Current challenges and best-practice protocols for microbiome analysis

Trimmomatic: a flexible trimmer for Illumina sequence data

Bolger, A. M., Lohse, M., & Usadel, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu170 · Cited by 65,548

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

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400

DADA2: High–resolution sample inference from Illumina amplicon data

Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0209-9 · Cited by 23,742

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

McMurdie, P. J., & Holmes, S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061217 · Cited by 21,942

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

Prokka: rapid prokaryotic genome annotation

Seemann, T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu153 · Cited by 18,937

Fast and sensitive protein alignment using DIAMOND

Buchfink, B., Xie, C., & Huson, D. H. (2015) · Nature Methods · doi:10.1038/nmeth.3176 · Cited by 14,201

Prodigal: prokaryotic gene recognition and translation initiation site identification

Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M., Larimer, F. W., & Hauser, L. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-119 · Cited by 12,692

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

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

Using microbiome information to understand and improve animal performance

Lourenco, J. M., & Welch, C. B. (2022) · Italian Journal of Animal Science · doi:10.1080/1828051x.2022.2077147 · Cited by 14

Crosstalk between mucosal microbiota, host gene expression, and sociomedical factors in the progression of colorectal cancer

Kim, N., Gim, J., Lee, B. J., Choi, B. I., Yoon, H. S., Kim, S. H., Joo, M. K., Park, J., & Kim, C. (2022) · Scientific Reports · doi:10.1038/s41598-022-17823-7 · Cited by 14

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

The prokaryotic and eukaryotic microbiome of Pacific oyster spat is shaped by ocean warming but not acidification

Zhong, K. X., Chan, A. M., Collicutt, B., Daspe, M., Finke, J. F., Foss, M., Green, T. J., Harley, C. D. G., Hesketh, A. V., Miller, K. M., et al. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.00052-24 · Cited by 12

Metagenomics Approaches to Investigate the Neonatal Gut Microbiome

Boudar, Z., Sehli, S., Janahi, S. E., Idrissi, N. A., Hamdi, S., Dini, N., Brim, H., Amzazi, S., Nejjari, C., Lloyd-Puryear, M. A., et al. (2022) · Frontiers in Pediatrics · doi:10.3389/fped.2022.886627 · Cited by 16

Precision nutrition through diet-gut microbiome interactions: Emerging insights driven by artificial intelligence, microbiome health metrics, and mechanistic modeling

Barrera-Suarez, M. A., Zhao, C., Karnatovskaia, L. V., & Sung, J. (2026) · Gut Microbes Reports · doi:10.1080/29933935.2026.2650247 · Cited by 16

Consumption of yacon flour and energy-restricted diet increased the relative abundance of intestinal bacteria in obese adults

Ribeiro, P. V. D. M., Veloso, T. G. R., de Oliveira, L. L., Mendes, N. P., & Alfenas, R. D. C. G. (2023) · Brazilian Journal of Microbiology · doi:10.1007/s42770-023-01140-w · Cited by 12

The effects of Cryptosporidium infection on gut fungi and enzyme abundance in Sus domesticus

(2023) · Asian Journal of Agriculture and Biology · doi:10.35495/ajab.2023.114 · Cited by 11

Intratumoral microorganisms in tumors of the digestive system

Xuan, M., Gu, X., Liu, Y., Li, Y., Li, Y., Huang, D., Li, J., & Xue, C. (2024) · Cell Communication and Signaling · doi:10.1186/s12964-023-01425-5 · Cited by 13

Environmentally Relevant Antibiotic Concentrations Exert Stronger Selection Pressure on River Biofilm Resistomes than AMR-Reservoir Effluents

Flores-Vargas, G., Bergsveinson, J., & Korber, D. R. (2024) · Antibiotics · doi:10.3390/antibiotics13060539 · Cited by 11

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

A review of neural networks for metagenomic binning

Herazo-Álvarez, J., Mora, M., Cuadros-Orellana, S., Vilches-Ponce, K., & Hernández-García, R. (2025) · Briefings in Bioinformatics · doi:10.1093/bib/bbaf065 · Cited by 11

Associations between self-reported psychological symptom severity and gut microbiota: further support for the microgenderome

Ganci, M., Suleyman, E., Butt, H., & Ball, M. (2022) · BMC Psychiatry · doi:10.1186/s12888-022-03947-7 · Cited by 13

The Pre-Analytical CEN/TS Standard for Microbiome Diagnostics—How Can Research and Development Benefit?

Stumptner, C., Stadlbauer, V., O’Neil, D., Gessner, A., Hiergeist, A., Zatloukal, K., & Abuja, P. M. (2022) · Nutrients · doi:10.3390/nu14091976 · Cited by 12

Biohacking the human gut microbiome for precision health and therapeutic innovation

Bautista, J., & López‐Cortés, A. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1776983 · Cited by 14

Impact of housing system on intestinal microbiota of laying hens – A systematic review

Pires, P. G. D. S., de Oliveira, G. S., McManus, C., dos Santos, V. M., & Moraes, P. D. O. (2024) · Research in Veterinary Science · doi:10.1016/j.rvsc.2024.105184 · Cited by 11

Overview of microbial studies in sandflies and their progress toward development of paratransgenic approach for the control of Leishmania sp.

Vaselek, S. (2024) · Frontiers in Tropical Diseases · doi:10.3389/fitd.2024.1369077 · Cited by 10

A Guide to Environmental DNA Extractions for Non‐Molecular Trained Biologists, Ecologists, and Conservation Scientists

Rieder, J., Jemmi, E., Hunter, M. E., & Adrian‐Kalchhauser, I. (2024) · Environmental DNA · doi:10.1002/edn3.70002 · Cited by 10

Comprehensive analysis of the interaction microbiome and prostate cancer: an initial exploration from multi-cohort metagenome and GWAS studies

Ye, G.-C., Peng, H., Xiang, J.-C., Miao, L.-T., Liu, C., Wang, S., & Xia, Q. (2025) · Journal of Translational Medicine · doi:10.1186/s12967-024-05937-7 · Cited by 14

Metagenomic insights of microbial functions under conventional and conservation agriculture

Thakur, S. S., Solano-González, S., Suravajhala, P., Jain, S. K., Yadav, S., Narayan, K. S., Raj, E. E., Kuzyakov, Y. V., & Ratnasari, A. (2025) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-025-04312-y · Cited by 10

Exploring the gut microbiome’s influence on cancer-associated anemia: Mechanisms, clinical challenges, and innovative therapies

Bangolo, A., Amoozgar, B., Habibi, M., Simms, E., Nagesh, V. K., Wadhwani, S., Wadhwani, N., Auda, A., Eliáš, D., Mansour, C., et al. (2025) · World Journal of Gastrointestinal Pharmacology and Therapeutics · doi:10.4292/wjgpt.v16.i2.105375 · Cited by 10

Interrogating Plant-Microbe Interactions with Chemical Tools: Click Chemistry Reagents for Metabolic Labeling and Activity-Based Probes

Lin, V. (2021) · Molecules · doi:10.3390/molecules26010243 · Cited by 10

Improving analysis of the vaginal microbiota of women undergoing assisted reproduction using nanopore sequencing

Lüth, T., Graspeuntner, S., Neumann, K., Kirchhoff, L., Masuch, A., Schaake, S., Lupatsii, M., Tse, R., Griesinger, G., Trinh, J., et al. (2022) · Journal of Assisted Reproduction and Genetics · doi:10.1007/s10815-022-02628-4 · Cited by 10

Microbiome and its implications in oncogenesis: a Mendelian randomization perspective.

Feng, K., