Teresa Teixeira Lopes, David Lopes, Isabel Bastos Moura, Isabel Soares Sousa, João Rodrigues, Camila Fernandes, Maria João Barreira, Carla Maia, Cristina Belo Correia, Cristina M. B. S. Pintado et al. · 2025 · The Microbe
  44. Ecosystem health shapes viral ecology in peatland soils
    James C. Kosmopoulos, William Pallier, Ashish A. Malik, Karthik Anantharaman · 2025 · Nature Microbiology
  45. The role of mycobiome in terroir and during Muscat grapes fermentation unveiled by multi-omic analysis
    Paola Di Gianvito, Vania Sáez, Maria Dimopoulou, Christina Papandreou, Nicola Francesca, Urška Vrhovšek, Kalliopi Rantsiou, Luca Cocolin, Panagiotis Arapitsas, Vasileios Englezos · 2026 · Food Research International
  46. Genome-Resolved Metagenomics Suggests Site-Specific Microbial Adaptations in Urban Soils Co-Contaminated with Hydrocarbons and Heavy Metals
    Morena India Mokoena, Rosina Nkuna, Tonderayi Sylvester Matambo · 2026 · Environments
  47. Environmental microbiome, resistome and plasmidome in agricultural areas with intensive poultry litter use: A metagenomic multicompartmental analysis of antimicrobial resistance gene dissemination
    Eliene dos Santos Lopes, Douglas Alfradique Monteiro, Cláudio Ernesto Taveira Parente, Lucy Seldin · 2026 · Journal of Hazardous Materials Advances
  48. Shotgun metagenome sequencing and informatics can accurately form a metagenome-assembled genome (MAG) of the bacterial tier 1 select agent Burkholderia pseudomallei for rapid public health response events
    Gregory A. Sprenger, Jay E. Gee, Mindy G. Elrod, Zachary P. Weiner, Christopher A. Gulvik · 2026 · Microbiology Spectrum
  49. Antibiotic resistance genes in drinking water: Absolute abundance, mobility, and hosts across the source-to-tap continuum
    Jie Liu, Renxin Zhao, Jin Huang, Uli Klümper, Ke Yu, Jiayu Zhang, Guijuan Zhang, Thomas Ulrich Berendonk, Ryo Honda, Yang Yu et al. · 2026 · Chemical Engineering Journal
  50. Enteropathy produced in mice by intergenerational transmission of small intestinal microbiota from undernourished children
    Kali M. Pruss, C.-Y. Kao, Alexandra E. Byrne, Robert Yuzen Chen, Blanda Di Luccia, Laura Karvelyte, Reyan Coskun, Mackenzie Lemieux, Keshav Nepal, Daniel M. Webber et al. · 2026 · Nature Microbiology
  51. Dimethylsulfoniopropionate metabolism shapes microbial ecology and physiological adaptation during the austral winter in Southern Ocean sea ice and seawater
    Z. Mayibongwe Buthelezi, Rian Pierneef, Oliver K. I. Bezuidt, M. Nello J. Gregori, Stéphane Pesant, Daniele Iudicone, Libby Hanwell, Jonathan D. Todd, Thulani Peter Makhalanyane · 2026 · Nature Communications
  52. Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets
    Chiara Vanni · 2021 · Methods in molecular biology
  53. Artificial intelligence reveals roles of gut microbiota in driving human colorectal cancer evolution
    Xuehua Wan · 2021 · WArtificial Intelligence in Cancer
  54. Recovery and Analysis of Long-Read Metagenome-Assembled Genomes
    Krithika Arumugam, Irina N. Bessarab, Mindia Haryono, Rohan B. H. Williams · 2023 · Methods in molecular biology
  55. Meta-transcriptomic identification of groundnut RNA viruses in western Kenya and the novel detection of groundnut as a host for Cauliflower mosaic virus
    Dennis Obonyo, George Ouma, Rachel Ikawa, Damaris A. Odeny · 2024 · Virology
  56. Systematic benchmarking of omics computational tools
    Sanjay Kumar, Manjusa Singh, Rajesh Kumar Sharma, Manish Gupta · 2024 · Elsevier eBooks
  57. Detection of mobile colistin resistance genes mcr-9.1 and mcr-10.1 in Enterobacter asburiae from Ecuadorian children
    Sara G. Cifuentes, Jay P. Graham, Gabriel A. Trueba, Paúl Cárdenas · 2024 · Microbiology Resource Announcements
