Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome

Fast and accurate short read alignment with Burrows-Wheeler transform

Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607

Gene Ontology: tool for the unification of biology

Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) · Nature Genetics · doi:10.1038/75556 · Cited by 43,206

KEGG: Kyoto Encyclopedia of Genes and Genomes

Kanehisa, M. (2000) · Nucleic Acids Research · doi:10.1093/nar/28.1.27 · Cited by 37,077

QIIME allows analysis of high-throughput community sequencing data

Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

Quast, C., Pruesse, E., Yilmaz, P., Gerken, J., Schweer, T., Yarza, P., Peplies, J., & Glöckner, F. O. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1219 · Cited by 33,055

KEGG: Kyoto Encyclopedia of Genes and Genomes

Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., & Kanehisa, M. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.1.29 · Cited by 31,232

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.

Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 21,481

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Grabherr, M. G., Haas, B. J., Yassour, M., Levin, J. Z., Thompson, D. A., Amit, I., Adiconis, X., Fan, L., Raychowdhury, R., Zeng, Q., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1883 · Cited by 21,201

Search and clustering orders of magnitude faster than BLAST

Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098

Edwardsiella ictaluri Almost Completely Occupies the Gut Microbiota of Fish Suffering from Enteric Septicemia of Catfish (Esc)

Yang, J., Lin, Y., Wei, Z., Wu, Z., Zhang, Q., Hao, J., Wang, S., & Li, A. (2023) · Fishes · doi:10.3390/fishes8010030 · Cited by 26

Acid Mine Drainage as Habitats for Distinct Microbiomes: Current Knowledge in the Era of Molecular and Omic Technologies

Lukhele, T., Selvarajan, R., Nyoni, H. H., Mamba, B. B., & Msagati, T. A. M. (2019) · Current Microbiology · doi:10.1007/s00284-019-01771-z · Cited by 24

Recent Advances and Developments in Bacterial Endophyte Identification and Application: A 20-Year Landscape Review

Mametja, N. M., Ramadwa, T. E., Managa, M., & Masebe, T. M. (2025) · Plants · doi:10.3390/plants14162506 · Cited by 23

Comparative Analysis of the Symbiotic Microbiota in the Chinese Mitten Crab (Eriocheir sinensis): Microbial Structure, Co-Occurrence Patterns, and Predictive Functions

Yang, J., Zhang, Q., Zhang, T., Wang, S., Hao, J., Wu, Z., & Li, A. (2023) · Microorganisms · doi:10.3390/microorganisms11030544 · Cited by 22

Adopting omics-based approaches to facilitate the establishment of microbial consortia to generate reproducible fermented foods with desirable properties

Zhang, E., Claesson, M. J., & Cotter, P. D. (2026) · npj Science of Food · doi:10.1038/s41538-026-00740-8 · Cited by 23

A systematic sequencing-based approach for microbial contaminant detection and functional inference

Park, S., Onizuka, S., Seki, M., Suzuki, Y., Iwata, T., & Nakai, K. (2019) · BMC Biology · doi:10.1186/s12915-019-0690-0 · Cited by 22

Synergies of Systems Biology and Synthetic Biology in Human Microbiome Studies

Ezzamouri, B., Shoaie, S., & Ledesma‐Amaro, R. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.681982 · Cited by 24

Impact of the Microbiota on Viral Infections

Campbell, D. E., Li, Y., Ingle, H., & Baldridge, M. T. (2023) · Annual Review of Virology · doi:10.1146/annurev-virology-111821-115754 · Cited by 22

Biofilm consumption shapes the intestinal microbiota of shrimp (Penaeus vannamei )

Garibay-Valdéz, E., Martínez‐Córdova, L. R., Vargas‐Albores, F., Gollas‐Galván, T., Lago‐Lestón, A., Calderón, K., & Martínez‐Porchas, M. (2018) · Aquaculture Nutrition · doi:10.1111/anu.12868 · Cited by 22

Metagenomic Studies in Inflammatory Skin Diseases

Godlewska, U., Brzoza, P., Kwiecień, K., Kwitniewski, M., & Cichy, J. (2020) · Current Microbiology · doi:10.1007/s00284-020-02163-4 · Cited by 24

