Shotgun metagenomics, from sampling to analysis

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

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Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

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Trimmomatic: a flexible trimmer for Illumina sequence data

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vegan: Community Ecology Package

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SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M. V., Kulikov, A. S., Lesin, V. M., Nikolenko, S., Pham, S., Prjibelski, A. D., et al. (2012) · Journal of Computational Biology · doi:10.1089/cmb.2012.0021 · Cited by 26,312

Metagenomic biomarker discovery and explanation

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Structure, function and diversity of the healthy human microbiome

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A human gut microbial gene catalogue established by metagenomic sequencing

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MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Li, D., Liu, C.-M., Luo, R., Sadakane, K., & Lam, T. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv033 · Cited by 10,133

A metagenome-wide association study of gut microbiota in type 2 diabetes

Qin, J., Li, Y., Cai, Z., Li, S., Zhu, J., Zhang, F., Liang, S., Zhang, W., Guan, Y., Shen, D., et al. (2012) · Nature · doi:10.1038/nature11450 · Cited by 6,762

Elucidating biofilm diversity on water lily leaves through 16S rRNA amplicon analysis: Comparison of four DNA extraction kits

Janssen, K., Low, S. L., Wang, Y., Mu, Q.-Y., Bierbaum, G., & Gee, C. T. (2021) · Applications in Plant Sciences · doi:10.1002/aps3.11444 · Cited by 13

Do you cov me? Effect of coverage reduction on species identification and genome reconstruction in complex biological matrices by metagenome shotgun high-throughput sequencing

Cattonaro, F., Spadotto, A., Radović, S., & Marroni, F. (2018) · F1000Research · doi:10.12688/f1000research.16804.1 · Cited by 14

Nanopore Electrochemistry for Pathogen Detection

Ju, Y., Pu, M., Sun, K., Song, G., & Geng, J. (2022) · Chemistry - An Asian Journal · doi:10.1002/asia.202200774 · Cited by 14

The human microbiota and infection prevention

Rafael Araos, B., & D’Agata, E. M. C. (2019) · Infection Control and Hospital Epidemiology · doi:10.1017/ice.2019.28 · Cited by 14

Precise Species Detection in Traditional Herbal Patent Medicine, Qingguo Wan, Using Shotgun Metabarcoding

Liu, J., Shi, M., Zhao, Q., Kong, W., Mu, W., Xie, H., Li, Z., Li, B., & Shi, L. (2021) · Frontiers in Pharmacology · doi:10.3389/fphar.2021.607210 · Cited by 15

A comprehensive evaluation of binning methods to recover human gut microbial species from a non-redundant reference gene catalog

Borderes, M., Gasc, C., Prestat, E., Ferrarini, M. G., Vinga, S., Boucinha, L., & Sagot, M. (2021) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqab009 · Cited by 15

Phylogeny and Metabolic Potential of the Methanotrophic Lineage MO3 in Beijerinckiaceae from the Paddy Soil through Metagenome-Assembled Genome Reconstruction

Cai, Y., Yun, J., & Jia, Z. (2022) · Microorganisms · doi:10.3390/microorganisms10050955 · Cited by 13

Soil development following glacier retreat shapes metagenomic and metabolomic functioning associated with asynchronous C and N accumulation

Huang, Y., Shi, W., Fu, Q., Qiu, Y., Zhao, J., Li, J., Lyu, Q., Yang, X., Xiong, J., Wang, W., et al. (2023) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2023.164405 · Cited by 13

Harnessing microfluidic technology for bacterial single-cell analysis in mammals

Guo, X., Shen, Q., Chen, Z., He, Z., & Yan, X. (2023) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2023.117168 · Cited by 13

Global scale phylogeography of functional traits and microdiversity in Prochlorococcus

Ustick, L. J., Larkin, A. A., & Martiny, A. C. (2023) · The ISME Journal · doi:10.1038/s41396-023-01469-y · Cited by 13

Predicting environmental stressor levels with machine learning: a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data

Hempel, C. A., Buchner, D., Mack, L., Brasseur, M. V., Tulpan, D., Leese, F., & Steinke, D. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1217750 · Cited by 14

Molecular Insights Into the Role of Gut Microbiota in Antibiotic Therapy Selection and Resistance Mitigation

