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QIIME allows analysis of high-throughput community sequencing data

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Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes

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Viruses in the sea

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Lysogenic Conversion by a Filamentous Phage Encoding Cholera Toxin

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Comparative Genomic Analysis Reveals Intestinal Habitat Adaptation of Ligilactobacillus equi Rich in Prophage and Degrading Cellulase

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Microbes and the Malnourished Child

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Temperate phages as self-replicating weapons in bacterial competitionPreprint

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Viruses Are Part of the Holobiont’s Fitness and Evolution

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A review on re-emerging bacteriophage therapy in the era of XDR

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Metagenomics and bioinformatics in microbial ecology: current status and beyond

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Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners

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Eukaryotic composition across seasons and social groups in the gut microbiota of wild baboons

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Gut Virome: What's the Role in Irritable Bowel Syndrome?

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Animal-associated jumbo phages as widespread and active modulators of gut microbiome ecology and metabolism

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Metagenomics and Single-Cell Omics Data Analysis for Human Microbiome Research

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Le système CRISPR-Cas

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Intestinal Microbiome in Health and Disease: Introduction

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Present scenario of antibiotic use in veterinary practice: importance of wastewater microbiology

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Nutrition and microbiota

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Bacteriophage-Driven Emergence of Novel Pathogens

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Metagenomics for Gut Microbes

Kumavath, R. N. (2018) · InTech eBooks · doi:10.5772/intechopen.68370 · Cited by 4

Statistical Methods for Human Microbiome Data Analysis

Chen, J. (2012) · ScholarlyCommons (University of Pennsylvania) · Cited by 4

Viral Sequence Identification in Metagenomes using Natural Language Processing TechniquesPreprint

Abdelkareem, A. O., Khalil, M. I., Elbehery, A. H. A., & Abbas, H. M. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.01.10.892158 · Cited by 4

A previously undescribed highly prevalent phage identified in a Danish enteric virome cataloguePreprint

Espen, L. V., Bak, E. G., Beller, L., Close, L., Deboutte, W., Juel, H. B., Nielsen, T., Sinar, D., Coninck, L. D., Frithioff‐Bøjsøe, C., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-273865/v1 · Cited by 4

Insight into the gut virome in patients with multiple sclerosisPreprint

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Fungal‐Bacterial Dysbiosis in IBD: Microbial Biomarkers of Disease Activity

Arribas‐Rodríguez, E., García‐Pizarro, M., Prado, Á. D., Santiago‐Carretero, M., Hernández, M., Jiménez, B. V., García‐Alonso, J., Barrio, J., Bouza, J. M. E., Arranz, E. M., et al. (2025) · MicrobiologyOpen · doi:10.1002/mbo3.70088 · Cited by 3

Extensive cultivation of human gut phages revealing undescribed Bacteroidaceae phages

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Effect of supplementation with synbiotics in metabolic syndrome: mechanisms and clinical implications

Abenavoli, L., YOSYPENKO, K., YURCHYSHENA, Y., Savytska, M., Lazarieva, O., Shvets, Y. V., Scarlata, G. G. M., Lynchak, O. V., & Falalyeyeva, T. M. (2026) · Minerva Gastroenterology · doi:10.23736/s2724-5985.25.04054-9 · Cited by 3

The Players Within the Intestinal Microbiome (Bacteria, Fungi, Parasites, and Viruses)

Liu, J., Fogarty, M. P., Lee, S. C., Dougherty, M., Ngobeni, R., Ge, Y., & Carroll, I. M. (2023) · Springer eBooks · doi:10.1007/978-3-031-46712-7_2 · Cited by 4

Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage

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Lyfe: learning to learn better

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Bacteriophage Diversity in Different Habitats and Their Role in Pathogen Control

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The role of the intestinal microbiota in the pathogenesis and treatment of inflammatory bowel diseases

Miyoshi, J., Qiao, Y., & Chang, E. B. (2017) · Seminars in Colon and Rectal Surgery · doi:10.1053/j.scrs.2017.09.005 · Cited by 3

ENVirT: inference of ecological characteristics of viruses from metagenomic data

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Reduced metagenomic sequencing (RMS) approach to determine the gut-associated phageome in mother-child

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Development and treatment of colorectal cancer: Insights from multi‐kingdom microbiota

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Metagenomic Analysis of the Tonsil Virome Highlights Its Diagnostic Potential for Rheumatoid Arthritis

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Unveiling the gut virome in human health and diseases

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Humankind versus Virus: Are we winning the battle but losing the war?