Influence mechanisms underlying the degradation of petroleum hydrocarbons in response to various nitrogen dosages supplementation through metatranscriptomics analysis

Ou, Y., Wu, M., Yu, Y., Liu, Z., Kang, H., Hu, M., Zhang, C., & Chen, X. (2025) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2024.137074 · Cited by 21

Tree Nut Consumption and Adipose Tissue Mass: Mechanisms of Action

Tindall, A. M., Petersen, K. S., Lamendella, R., Shearer, G. C., Murray‐Kolb, L. E., Proctor, D. N., & Kris‐Etherton, P. M. (2018) · Current Developments in Nutrition · doi:10.1093/cdn/nzy069 · Cited by 21

White spot syndrome virus impact on the expression of immune genes and gut microbiome of black tiger shrimp Penaeus monodon

Jatuyosporn, T., Laohawutthichai, P., Ochoa‐Romo, J. P., Gallardo-Becerra, L., Sánchez, F., Tassanakajon, A., Ochoa‐Leyva, A., & Krusong, K. (2023) · Scientific Reports · doi:10.1038/s41598-023-27906-8 · Cited by 20

Microbiome in Eosinophilic Esophagitis—Metagenomic, Metatranscriptomic, and Metabolomic Changes: A Systematic Review

Busing, J. D., Buendia, M. A., Choksi, Y. A., Hiremath, G. S., & Das, S. R. (2021) · Frontiers in Physiology · doi:10.3389/fphys.2021.731034 · Cited by 20

Microbial ecosystem disruption under persistent organic pollutant stress: Consequences for soil biogeochemistry and environmental sustainability – A review

Ullah, S., Hussain, B., Iqbal, N., Raza, M. M., Salam, M., Vasudhevan, P., Sani, S. G. A. S., & Pu, S. (2025) · Environmental Chemistry and Ecotoxicology · doi:10.1016/j.enceco.2025.10.017 · Cited by 23

Application of viromics: a new approach to the understanding of viral infections in humans

Ramamurthy, M., Sankar, S., Kannangai, R., Nandagopal, B., & Sridharan, G. (2017) · VirusDisease · doi:10.1007/s13337-017-0415-3 · Cited by 19

Overview of Trends in the Application of Metagenomic Techniques in the Analysis of Human Enteric Viral Diversity in Africa’s Environmental Regimes

Osunmakinde, C. O., Selvarajan, R., Sibanda, T., Mamba, B. B., & Msagati, T. A. M. (2018) · Viruses · doi:10.3390/v10080429 · Cited by 20

Combining metagenomics and metatranscriptomics to study human, animal and environmental resistomes

Wang, Y., Hu, Y., & Gao, G. F. (2020) · Medicine in Microecology · doi:10.1016/j.medmic.2020.100014 · Cited by 20

RNA beyond humans

Chauhan, N. S., Monika, Kumar, T., Sharma, P., & Goyal, K. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-817193-6.00005-4 · Cited by 19

A review of bacteriophage and their application in domestic animals in a post-antibiotic era

Guo, X., Luo, G., Hou, F., Zhou, C., Liu, X., Lei, Z., Niu, D. X., Ran, T., & Tan, Z. (2024) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2024.174931 · Cited by 18

Sputum metagenomics in bronchiectasis reveals pan-European variation: an EMBARC-BRIDGE study

Thng, K. X., Tiew, P. Y., Aogáin, M. M., Narayana, J. K., Jaggi, T. K., Ivan, F. X., Shuttleworth, M. K., Long, M. B., Richardson, H., Lind, H., et al. (2025) · European Respiratory Journal · doi:10.1183/13993003.00054-2025 · Cited by 22

Speculations on the clinical significance of asymptomatic viral infections

Gentile, G., & Micozzi, A. (2016) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2016.07.016 · Cited by 18

Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples

Afonso, C. L., & Afonso, A. M. (2023) · Veterinary Sciences · doi:10.3390/vetsci10120690 · Cited by 17

From the Gut to the Brain: Is Microbiota a New Paradigm in Parkinson’s Disease Treatment?