Andreescu, M. (2023) · Cureus · doi:10.7759/cureus.50318 · Cited by 14

Metaproteomics analysis of anaerobic digestion of food waste by the addition of calcium peroxide and magnetite

Zhu, L., Li, W., Liu, Y., Li, J., Xu, L., Gu, L., Chen, C., Cao, Y., & He, Q. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.01451-23 · Cited by 13

Integrating functional metagenomics to decipher microbiome–immune interactions

Sardar, P., Almeida, A., & Pedicord, V. A. (2024) · Immunology and Cell Biology · doi:10.1111/imcb.12798 · Cited by 15

Functional prediction based on 16S rRNA metagenome data from bacterial microbiota associated with macroalgae from the Peruvian coast

Vigil, B. E., Ascue, F., Ayala-Tocto, R. Y., Murúa, P., Calderón, M. S., & Bustamante, D. E. (2024) · Scientific Reports · doi:10.1038/s41598-024-69538-6 · Cited by 13

Fairy: fast approximate coverage for multi-sample metagenomic binning

Shaw, J., & Yu, Y. W. (2024) · Microbiome · doi:10.1186/s40168-024-01861-6 · Cited by 14

Perspectives on Microbiome Therapeutics in Infectious Diseases: A Comprehensive Approach Beyond Immunology and Microbiology

Seo, H., Kim, S., Beck, S., & Song, H. (2024) · Cells · doi:10.3390/cells13232003 · Cited by 15

Improving Whole Biodiversity Monitoring and Discovery With Environmental DNA Metagenomics

Curto, M., Veríssimo, A., Riccioni, G., Santos, C. D., Ribeiro, F., Jentoft, S., Alves, M. J., & Gante, H. F. (2025) · Molecular Ecology Resources · doi:10.1111/1755-0998.14105 · Cited by 13

Mining the Microbiome and Microbiota-Derived Molecules in Inflammatory Bowel Disease

Bekkers, M., Stojkovic, B., & Kaiko, G. E. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222011243 · Cited by 15

MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration

Saenz, C., Nigro, E., Gunalan, V., & Arumugam, M. (2022) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2022.846922 · Cited by 17

Diversity and Metabolic Potential of a PAH-Degrading Bacterial Consortium in Technogenically Contaminated Haplic Chernozem, Southern Russia

Delegan, Y. A., Sushkova, S. N., Minkina, T., Филонов, А. Е., Kocharovskaya, Y., Demin, K. A., Gorovtsov, A. V., Rajput, V. D., Валерьевна, З. И., Grigoryeva, T. V., et al. (2022) · Processes · doi:10.3390/pr10122555 · Cited by 13

High-Throughput Sequencing and Metagenomic Data Analysis

Shuikan, A. M., Alharbi, S. A., Alkhalifah, D. H. M., & Hozzein, W. N. (2019) · IntechOpen eBooks · doi:10.5772/intechopen.89944 · Cited by 13

IDMIL: an alignment-free Interpretable Deep Multiple Instance Learning (MIL) for predicting disease from whole-metagenomic data

Rahman, M. A., & Rangwala, H. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa477 · Cited by 15

Environmental DNA for Biodiversity Monitoring of Coral Reefs

Richards, Z. T., Stat, M., Heydenrych, M. J., & DiBattista, J. D. (2022) · Coral reefs of the world · doi:10.1007/978-3-031-07055-6_13 · Cited by 13

Computational haplotype recovery and long-read validation identifies novel isoforms of industrially relevant enzymes from natural microbial communitiesPreprint

Nicholls, S. M., Aubrey, W., Edwards, A., Grave, K. D., Huws, S., Schietgat, L., Soares, A., Creevey, C. J., & Clare, A. J. (2018) · Research Portal (Queen's University Belfast) · doi:10.1101/223404 · Cited by 7

Unlocking the Hidden Microbiome of Food: The Role of Metagenomics in Analyzing Fresh Produce, Poultry, and Meat

Martínez, T. M. G., Rodríguez, B., Rodríguez-Montaño, M., Alfau, J., Reyes, C., Fernandez, Y., Ramos, R. T. J., Franco, E. F., & Maroto-Martín, L. O. (2025) · Applied Microbiology · doi:10.3390/applmicrobiol5010026 · Cited by 17

Interaction between the breast tumor microenvironment and gut microbiome

Tang, G., Millar, E. K. A., Graham, P., & Beretov, J. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2514136 · Cited by 14