Gaddi, A. V., Capello, F., Andrisano, V., Aspriello, S. D., Bertolotti, M., Bonsanto, F., Britti, D., Castagnetti, A., Casu, G., Cicero, A. F. G., et al. (2020) · Mediterranean Journal of Nutrition and Metabolism · doi:10.3233/mnm-200415 · Cited by 3

Phylogenomics of the Liquorilactobacillus Genus

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The Microbiome–Gut–Brain Axis and the Consequences of Infection and Dysbiosis

Bienenstock, J., Kunze, W., & Forsythe, P. (2016) · The American Journal of Gastroenterology Supplements · doi:10.1038/ajgsup.2016.12 · Cited by 4

The Mucosal Microbiome

Jacobs, J. P., & Braun, J. G. (2015) · Elsevier eBooks · doi:10.1016/b978-0-12-415847-4.00005-7 · Cited by 4

Metagenomic Approaches for Investigating the Role of the Microbiome in Gut Health and Inflammatory Diseases

Carvalho, R. D. D. O., Carmo, F. L. R. D., da Silva, S. H., Cordeiro, B. F., Vaz, A. B. M., Gimenez, E. G. T., Goulart, L., Goés‐Neto, A., Loir, Y. L., Jan, G., et al. (2018) · InTech eBooks · doi:10.5772/intechopen.72031 · Cited by 4

Breastfeeding influences the neonatal virome

Bushman, F. D., & Liang, G. (2021) · Nature · doi:10.1038/d41586-021-01112-w · Cited by 3

Reads Binning Improves the Assembly of Viral Genome Sequences From Metagenomic Samples

Song, K. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.664560 · Cited by 3

Virome of the Healthy Human Eye

Shivaji, S. (2022) · Springer eBooks · doi:10.1007/978-981-19-1754-7_8 · Cited by 3

Phage Therapy: Genomics to Applications and Future Prospects

Jaiswal, A. (2022) · Springer eBooks · doi:10.1007/978-981-19-1854-4_5 · Cited by 3

Tracking the Rules of Transmission and Introgression with Networks

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Practical Applications of Bacteriophage Therapy: Biofilms to Bedside

Jacobs, A. C., Dugan, J. W., Duplessis, C. A., Rouse, M. D., Deshotel, M., Simons, M. P., Biswas, B., Nikolich, M. P., Stockelman, M. G., Tyner, S. D., et al. (2019) · Springer eBooks · doi:10.1007/978-981-13-9871-1_21 · Cited by 3

crAssphage abundance and genomic selective pressure correlate with altered bacterial abundance in the fecal microbiota of South African mother-infant dyadsPreprint

Brown, B. P., Wendoh, J. M., Chopera, D., Havyarimana, E., Jaumdally, S. Z., Nyangahu, D. D., Gray, C. M., Martin, D. P., Varsani, A., & Jaspan, H. B. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/582015 · Cited by 3

Prophage regulation of Shewanella fidelis 3313 motility and biofilm formation with implications for gut colonization dynamics in Ciona robustaPreprint

Natarajan, O., Gibboney, S. L., Young, M. N., Lim, S. J., Nguyen, F., Pluta, N., Atkinson, C. G. F., Liberti, A., Kees, E. D., Leigh, B. A., et al. (2025) · eLife · doi:10.7554/elife.103107 · Cited by 3

A Genome of Temperate Enterococcus Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences

Pchelin, I. M., Tkachev, P. V., Валерьевич, А. Д., Gorshkov, A. N., Drachko, D. O., Zlatogursky, V. V., Dmitriev, A. V., & Goncharov, A. Е. (2023) · Viruses · doi:10.3390/v15010216 · Cited by 2

Human Gut Bacteriophageome: Insights Into Drug Resistance Mechanisms in Tuberculosis

Jafari, E., Azizian, R., Tabasi, M., Banakar, M., & Lankarani, K. B. (2025) · Interdisciplinary Perspectives on Infectious Diseases · doi:10.1155/ipid/8811027 · Cited by 3

Phage Probiotics

Wong, S. L. (2016) · SpringerBriefs in biochemistry and molecular biology · doi:10.1007/978-3-319-45791-8_5 · Cited by 2

Bacterial Contamination of the Surgical Site at the Time of Elective Caesarean Section in Belgian Blue Cows—Part 2: Identified by 16Sr DNA Amplicon Sequencing

Djebala, S., Coria, E., Munaut, F., Gille, L., Eppe, J., Moula, N., Taminiau, B., Daube, G., & Bossaert, P. (2023) · Veterinary Sciences · doi:10.3390/vetsci10020094 · Cited by 2

Moderate bacteriophages: the secret weapon of bacteria or their Achilles heel?