Vilela, C., Araújo, B., Soares-Guedes, C., Caridade-Silva, R., Martins‐Macedo, J., Teixeira, C., Gomes, E. D., Prudêncio, C., Vieira, M., & Teixeira, F. G. (2024) · Cells · doi:10.3390/cells13090770 · Cited by 18

Pharmacometabolomics Informs Viromics toward Precision Medicine

Balasopoulou, A., Patrinos, G. P., & Κάτσιλα, Θ. (2016) · Frontiers in Pharmacology · doi:10.3389/fphar.2016.00411 · Cited by 16

Informal nutrition symposium: leveraging the microbiome (and the metabolome) for poultry production

Lee, M. D., Ipharraguerre, I. R., Arsenault, R. J., Lyte, M., Lyte, J. M., Humphrey, B. D., Angel, R., & Korver, D. R. (2021) · Poultry Science · doi:10.1016/j.psj.2021.101588 · Cited by 16

Gut bacterial community profile in Pacific white shrimp Litopenaeus vannamei following 5‐aminolevulinic acid supplementation

Pedrosa‐Gerasmio, I. R., Nozaki, R., Kondo, H., & Hırono, I. (2020) · Aquaculture Research · doi:10.1111/are.14750 · Cited by 15

Metatranscriptomic and metataxonomic insights into the ultra-small microbiome of the Korean fermented vegetable, kimchi

Lee, H., Yoon, S., Dang, Y.-M., Yun, J., Jeong, H., Kim, K., Bae, J., & Ha, J. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1026513 · Cited by 14

Oral bacteriophages: metagenomic clues to interpret microbiomes

Banar, M., Rokaya, D., Azizian, R., Khurshid, Z., & Banakar, M. (2024) · PeerJ · doi:10.7717/peerj.16947 · Cited by 14

Bio‐therapeutics from human milk: prospects and perspectives

Singh, K. S., Singh, B. P., Rokana, N., Singh, N., Kaur, J., Singh, A., & Panwar, H. (2021) · Journal of Applied Microbiology · doi:10.1111/jam.15078 · Cited by 16

Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community

Kang, Y., Ji, X., Guo, L., Xia, H., Yang, X., Xie, Z., Shi, X., Wu, R., Feng, D., Wang, C., et al. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.00769-21 · Cited by 13

Current Understanding of Bacterial Endophytes, Their Diversity, Colonization and Their Roles in Promoting Plant Growth

Maela, M. P., & Serepa‐Dlamini, M. H. (2019) · Applied Microbiology open access · doi:10.4172/2471-9315.19.5.157 · Cited by 13

The Role of the Gut Microbiome in Hematological Cancers

Hussein, N., Rajasuriar, R., Khan, A. M., Lim, Y. A. L., & Gan, G. G. (2023) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-23-0080 · Cited by 12

High temperature aggravated hypoxia-induced intestine toxicity on juvenile Chinese mitten crab (Eriocheir sinensis)

Deng, D., Hu, S., Lin, Z., Geng, J., Qian, Z., Zhang, K., Ning, X., Cheng, Y., Zhang, C., & Yin, S. (2024) · Comparative Biochemistry and Physiology Part D Genomics and Proteomics · doi:10.1016/j.cbd.2024.101288 · Cited by 12

Advances in omics data for eosinophilic esophagitis: moving towards multi-omics analyses

Matsuyama, K., Yamada, S., Sato, H., Zhan, J., & Shoda, T. (2024) · Journal of Gastroenterology · doi:10.1007/s00535-024-02151-6 · Cited by 12

Methods in microbiome research

Iyer, N. R. (2016) · Lab Animal · doi:10.1038/laban.1093 · Cited by 12

Complementary Methodologies To Investigate Human Gut Microbiota in Host Health, Working towards Integrative Systems Biology

Méndez–García, C., Barbas, C., Ferrer, M., & Rojo, D. (2017) · Journal of Bacteriology · doi:10.1128/jb.00376-17 · Cited by 13