Microbiome signatures and their role in uveitis: Pathogenesis, diagnostics, and therapeutic perspectives

Agrawal, K., Hong, A. S. Y., Cifuentes‐González, C., Kumar, V. S., Rojas-Carabali, W. A., Zhang, S., Wang, Q., de‐la‐Torre, A., Gijs, M., Gill, T., et al. (2025) · Progress in Retinal and Eye Research · doi:10.1016/j.preteyeres.2025.101409 · Cited by 13

Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections

Papamentzelopoulou, M., Vrioni, G., & Pitiriga, V. C. (2025) · Antibiotics · doi:10.3390/antibiotics14121257 · Cited by 13

Next-generation sequencing approaches for soil microbiome research

Reznikova, D. A., Barannikova, M. V., Shnakhova, L. M., Mitkin, N. A., & Vatlin, A. A. (2026) · Frontiers in Soil Science · doi:10.3389/fsoil.2025.1706999 · Cited by 14

Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts

McCallum, G. E., Rossiter, A. E., Quraishi, M. N., Iqbal, T. H., Kuehne, S. A., & van Schaik, W. (2023) · Microbial Genomics · doi:10.1099/mgen.0.001030 · Cited by 12

Metagenome of Gut Microbiota Provides a Novel Insight into the Pathogenicity of Balantioides coli in Weaned Piglets

He, K., Xiong, J., Yang, W., Zhao, L., Wang, T., Qian, W., Hu, S., Wang, Q., Aleem, M. T., Miao, W., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241310791 · Cited by 12

Mercury methylation in boreal aquatic ecosystems under oxic conditions and climate change: a review

Rodríguez, J. (2023) · Frontiers in Marine Science · doi:10.3389/fmars.2023.1198263 · Cited by 12

Microbial composition and function in reclaimed mine sites along a reclamation chronosequence become increasingly similar to undisturbed reference sites

Singh, J. P., Bottos, E. M., Hamme, J. D. V., & Fraser, L. H. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2024.170996 · Cited by 12

Metagenomic analysis of the microbial communities and associated network of nitrogen metabolism genes in the Ryukyu limestone aquifer

Maruyama, R., Yasumoto, K., Mizusawa, N., Iijima, M., Yasumoto-Hirose, M., Iguchi, A., Hermawan, O. R., Hosono, T., Takada, R., Song, K.-H., et al. (2024) · Scientific Reports · doi:10.1038/s41598-024-54614-8 · Cited by 12

A practical introduction to holo-omics

Odriozola, I., Rasmussen, J. A., Gilbert, M. T. P., Limborg, M. T., & Alberdi, A. (2024) · Cell Reports Methods · doi:10.1016/j.crmeth.2024.100820 · Cited by 14

Nanopore R10.4 metagenomic detection of blaCTX-M/blaDHA antimicrobial resistance genes and their genetic environments in stool

Campos-Madueno, E. I., Aldeia, C., & Endimiani, A. (2024) · Nature Communications · doi:10.1038/s41467-024-51929-y · Cited by 13

Rapid identification of antibiotic resistance gene hosts by prescreening ARG-like reads

Su, Z. G., Gu, A. Z., Wen, D., Li, F., Huang, B., Mu, Q., & Chen, L. (2024) · Environmental Science and Ecotechnology · doi:10.1016/j.ese.2024.100502 · Cited by 12

Evaluation of DNA Extraction Methods for Microbial Community Profiling in Deadwood Decomposition

Zhang, Y., Song, Z., & Schilling, J. S. (2024) · MicrobiologyOpen · doi:10.1002/mbo3.70007 · Cited by 12

Maternal Prenatal Stress and the Offspring Gut Microbiome: A Cross‐Species Systematic Review

Graf, M. D., Murgueitio, N., Vogel, S. C., Hicks, L., Carlson, A. L., Propper, C. B., & Kimmel, M. (2024) · Developmental Psychobiology · doi:10.1002/dev.70005 · Cited by 13

Transgenerational effects on the gene transcriptome of chicken liver

Gao, M., Chen, Y., Fan, H., Chen, S., Wang, H., Nie, W., Guo, Y., & Lv, Z. (2024) · Animal Advances · doi:10.48130/animadv-0024-0003 · Cited by 13