  58. HairSplitter: haplotype assembly from long, noisy reads
    Roland Faure, Dominique D. Lavenier, Jean‐François Flot · 2024 · Peer Community Journal
  59. Response of marine microbes to iron contained in colloids of glacial origin: a Kerguelen Island case study
    Rhea Thoppil, Stéphane Blain, Rui Zhang, Audrey Guéneuguès, Olivier Crispi, Philippe Catala, Barbara Marie, Ingrid Obernosterer · 2025 · ISME Communications
  60. Uncovering tissue-specific endophytic microbiota composition and activity in Rhizophora mangle L.: a metagenomic and metatranscriptomic approach
    Valentina Cárdenas‐Hernández, César Alejandro Lemos-Lucumí, Nelson Toro‐Perea · 2025 · PeerJ
  61. Clin-mNGS: Automated Pipeline for Pathogen Detection from Clinical Metagenomic Data
    Akshatha Prasanna, Vidya Niranjan · 2020 · Current Bioinformatics
  62. Rhizosphere Metagenomics: Methods and Challenges
    Abiramavalli Moorthy, Usha Balasundaram · 2021 · Rhizosphere biology
  63. Influence of soil management for soybean production under microbial diversity in amazon soils
    Oscar Victor Cardenas Alegria, Carlos Willian Dias Dantas, Elaine Maria Silva Guedes Lobato, Sandro Patroca Da Silva, Cássia Nazaré de Sousa Moraes, Ana Cecília Ribeiro Cruz, Rommel Thiago Jucá Ramos, Adriana Ribeiro Carneiro · 2022 · Frontiers in Environmental Science
  64. Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers
    Hajra Qayyum, Muhammad Faheem Raziq, Haseeb Manzoor, Syed Shujaat Ali Zaidi, Amjad H. Ali, Masood Ur Rehman Kayani · 2025 · Interdisciplinary Sciences Computational Life Sciences
  65. Improving Metagenomic Assemblies Through Data Partitioning: A GC Content Approach
    Fábio Malcher Miranda, Cassio Batista, Artur Silva, Jefferson Magalhaes De Morais, Nelson Neto, Rommel Thiago Jucá Ramos · 2018 · Lecture notes in computer science
  66. Metagenomes, Metagenome-Assembled Genomes, and Metatranscriptomes from Polychlorinated Biphenyl-Contaminated Sediment Microcosms
    Jessica M. Ewald, Jerald L. Schnoor, Timothy E. Mattes · 2022 · Microbiology Resource Announcements
  67. Assessing taxonomic metagenome profilers with OPAL
    Fernando Meyer, Andreas Bremges, Peter Belmann, Stefan Janssen, Alice Carolyn McHardy, David Koslicki · 2018 · bioRxiv (Cold Spring Harbor Laboratory)
  68. Size-fractionated microbiome observed during an eight-month long sampling in Jiaozhou Bay and the Yellow Sea
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  69. Diversity and biogeochemical roles of DNA viruses in Antarctic sea ice
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  70. “Quasigenus” among Phycodnaviridae : A diversity of chlorophyte-infecting viruses in response to a dense algal culture in a high-rate algal pond
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  71. Bioinformatic methods for genome-centric metagenomics
    Rhys Newell · 2023 · Queensland University of Technology
  72. Comprehensive Assessment of Eleven de novo HiFi Assemblers on Complex Eukaryotic Genomes and Metagenomes
    Wenjuan Yu, Haohui Luo, Jinbao Yang, Shengchen Zhang, Heling Jiang, Xianjia Zhao, Xingqi Hui, Da Sun, Liang Li, Xiu-qing Wei et al. · 2023 · bioRxiv (Cold Spring Harbor Laboratory)
  73. Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs
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  74. Assessing the performance of current strain resolution tools on long-read metagenomes
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  75. Evaluation of Metagenome Binning: Advances and Challenges
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  76. Genome-Resolved Metagenomics of Rice Straw Degradation Experiments in Colombian Fields
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  77. Microbial Communities Driving Pollution Degradation in Contaminated Environments