Detoxification of toxic heavy metals by serine protease inhibitor isolated from polluted soil

Mukherjee, A., Yadav, R. K., Marmeisse, R., Fraissinet‐Tachet, L., & Reddy, M. S. (2019) · International Biodeterioration & Biodegradation · doi:10.1016/j.ibiod.2019.104718 · Cited by 12

Fecal microbiota cooperative metabolism of pectins derived from apple pomace: A functional metagenomic study

Calvete‐Torre, I., Sabater, C., Margollés, A., & Ruíz, L. (2023) · LWT · doi:10.1016/j.lwt.2023.115362 · Cited by 11

Field Metagenomics of Bacterial Community Involved in Bioremediation of Crude Oil-Polluted Soil

Ezekoye, C. C., Chikere, C. B., & Okpokwasili, G. C. (2018) · Journal of Bioremediation & Biodegradation · doi:10.4172/2155-6199.1000449 · Cited by 11

Single-cell RNA-Seq reveals intracellular microbial diversity within immune cells during SARS-CoV-2 infection and recovery

Yadav, S. K., Mehta, P., Soni, J., Chattopadhyay, P., Devi, P., Habyarimana, T., Tardalkar, K., Joshi, M. G., & Pandey, R. (2023) · iScience · doi:10.1016/j.isci.2023.108357 · Cited by 13

Water microbiome dynamics of Pacific white shrimp Penaeus vannamei infected with Vibrio parahaemolyticus strains responsible for acute hepatopancreatic necrosis disease

Aguilar-Rendón, K. G., Soto-Rodríguez, S. A., Gómez‐Gil, B., Lozano‐Olvera, R., & Yáñez‐Rivera, B. (2022) · Aquaculture · doi:10.1016/j.aquaculture.2021.737871 · Cited by 11

Role of gene regulation and inter species interaction as a key factor in gut microbiota adaptation

Gao, S., Khan, M. I., Kalsoom, F., Liu, Z., Chen, Y., & Chen, Z. (2022) · Archives of Microbiology · doi:10.1007/s00203-022-02935-5 · Cited by 11

Transcriptomics

Rajawat, J. (2018) · Springer eBooks · doi:10.1007/978-981-13-2925-8_3 · Cited by 10

Microbiome measurement: Possibilities and pitfalls

Radjabzadeh, D., Uitterlinden, A. G., & Kraaij, R. (2017) · Best Practice & Research Clinical Gastroenterology · doi:10.1016/j.bpg.2017.10.008 · Cited by 10

Microorganisms: the secret agents of the biosphere, and their key roles in biotechnology

de Oliveira, V. M., Andreote, F. D., Cardoso, P., Castro‐Gamboa, I., Costa-Lotufo, L. V., Polizeli, M. D. L. T. D. M., Thiemann, O. H., & Setúbal, J. C. (2022) · Biota Neotropica · doi:10.1590/1676-0611-bn-2022-1343 · Cited by 10

Impact of different oral treatments on the composition of the supragingival plaque microbiome

Rabe, A., Salazar, M. G., Michalik, S., Kocher, T., Below, H., Völker, U., & Welk, A. (2022) · Journal of Oral Microbiology · doi:10.1080/20002297.2022.2138251 · Cited by 10

MICROBIOTA DA PELE: NOVOS DESAFIOS

Sivieri, K., Crespo, C. D. C., Novak, J., Tobara, J. C., & Martins, W. K. (2021) · Arquivos Catarinenses de Medicina · doi:10.63845/e6zenk26 · Cited by 10

Whole-genome of Mexican-crAssphage isolated from the human gut microbiome

Cervantes-Echeverría, M., Equihua-Medina, E., Cornejo‐Granados, F., Hernández-Reyna, A., Sánchez, F., López-Contreras, B. E., Canizales‐Quinteros, S., & Ochoa‐Leyva, A. (2018) · BMC Research Notes · doi:10.1186/s13104-018-4010-5 · Cited by 10

Impact of Next‐generation Sequencing in Elucidating the Role of microRNA Related to Multiple Abiotic Stresses