Advancing molecular macrobenthos biodiversity monitoring: a comparison between Oxford Nanopore and Illumina based metabarcoding and metagenomics

Doorenspleet, K., Mailli, A. A., van der Hoorn, B., Beentjes, K. K., Backer, A. D., Derycke, S., Murk, A. J., Reiss, H., & Nijland, R. (2025) · PeerJ · doi:10.7717/peerj.19158 · Cited by 12

A P4 medicine perspective of gut microbiota and prediabetes: Systems analysis and personalized intervention

Huang, Q., Fang, Q., & Hu, Z. (2020) · Journal of Translational Internal Medicine · doi:10.2478/jtim-2020-0020 · Cited by 13

Metagenomics-Based Proficiency Test of Smoked Salmon Spiked with a Mock Community

Sala, C., Mordhorst, H., Grützke, J., Brinkmann, A., Petersen, T. N., Poulsen, C. S., Cotter, P. D., Crispie, F., Ellis, R. J., Castellani, G., et al. (2020) · Microorganisms · doi:10.3390/microorganisms8121861 · Cited by 13

Computational analyses of bacterial strains from shotgun reads

Ventolero, M. F. H., Wang, S., Hu, H., & Li, X. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac013 · Cited by 10

Evaluation of Host Depletion and Extraction Methods for Shotgun Metagenomic Analysis of Bovine Vaginal Samples

Ong, C. T., Boe-Hansen, G. B., Ross, E. M., Blackall, P. J., Turni, C., Hayes, B. J., & Tabor, A. E. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.00412-21 · Cited by 13

MegaD: Deep Learning for Rapid and Accurate Disease Status Prediction of Metagenomic Samples

Mreyoud, Y., Song, M., Lim, J., & Ahn, T.-H. (2022) · Life · doi:10.3390/life12050669 · Cited by 13

Exploring the Bacteriome and Resistome of Humans and Food-Producing Animals in Brazil

de Carvalho, F. M., Valiatti, T. B., Santos, F. F., Silveira, A. C. D. O., Guimarães, A. P. C., Gerber, A. L., Souza, C. D. O., Cassu-Corsi, D., Brasiliense, D. M., Castelo‐Branco, D. D. S. C. M., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.00565-22 · Cited by 13

The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data

Hu, X., Haas, J., & Lathe, R. (2022) · BMC Microbiology · doi:10.1186/s12866-022-02671-2 · Cited by 13

Molecular genetic testing methodologies in hematopoietic diseases: current and future methods

Sridhar, K., Singh, A., Butzmann, A., Jangam, D., & Ohgami, R. S. (2019) · International Journal of Laboratory Hematology · doi:10.1111/ijlh.13024 · Cited by 13

Taking a look on fungi in cystic fibrosis: More questions than answers

Martín-Gómez, M. T. (2020) · Revista Iberoamericana de Micología · doi:10.1016/j.riam.2019.10.004 · Cited by 11

Complete Mitochondrial Genomes and Bacterial Metagenomic Data From Two Species of Parasitic Avian Nasal-Mites (Rhinonyssidae: Mesostigmata)

Osuna‐Mascaró, C., Doña, J., Johnson, K. P., Esteban, R., & de Rojas, M. (2020) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2020.00142 · Cited by 12

Feasibility of applying shotgun metagenomic analyses to grapevine leaf, rhizosphere and soil microbiome characterisation

Azevedo-Silva, D., Rasmussen, J. A., Carneiro, M., Gilbert, M. T. P., & Azevedo, H. (2021) · Australian Journal of Grape and Wine Research · doi:10.1111/ajgw.12508 · Cited by 18

Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn GraphsPreprint

Benoit, G., Raguideau, S., James, R. S., Phillippy, A. M., Chikhi, R., & Quince, C. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.07.548136 · Cited by 12

Harnessing intratumoral microbiota: new horizons in immune microenvironment and immunotherapy

Zhang, J., You, Z., Li, X., Hu, J., Li, J., & Jing, Z. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-025-06916-2 · Cited by 14

Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand

Arunrat, N., Mhuantong, W., & Sereenonchai, S. (2025) · Microbial Ecology · doi:10.1007/s00248-025-02598-x · Cited by 11

Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health

da Silva, A. C., Lapkin, J., Yin, Q., Muller, E., & Almeida, A. (2026) · Cell Host & Microbe · doi:10.1016/j.chom.2026.01.013 · Cited by 17