Евдокимова, Н. В., & Черненькая, Т. В. (2023) · Zhurnal «Patologicheskaia fiziologiia i eksperimental`naia terapiia» · doi:10.25557/0031-2991.2023.01.117-123 · Cited by 2

Interactions between gut microorganisms and the role of their metabolites in host health

Zhao, F., Zhao, J., Ma, R., & Sun, Z. (2024) · Chinese Science Bulletin (Chinese Version) · doi:10.1360/tb-2024-0709 · Cited by 2

Virome and Microbiome Interaction and Their Implication in the Human Gut Health

AboNahas, H. H., El‐Maradny, Y. A., Gezaf, S. A., Nouh, F. A. A., AboNahas, Y. H., Landa‐Acuña, D., Gil-Polo, A., Saied, E. M., & Abdel-Azeem, A. M. (2022) · Springer eBooks · doi:10.1007/978-981-16-1626-6_4 · Cited by 2

Prophage regulation of Shewanella fidelis 3313 motility and biofilm formation with implications for gut colonization dynamics in Ciona robusta

Natarajan, O., Gibboney, S. L., Young, M. N., Lim, S. J., Nguyen, F., Pluta, N., Atkinson, C. G. F., Liberti, A., Kees, E. D., Leigh, B. A., et al. (2025) · eLife · doi:10.7554/elife.103107.3 · Cited by 2

Prevalence and Characterization of CRISPR Locus 2.1 Spacers in Escherichia coli Isolates Obtained from Feces of Animals and Humans

Shin, H., Kim, Y.-J., Unno, T., & Hur, H. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.04934-22 · Cited by 2

Exploring the Potential of Bacteriophages on Earth and Beyond

Mohanty, A., Shaw, B., Pradeep, N., Singh, N. K., & Venkateswaran, K. (2023) · Journal of the Indian Institute of Science · doi:10.1007/s41745-023-00361-0 · Cited by 2

The human microbiome and modern approaches to its preservation (analytical review)

Bobyr, V. V., Nazarchuk, O. A., Paliy, V. G., Kryzhanovska, A. V., Bobyr, N. A., Власенко, І. Г., & Zhemera, N. A. (2023) · Reports of Vinnytsia National Medical University · doi:10.31393/reports-vnmedical-2023-27(3)-23 · Cited by 2

Intestivirid Acquisition Increases Across Infancy in a Wild Primate Population

Schneider‐Crease, I. A., Moya, I. L., Chiou, K. L., Baniel, A., Haile, A. A., Kebede, F., Abebe, B., Lu, A., Bergman, T. J., Snyder‐Mackler, N., et al. (2025) · Molecular Ecology · doi:10.1111/mec.17801 · Cited by 2

How the Other Half Lives: CRISPR-Cas’s Influence on Bacteriophages

Bonomo, M. E., & Deem, M. W. (2017) · Springer eBooks · doi:10.1007/978-3-319-61569-1_4 · Cited by 2

Targeted Delivery of Bacteriophages to the Gastrointestinal Tract and Their Controlled Release

Malik, D. J. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-815249-2.00019-1 · Cited by 2

Understanding the Link Between the Urinary Microbiome and Urinary Lithiasis Disease

Suryavanshi, M. V., Poddar, M., & Rekha, P. D. (2021) · Springer eBooks · doi:10.1007/978-981-16-5617-0_12 · Cited by 2

Gut virome profile in healthy Saudi children

Mouzan, M. I. E., Assiri, A. A., Sarkhy, A. A. A., & Alasmi, M. (2023) · Saudi Journal of Gastroenterology · doi:10.4103/sjg.sjg_444_22 · Cited by 2

Human Microbiomes and Disease for the Biomedical Data Scientist

Golob, J. L. (2023) · Annual Review of Biomedical Data Science · doi:10.1146/annurev-biodatasci-020722-043017 · Cited by 2

Detection of Bacteriophages: Sequence-Based Systems

Owen, S. V., Perez-Sepulveda, B. M., & Adriaenssens, E. M. (2021) · Springer eBooks · doi:10.1007/978-3-319-41986-2_19 · Cited by 2

Human Virome

Yankovsky, D. S., Дымент, Г. С., Berezhniy, V. V., Kitam, V. O., & Химич, Н. В. (2019) · SOVREMENNAYA PEDIATRIYA · doi:10.15574/sp.2019.97.49 · Cited by 2

A network-based integrated framework for predicting virus-host interactionsPreprint

Wang, W., Ren, J., Tang, K., Dart, E., Ignacio-Espinoza, J. C., Fuhrman, J. A., Braun, J., Sun, F., & Ahlgren, N. A. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/505768 · Cited by 2

Paving the Way to Unveil the Diversity and Evolution of Phage Genomes

Reyes, A., & Vives, M. J. (2020) · Viruses · doi:10.3390/v12090905 · Cited by 2

Enteric phageome alternations in Type 2 diabetes diseasePreprint

Chen, Q., Ma, X., Li, C., Shen, Y., Zhu, W., Zhang, Y., Guo, X., Zhou, J. W., & Liu, C. (2019) · doi:10.21203/rs.2.17361/v1 · Cited by 2