Goswami, K., Tripathi, A., Gautam, B., & Mishra, N. S. (2019) · doi:10.1002/9781119463665.ch20 · Cited by 10

Genomic insights into novel extremotolerant bacteria isolated from the NASA Phoenix mission spacecraft assembly cleanrooms

Schultz, J., Jamil, T., Sengupta, P., Sivabalan, S. K. M., Rawat, A., Patel, N. S., Krishnamurthi, S., Alam, I. S., Singh, N. K., Raman, K., et al. (2025) · Microbiome · doi:10.1186/s40168-025-02082-1 · Cited by 9

Adaptations, diversity, and biotechnological potential of thermophilic microorganisms: exploring culture-dependent and culture-independent approaches in extreme environments

Gupta, S., Bhargava, V., Kaur, J., & Lata, P. (2025) · 3 Biotech · doi:10.1007/s13205-025-04382-7 · Cited by 9

Human Gut Microbiome Analysis and Multi-omics Approach

Sirangelo, T. M. (2018) · International Journal of Pharma Medicine and Biological Sciences · doi:10.18178/ijpmbs.7.3.52-57 · Cited by 9

Oral microbial diversity analysis among atrophic glossitis patients and healthy individuals

Li, H., Sun, J.-L., Wang, X.-Y., & Shi, J. (2021) · Journal of Oral Microbiology · doi:10.1080/20002297.2021.1984063 · Cited by 6

Oncobiome at the Forefront of a Novel Molecular Mechanism to Understand the Microbiome and Cancer

la Vega, H. A., Alonso-Luna, O., Ali-Pérez, J., López‐Camarillo, C., & Ruíz‐García, E. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-24100-1_10 · Cited by 8

Taxonomic diversity and functional potential of microbial communities in oyster calcifying fluid

Unzueta‐Martínez, A., & Girguis, P. R. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.01094-24 · Cited by 9

The Feasibility of Phage Therapy for Periodontitis

Zhen, C., Guo, Z., Lin, H., Tian, Y., Zhang, P., Chen, H., Wang, Y., & Shen, Y. (2021) · Future Microbiology · doi:10.2217/fmb-2020-0161 · Cited by 8

kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes

Defazio, G., Tangaro, M. A., Pesole, G., & Fosso, B. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae680 · Cited by 7

Increasing Reproducibility in Oral Microbiome Research

Gopinath, D., & Menon, R. K. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1518-8_1 · Cited by 7

On the core bacterial flora of Ixodes persulcatus (Taiga tick)

Sui, S., Yang, Y., Sun, Y. E., Wang, X., Wang, G., Shan, G., Wang, J., & Yu, J. M. (2017) · PLoS ONE · doi:10.1371/journal.pone.0180150 · Cited by 7

Applying 3D cultures and high-throughput technologies to study host-pathogen interactions

Martinis, E. C. P. D., Alves, V. F., Pereira, M. G., Andrade, L. N., Abichabki, N. D. L. M., Abramova, A., Dannborg, M., & Bengtsson‐Palme, J. (2025) · Frontiers in Immunology · doi:10.3389/fimmu.2025.1488699 · Cited by 6

The Bacterial Composition of the Gut Microbiota of Mexicans with Overweight and Obesity: A Systematic Review

Samudio-Cruz, M. A., Luna‐Angulo, A. B., Cabrera-Ruiz, E., Landa‐Solís, C., Rangel‐López, E., Carrillo‐Mora, P., Ríos-Martínez, J., Toledo-Pérez, R., Paniagua‐Pérez, R., Martínez-Canseco, C. J., et al. (2025) · Microorganisms · doi:10.3390/microorganisms13081727 · Cited by 8

Alterations of gut viral signals in atrial fibrillation: complex linkage with gut bacteriome

Zuo, K., Li, J., Chen, F., Zhong, J., Xu, L., & Yang, X. (2022) · Aging · doi:10.18632/aging.204222 · Cited by 6

Long-read sequencing reveals the shell microbiome of apparently healthy American lobsters Homarus americanus from Atlantic Canada