Exploring Diversity of Bacterial Endophyte Communities Using Advanced Sequencing Technology

Tamošiūnė, I., Andriūnaitė, E., Stanys, V., & Baniulis, D. (2019) · Springer eBooks · doi:10.1007/978-981-13-8495-0_20 · Cited by 11

Taxonomy, Sequence Variance and Functional Profiling of the Microbial Community of Long-Ripened Cheddar Cheese Using Shotgun Metagenomics

Mohamed, H. M., Barzideh, Z., Siddiqi, M., & LaPointe, G. (2023) · Microorganisms · doi:10.3390/microorganisms11082052 · Cited by 13

Exploring PETase-like enzyme from shotgun metagenome and co-expressing Colicin E7 in Escherichia coli for effective PET degradation

Effendi, S. S. W., Hu, R.-E., Hsiang, C., Ting, W., Huang, C., & Ng, I. (2024) · Process Biochemistry · doi:10.1016/j.procbio.2024.03.001 · Cited by 11

Cascade effects of forest thinning on microbial composition and function of various tree species and multiple decomposition time series: Insights from deadwood decomposition in tropical forests

Anderson, D. W., & Wu, Y.-T. (2024) · Forest Ecology and Management · doi:10.1016/j.foreco.2024.121817 · Cited by 11

Atherosclerosis, gut microbiome, and exercise in a meta-omics perspective: a literature review

Tang, H., Huang, Y., Yuan, D., & Liu, J. (2024) · PeerJ · doi:10.7717/peerj.17185 · Cited by 14

Limited variation in microbial communities across populations of Macrosteles leafhoppers (Hemiptera: Cicadellidae)

Mulio, S. Å., Zwolińska, A., Klejdysz, T., Prus-Frankowska, M., Michalik, A., Kolasa, M. R., & Łukasik, P. (2024) · Environmental Microbiology Reports · doi:10.1111/1758-2229.13279 · Cited by 11

Benchmarking short-, long- and hybrid-read assemblers for metagenome sequencing of complex microbial communities

Goussarov, G., Mysara, M., Cleenwerck, I., Claesen, J., Leys, N., Vandamme, P. A. R., & Houdt, R. V. (2024) · Microbiology · doi:10.1099/mic.0.001469 · Cited by 11

PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification

Ghezzi, H., Fan, Y. M., Ng, K. M., Burckhardt, J. C., Pepin, D. M., Lin, X., Ziels, R. M., & Tropini, C. (2024) · mSphere · doi:10.1128/msphere.00360-24 · Cited by 11

Analytical aspects of metagenomic and volatilomic approaches that advance table olive integrity research

Langari, D., & Mantzouridou, F. T. (2024) · Exploration of Foods and Foodomics · doi:10.37349/eff.2024.00052 · Cited by 11

A Proteogenomic Approach to Unveiling the Complex Biology of the Microbiome

Pavelescu, L. A., Profir, M., Enache, R. M., Roşu, O. A., Creţoiu, S. M., & Gașpar, B. S. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms251910467 · Cited by 10

NovoLign: metaproteomics by sequence alignment

Kleikamp, H. B. C., van der Zwaan, R., van Valderen, R. D., van Ede, J. M., Pronk, M., Schaasberg, P., Allaart, M. T., van Loosdrecht, M. C. M., & Pabst, M. (2024) · ISME Communications · doi:10.1093/ismeco/ycae121 · Cited by 9

Therapeutic Modulation of the Microbiome in Oncology: Current Trends and Future Directions

Saraswat, I., & Goel, A. (2024) · Current Pharmaceutical Biotechnology · doi:10.2174/0113892010353600241109132441 · Cited by 12

Land use patterns change N and P cycling bacterial diversity in an acidic karst soil

Li, Z., Qin, W., You, Y., Chen, J., Zhao, X., Dong, R., Gu, X., Cui, S., Chen, C., Stirling, E., et al. (2024) · Agriculture Ecosystems & Environment · doi:10.1016/j.agee.2024.109389 · Cited by 11

High throughput single cell metagenomic sequencing with semi-permeable capsules: unraveling microbial diversity at the single-cell level in sewage and fecal microbiomes