CRISPR‐Cas Systems: Core Features and Common Mechanisms

Barrangou, R., Marraffini, L. A., & Sontheimer, E. J. (2022) · Wiley eBooks · doi:10.1002/9781683673798.ch1 · Cited by 2

Microbial network assembly in bat flies with differing host specificity from North Africa

Corduneanu, A., Bendjeddou, M. L., Sándor, A. D., Mihalca, A. D., Hornok, S., Péter, Á., Khelfaoui, F., Aželytė, J., Obregón, D., Mateos‐Hernández, L., et al. (2025) · International Microbiology · doi:10.1007/s10123-025-00720-0 · Cited by 1

Anticancer Effect of Icaritin on Prostate Cancer via Regulating Abundance of Akkermansiaceae and Vitamin K2 in Intestinal Fecal

Hu, J., Liang, Y., Wu, X., Huang, J., & Jiang, H. (2026) · Cancers · doi:10.3390/cancers18050804 · Cited by 1

Bacteriophage-mediated gut microbiota regulation: a bibliometric landscape analysis (2005–2024)

Yin, J., Wang, H., Cui, Y., Zhou, X., Zhang, S., & Yin, H. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1768117 · Cited by 1

Temporal dynamics of gut microbiota and virome in preterm infants: insights from longitudinal metagenomic analysis

Huang, J., Yan, X., Su, Q., Tu, H., Yu, Z., Dong, L., & Wu, B. (2026) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2026.1598786 · Cited by 1

Oxidative stress constrains evolution of bacteriophage host-range diversity

Meynard-Doumenc, C., Lamy-Besnier, Q., Brot, L., Messika, M., Wolfromm, A., Grill, J.-P., & Sordi, L. D. (2026) · The ISME Journal · doi:10.1093/ismejo/wrag090 · Cited by 1

Microbial shifts in early life: the pediatric gut microbiome and its role in health and disease

Waghmode, S., Viswanathan, R., Koligudde, V., Umare, P., & Lavania, M. (2026) · Gut Microbes · doi:10.1080/19490976.2026.2681763 · Cited by 1

The gut-liver-immune axis: structural basis, cellular architecture, molecular mediators, and disease-specific manifestations

Yoon, S. J., Eom, J. A., & Suk, K. T. (2026) · Frontiers in Immunology · doi:10.3389/fimmu.2026.1864805 · Cited by 1

Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities

Meijer, J., Skiadas, P., Rainey, P. B., Hogeweg, P., & Dutilh, B. E. (2026) · Science Advances · doi:10.1126/sciadv.aeb8246 · Cited by 1

Next-Generation Sequencing in Viral Diagnosis

Jancy, M. S., Nehru, M., Arunan, S., & Prabhu, V. (2025) · Methods in molecular biology · doi:10.1007/978-1-0716-4546-8_13 · Cited by 1

Alternating High‐Fat and Polysaccharide Diets Modulates Gut Phage‐Bacterial Interplay

Zhao, F., Zhang, R., Wei, R., Fan, H., Hu, Y., Shi, W., & Wang, J. (2026) · Advanced Science · doi:10.1002/advs.202516916 · Cited by 1

The Human Virome in Infectious Diseases: Insights from Chronic and Acute Infections Across Body Sites—A Narrative Review

Feletti, R., Mori, A., Zaffagnini, A., Castilletti, C., & Pomari, E. (2026) · Microorganisms · doi:10.3390/microorganisms14050969 · Cited by 2

Animal gut microbes and microbiomes in the 21st century and beyond

Zhang, Z., Jiang, F., Li, Z. Y., Lin, L., Qi, B., Han, D., Ran, C., Mao, S., Wang, J., Zhou, Z., et al. (2026) · Science China Life Sciences · doi:10.1007/s11427-026-3312-5 · Cited by 1

Diet, mycobiome and virome: from mucosal immunity to gut–brain axis regulation

Medoro, A., Castagnetti, A., Intrieri, M., Scapagnini, G., & Davinelli, S. (2026) · Frontiers in Nutrition · doi:10.3389/fnut.2026.1873950 · Cited by 2

A Metaviromic Analysis of Viral Communities in the Feces of Unexplained Acute Gastroenteritis

Baek, I. H., Kim, S. A., Kim, J., Park, H. K., & Kim, W. (2013) · Journal of Bacteriology and Virology · doi:10.4167/jbv.2013.43.4.290 · Cited by 1

Fame and Future of Fecal Transplantations: Developing Next-Generation Therapies with Synthetic Microbiomes

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“Aging Gut Microbiota and Colorectal Cancer Pathways Correlations”

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