Koepper, S., Clark, K. F., McClure, J. T., Revie, C. W., Stryhn, H., & Thakur, K. K. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1245818 · Cited by 6

Relevance of Metatranscriptomics in Symbiotic Associations Between Plants and Rhizosphere Microorganisms

Bharti, M. K., Siddique, R. A., Ranjan, K., Chandra, D., & Singh, N. P. (2021) · Springer eBooks · doi:10.1007/978-981-15-9758-9_3 · Cited by 6

Metagenomic Approaches for Studying Plant–Microbe Interactions

Mohan, S. M., & Pola, S. (2022) · Springer eBooks · doi:10.1007/978-981-19-3696-8_12 · Cited by 6

Application of Metatranscriptomics in Wastewater Treatment Processes

Ekwanzala, M. D., Budeli, P., & Unuofin, J. O. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-821881-5.00008-8 · Cited by 6

MG7: Configurable and scalable 16S metagenomics data analysisPreprint

Alekhin, A., Kovach, E., Manrique, M., Pareja-Tobes, P., Pareja, E., Tobes, R., & Pareja-Tobes, E. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/027714 · Cited by 6

Children with eosinophilic esophagitis non‐responsive to combination therapy have distinct esophageal transcriptomic and microbiome profile

Hiremath, G. S., Choksi, Y. A., Correa, H., Jacobse, J., Das, S. R., Ma, S., Goettel, J. A., & Rajagopala, S. V. (2024) · Allergy · doi:10.1111/all.16208 · Cited by 5

Treatment of xerostomia in Sjögren’s syndrome – what effect does it have on the oral microbiome?

Muszyński, D., Kucharski, R., Marek-Trzonkowska, N. M., Kalinowska, M., Brzóska, A., Bolcewicz, M., Kalinowski, L., & Kaźmierczak-Siedlecka, K. (2025) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2025.1484951 · Cited by 5

Seed inoculation of Hartmannibacter diazotrophicus does not alter the rhizosphere bacterial microbiome of wheat and barley in a three-year field trial

Quiroga, S., Ratering, S., Rosado-Porto, D., Rekowski, A., Schulz, F., Zörb, C., & Schnell, S. (2024) · Applied Soil Ecology · doi:10.1016/j.apsoil.2024.105823 · Cited by 5

Functional and taxonomic classification of a greenhouse water drain metagenome

López-Leal, G., Cornejo‐Granados, F., Hurtado-Ramírez, J. M., Mendoza-Vargas, A., & Ochoa‐Leyva, A. (2018) · Standards in Genomic Sciences · doi:10.1186/s40793-018-0326-y · Cited by 5

Microbiome-MX 2018: microbiota and microbiome opportunities in Mexico, a megadiverse country

Cornejo‐Granados, F., de la Barca, A. M. C., Torres, N., Martínez‐Romero, E., Torres, J., López‐Vidal, Y., Soberón, X., Partida‐Martínez, L. P., Pinto-Cardoso, S. M., Alcaraz, L. D., et al. (2019) · Research in Microbiology · doi:10.1016/j.resmic.2019.03.001 · Cited by 5

Fate of pathogens and viruses in hospital wastewater and their treatment methods

Talan, A., & Tyagi, R. D. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-819722-6.00005-5 · Cited by 5

The secondary bacterial infection caused by WSSV outbreaks impacts shrimp Marsupenaeus japonicus’ growth as well as its intestinal microbiota’s composition and function

He, Z., Zhao, J., Liao, X., Chen, X., Fu, Z., Sun, C., & Ni, Z. (2020) · Israeli Journal of Aquaculture - Bamidgeh · doi:10.46989/001c.21687 · Cited by 5

Differential roles of nitrogen and phosphorus in petroleum hydrocarbon biodegradation: Metatranscriptomic insights from soil bioremediation

Ou, Y., Zhang, C., Wu, M., Yu, Y., Zhang, X., Hu, M., Gao, H., & Wu, X. (2025) · Journal of environmental chemical engineering · doi:10.1016/j.jece.2025.118412 · Cited by 4

Fecal Microbiota Transplantation in Animals: Therapeutics, Conservation, and Farming