Ling, M., Szarvas, J., Kurmauskaitė, V., Kiseliovas, V., Žilionis, R., Avot, B. J. P., Munk, P., & Aarestrup, F. M. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1516656 · Cited by 14

De novo discovery of conserved gene clusters in microbial genomes with Spacedust

Zhang, R.-S., Mirdita, M., & Soeding, J. (2025) · bioRxiv · doi:10.1038/s41592-025-02816-x · Cited by 10

Systematic and synthetic approaches to rewire regulatory networks

Park, J., & Wang, H. H. (2018) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2017.12.009 · Cited by 11

The contribution of respiratory microbiome analysis to a treatable traits model of care

Taylor, S., O’Farrell, H. E., Simpson, J. L., Yang, I. A., & Rogers, G. B. (2018) · Respirology · doi:10.1111/resp.13411 · Cited by 11

A Battery of Soil and Plant Indicators of NBS Environmental Performance in the Context of Global Change

Andrés, P., Doblas‐Miranda, E., Mattana, S., Molowny‐Horas, R., Vayreda, J., Guardiola, M., Pino, J., & Gordillo, J. (2021) · Sustainability · doi:10.3390/su13041913 · Cited by 11

Quantifying and Cataloguing Unknown Sequences within Human Microbiomes

Modha, S., Robertson, D. L., Hughes, J., & Orton, R. J. (2022) · mSystems · doi:10.1128/msystems.01468-21 · Cited by 11

Complex impacts of hydraulic fracturing return fluids on soil microbial community respiration, structure and functional potentials

Zhong, C., Nesbø, C. L., von Gunten, K., Zhang, Y., Shao, X., Jin, R., Konhauser, K. O., Goss, G. G., Martin, J. W., He, Y., et al. (2022) · Environmental Microbiology · doi:10.1111/1462-2920.16009 · Cited by 11

State-Space-Based Framework for Predicting Microbial Interaction Variability in Wastewater Treatment Plants

Yu, Z., Huang, Y. L., Gan, Z., Meng, Y., & Meng, F. (2022) · Environmental Science & Technology · doi:10.1021/acs.est.2c02844 · Cited by 11

How a holobiome perspective could promote intensification, biosecurity and eco-efficiency in the shrimp aquaculture industry

Gutiérrez-Pérez, E. D., Vázquez‐Juárez, R., Magallón‐Barajas, F. J., Martínez, M. Á., Escobar‐Zepeda, A., & Magallón‐Servín, P. (2022) · Frontiers in Marine Science · doi:10.3389/fmars.2022.975042 · Cited by 12

Laser printing: trends and perspectives

Chichkov, B. (2022) · Applied Physics A · doi:10.1007/s00339-022-06158-9 · Cited by 10

Pathways for Understanding Blue Carbon Microbiomes with Amplicon Sequencing

Hurtado-McCormick, V., Trevathan‐Tackett, S. M., Bowen, J. L., Connolly, R. M., Duarte, C. M., & Macreadie, P. I. (2022) · Microorganisms · doi:10.3390/microorganisms10112121 · Cited by 11

Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge

Abdulkadir, N., Saraiva, J., Schattenberg, F., Toscan, R. B., Corrêa, F. B., Harms, H., Müller, S., & da Rocha, U. N. (2023) · Microorganisms · doi:10.3390/microorganisms11010175 · Cited by 13

Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis

Panda, A., & Tuller, T. (2023) · npj Biofilms and Microbiomes · doi:10.1038/s41522-023-00372-w · Cited by 11

Coriolis: enabling metagenomic classification on lightweight mobile devices

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Theoretical and Simulation-Based Investigation of the Relationship between Sequencing Effort, Microbial Community Richness, and Diversity in Binning Metagenome-Assembled Genomes

Royalty, T. M., & Steen, A. D. (2019) · mSystems · doi:10.1128/msystems.00384-19 · Cited by 13

Molecular sequencing technologies in the diagnosis and management of prosthetic joint infections

Gamie, Z., Karthikappallil, D., Gamie, E., Stamiris, S., Kenanidis, E. I., & Tsiridis, E. E. (2021) · Expert Review of Molecular Diagnostics · doi:10.1080/14737159.2021.1894929 · Cited by 11

Functional diversity of bacterial communities in the rhizosphere of maize grown on a soil under organic and inorganic fertilization

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Influence of site and smoking on malignant transformation in the oral cavity: Is the microbiome the missing link?