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  78. Recent toolset of metagenomics for taxonomical and functional annotation of marine associated viruses: A review
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  79. Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics
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  80. Flowtigs: Safety in flow decompositions for assembly graphs
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  81. Simple, reference-independent assessment to empirically guide correction and polishing of hybrid microbial community metagenomic assembly
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  82. Methodological aspects of investigating the resistome in pig farm environments
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  83. Ecological insights into circular putative plasmids in Stylissa carteri microbiomes across the Indo-Pacific
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  84. Soil microbiome analysis of Uruguayan grasslands and croplands reveals losses of microbial diversity and necromass recycling traits
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  91. Soil microbial adaptation to carbon deprivation: shifts in lignocellulolytic gene profiles following long-term plant exclusion
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  92. Unraveling microbial life from a high-altitude hydrothermal system in the Andes plateau and their potential for nitrogen transformations
    Coral Pardo-Esté, Juan Castro‐Severyn, Jacqueline Aldridge, Diego Álvarez-Saravia, Lenka Kurte, Polette Aguilar‐Muñoz, Pablo Paquis, Vilma Pérez, David Medina, Wade H Jeffrey et al. · 2025 · Engineering Microbiology
  93. Urban Wastewater Metagenomics Reveals the Antibiotic Resistance Gene Distribution Across Latvian Municipalities
    Edgars Liepa, Maija Ustinova, Dita Gudrā, Ance Roga, Ineta Kalniņa, Brigita Dejus, Sandis Dejus, Mārtiņš Strods, Laura Elīna Tomsone, Juris Ķibilds et al. · 2026 · Microorganisms
  94. ChromoMapper: a new tool to quickly compare large genome assemblies
    Elvira Toscano, Elena Cimmino, Angelo Sabato Boccia, Leandra Sepe, Giovanni Paolella · 2026 · Bioinformatics Advances
  95. Shotgun metagenomic dataset of seawater bacterial communities from Pari Islands, Indonesia
    Buntora Pasaribu, Christopher Vincent Mishael Dilens, Muhammad Wahyudin Lewaru, Diah Ayuningrum, Mufti Petala Patria, Donny Juliandri Prihadi, Noir Primadona Purba, Mochamad Untung Kurnia Agung, Ismail Maqbul, SULISTIOWATI SULISTIOWATI · 2026 · Microbiology Resource Announcements
  96. Weather conditions structure the taxonomic and functional diversity of the aeolian dust microbiome
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  97. Identification and characterization of a novel orthoreovirus from American eels, Anguilla rostrata
    Jin-Xian Yang, Ying-Ying Li, Bin Sun, Qiang Chen, Jun Qing Ge · 2026 · Microbiology Spectrum
  98. Elucidating the Functional and Taxonomic Diversity of Soil Microbial Communities From Three Commercial Soybean Farms in South Africa
    Khumbudzo Ndhlovu, Adeola Salawu-Rotimi, Francina Lebogang Bopape, Prudence Nompumelelo Mtsweni, Olubukola Oluranti Babalola, Ahmed Idris Hassen · 2026 · Environmental Microbiology Reports
  99. Long‐Term Effects of Straw‐Biochar Application and Fertilization Gradients on Black Soil Carbon Sequestration via Prokaryote‐Fungus‐Protist Interactions and Metagenomic‐Metabolite Linkages
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  100. Bioinformatics roadmap for characterizing the gut microbiome to study its interactions and associations with the gut mucosal immune system
    Muhammad Zohaib Anwar, Miguel Darío Prieto, William Hsiao · 2026 · Mucosal Immunology