Reveles, K. R., Meehan, J., & Tillotson, G. (2025) · Microorganisms · doi:10.3390/microorganisms13112465 · Cited by 5

Mosquito-borne viruses in Australia: An emerging trend of increasing prevalence in Northern Queensland

Hosen, M. E., Dunsdon, S., & Sarker, S. (2026) · Virology · doi:10.1016/j.virol.2026.110825 · Cited by 5

Methods for studying the forest tree microbiome

Blumenstein, K., Terhonen, E., Sun, H., & Asiegbu, F. O. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-822542-4.00016-4 · Cited by 4

Storage media and RNA extraction approaches substantially influence the recovery and integrity of livestock fecal microbial RNA

Koorakula, R., Ghanbari, M., Schiavinato, M., Wegl, G., Dohm, J. C., & Domig, K. J. (2022) · PeerJ · doi:10.7717/peerj.13547 · Cited by 8

Gut Microbiome and Small RNA Integrative-Omic Perspective of Meconium and Milk-FED Infant Stool Samples

Kazakova, P., Abasolo-Zabalo, N., de Cripan, S. M., Marquès, E., Cereto‐Massagué, A., García, L., Canela-Canela, N., Tormo, R., & Torrell-Galceran, H. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24098069 · Cited by 3

Advancing Our Understanding of Plant–Microbe Interactions through Integrating Multiomics and Stable Isotopes for Sustainable Agriculture

Jyoti, P., Bhardwaj, J., Kaushal, G., & Yadav, S. K. (2025) · ACS Agricultural Science & Technology · doi:10.1021/acsagscitech.5c00098 · Cited by 3

Mass Spectrometry-Based Proteomics of Minor Species in the Bulk: Questions to Raise with Respect to the Untargeted Analysis of Viral Proteins in Human Tissue

Aziz, S., Rasheed, F., Zahra, R., & König, S. (2023) · Life · doi:10.3390/life13020544 · Cited by 3

Differences in diversity and community composition of the shell microbiome of apparently healthy lobsters Homarus americanus across Atlantic Canada

Koepper, S., Clark, K. F., McClure, J. T., Revie, C. W., Stryhn, H., & Thakur, K. K. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1320812 · Cited by 3

Novel insight into the mechanisms of neurotoxicity induced by glufosinate-ammonium via the microbiota-intestine-brain axis in Chinese mitten crab (Eriocheir sinensis)

Feng, H., Song, L., Wu, Y., Zhao, F., Zhu, F., Song, Z., Zhang, K., Jiang, J., Cai, X., Yin, S., et al. (2025) · Pesticide Biochemistry and Physiology · doi:10.1016/j.pestbp.2025.106426 · Cited by 2

Comprehensive Advances on Probiotic-Fermented Medicine and Food Homology

Bu, D., Cheng, Y., Gao, W., Han, F., & Dong, H. (2025) · Fermentation · doi:10.3390/fermentation11120682 · Cited by 2

Predictive bioinformatics models in natural farming practices-bridging science and sustainability

Kumar, P., Sharma, S., Sharma, S., VERMA, S., & Chandel, R. S. (2026) · Environmental Sustainability · doi:10.1007/s42398-025-00411-6 · Cited by 2

Integrating metagenomics and metatranscriptomics into Orthoflavivirus diagnosis: a transformative approach for clinical virology

Hosen, M. E., Horwood, P. F., & Sarker, S. (2026) · Journal of General Virology · doi:10.1099/jgv.0.002247 · Cited by 2

Time to Agree: the Efforts to Standardize Molecular Microbiological Methods (MMM) for Detection of Microorganisms in Natural and Engineered Systems

de Paula, R. M., Gieg, L. M., Duncan, K. E., Tsesmetzis, N., Eckert, R. B., & Skovhus, T. L. (2021) · NACE CORROSION Conference · doi:10.5006/c2021-16986 · Cited by 2

Garlic (Allium sativum) as a dietary ingredient can cause dysbiosis in the microbiota of the California yellowtail (Seriola dorsalis) at high concentrations