Galvin, S., Moran, G. P., & Healy, C. M. (2023) · Frontiers in Oral Health · doi:10.3389/froh.2023.1166037 · Cited by 12

Applications and Challenges of Real-time Mobile DNA Analysis

Ko, S. Y., Sassoubre, L. M., & Żola, J. (2018) · IEEE Workshop on Mobile Computing Systems and Applications (WMCSA) · doi:10.1145/3177102.3177114 · Cited by 11

Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virusPreprint

Chen, N. F. G., Chaguza, C., Gagne, L. A., Doucette, M., Smole, S., Buzby, E., Hall, J., Ash, S., Harrington, R., Cofsky, S., et al. (2022) · medRxiv · doi:10.1101/2022.10.14.22280783 · Cited by 11

Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control

Gomes, E., Mesquita, T. G., Serra, P., Araújo, D., Almeida, C., Machado, A., Oliveira, R., & Castro, J. (2026) · Antibiotics · doi:10.3390/antibiotics15030262 · Cited by 10

Exploring lactic acid bacteria from fresh fruits, vegetables, and edible flowers: from biodiversity valorisation to food applications

Presutto, E., Capozzi, V., Chiara, M., Drider, D., Spano, G., & Fragasso, M. (2026) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-026-04872-7 · Cited by 10

Metagenomic insights into novel microbial lineages with distinct ecological functions in the Arctic glacier foreland ecosystems

Venkatachalam, S., Vipindas, P. V., Jabir, T., Jain, A., & Krishnan, K. P. (2023) · Environmental Research · doi:10.1016/j.envres.2023.117726 · Cited by 12

Metagenomic binning analyses of swine manure composting reveal mechanism of nitrogen cycle amendment using kaolin

Li, H., Zhao, Z., Shi, M., Luo, B., Wang, G., Wang, X., Gu, J., Song, Z., Sun, Y., Li, Z., et al. (2023) · Bioresource Technology · doi:10.1016/j.biortech.2023.130156 · Cited by 10

Antimicrobial resistance landscape in a metropolitan city context using open drain wastewater-based metagenomic analysis

Madhukar, M. K., Singh, N., Iyer, V. R., Sowpati, D. T., Tallapaka, K. B., Mishra, R. K., & Moharir, S. C. (2024) · Environmental Research · doi:10.1016/j.envres.2024.118556 · Cited by 14

Insights into the seasonal changes in the taxonomic and functional diversity of bacteria in the eastern Arabian Sea: Shotgun metagenomics approach

Parab, A. S., & Manohar, C. S. (2024) · Marine Environmental Research · doi:10.1016/j.marenvres.2024.106616 · Cited by 10

Effects of iron-carbon on nitrogen metabolism of floc and aerobic granular sludge

Pan, K., Zhou, Q., Guo, T., Chen, Y., Li, F., Ding, M., Ma, X., & Li, J. (2024) · Bioresource Technology · doi:10.1016/j.biortech.2024.131376 · Cited by 10

Genomic surveillance for tackling emerging plant diseases, with special reference to wheat blast

Islam, T. (2024) · CABI Reviews · doi:10.1079/cabireviews.2024.0050 · Cited by 10

Microbial communities indicate fine differences in pollution levels by emerging contaminants

Griffero, L., Pereira-Flores, E., Lescano, C., Rodríguez–Gallego, L., Parada, A. P., & Alonso, C. (2024) · Ecological Indicators · doi:10.1016/j.ecolind.2024.112875 · Cited by 10

Metagenomic insights of microbial functions under conventional and conservation agriculture

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An Introduction to Whole-Metagenome Shotgun Sequencing Studies

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An introduction to the analysis of shotgun metagenomic data

Sharpton, T. J. (2014) · Frontiers in Plant Science · doi:10.3389/fpls.2014.00209 · Cited by 708

Building on basic metagenomics with complementary technologies

Warnecke, F., & Hugenholtz, P. (2007) · Genome biology · doi:10.1186/gb-2007-8-12-231 · Cited by 62

Benchmarking shotgun metagenomics

(2026) · Nature Microbiology · doi:10.1038/s41564-026-02344-0

Metagenome Analysis

Meyerdierks, A., & Glöckner, F. O. (2010) · Springer eBooks · doi:10.1007/978-90-481-8639-6_2 · Cited by 5