Valenzuela-Gutiérrez, R., Lago‐Lestón, A., Cicala, F., Hernández-Rodríguez, M., Barón-Sevilla, B., Armuelles-Bernal, C. E., Vargas‐Albores, F., Garibay-Valdéz, E., Gómez-Reyes, R., & Martínez‐Porchas, M. (2023) · Aquaculture International · doi:10.1007/s10499-023-01301-6 · Cited by 2

Alterations in microbiome of COVID-19 patients and its impact on forensic investigations

Mir, T. U. G., Manhas, S., Wani, A. K., Akhtar, N., Shukla, S., & Prakash, A. (2023) · Science & Justice · doi:10.1016/j.scijus.2023.12.002 · Cited by 2

Navigating Evolving Challenges in Blood Safety

Pourkarim, M. R. (2024) · Viruses · doi:10.3390/v16010123 · Cited by 2

Multi-omics in Gut Microbiome

Mathuria, A., Chaudhary, A., Sharma, H., & Mani, I. (2024) · Springer eBooks · doi:10.1007/978-981-97-1844-3_9 · Cited by 4

Multi-metal tolerance of DHHC palmitoyl transferase-like protein isolated from metal contaminated soil

Mukherjee, A., Thakur, B., Pandey, A. K., Marmeisse, R., Fraissinet‐Tachet, L., & Reddy, S. M. (2020) · Ecotoxicology · doi:10.1007/s10646-020-02301-5 · Cited by 2

Role of the Microbiome in Pancreatic Cancer

Kurtom, S., Sethi, V., & Dudeja, V. (2021) · Springer eBooks · doi:10.1007/978-3-030-53786-9_19 · Cited by 2

Metagenómica y metatranscriptómica para mitigar las emisiones de metano por animales rumiantes

Martínez-Muñoz, D. S., Rivera-Cerón, F., Palacios-Solórzano, I., Ramírez-Martínez, B. A., Molina‐Aguilar, C., & Moguel, B. (2022) · TIP Revista Especializada en Ciencias Químico-Biológicas · doi:10.22201/fesz.23958723e.2022.430 · Cited by 3

Det orale mikrobiom - en opdatering for tandplejeteamet

Kilian, M., Chapple, I., Hannig, M., Marsh, P. D., Meuric, V., Pedersen, A. M. L., Tonetti, M. S., Wade, W. G., & Zaura, E. (2017) · Den norske tannlegeforenings Tidende · doi:10.56373/2017-5-4 · Cited by 2

Metatranscriptomics: A Recent Advancement to Explore and Understand Rhizosphere

Bajpai, R., Meher, J., Rashid, M. M., & Lingayat, D. (2021) · Springer eBooks · doi:10.1007/978-981-15-9758-9_26 · Cited by 2

Metagenomic Analysis and Their Application

Ghosh, A., Metha, A., & Khan, M. A. (2025) · Elsevier eBooks · doi:10.1016/b978-0-323-95502-7.00286-4 · Cited by 2

Soil Biological Processes in Urban Soils

Gleeson, D. B. (2022) · Progress in soil science · doi:10.1007/978-3-030-87316-5_8 · Cited by 1

Human Microbiome Acquisition and Bioinformatic Challenges in Metagenomic Studies

D’Argenio, V. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19020383 · Cited by 56

Understanding human health through metatranscriptomics

Ojala, T., Kankuri, E. M., & Kankainen, M. (2023) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2023.02.002 · Cited by 113

Studying the Human Gut Microbiota in the Trans-Omics Era - Focus on Metagenomics and Metabonomics

Tuohy, K. M., Gougoulias, C., Shen, Q., Walton, G., Fava, F., & Ramnani, P. (2009) · Current Pharmaceutical Design · doi:10.2174/138161209788168182 · Cited by 77

Metagenomics approaches for studying the human microbiome

Eskeziyaw, B. M., & Mengistu, D. Y. (2024) · All Life · doi:10.1080/26895293.2024.2350166 · Cited by 9

Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics

Ojala, T., Häkkinen, A.-E., Kankuri, E. M., & Kankainen, M. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.05.004 · Cited by 81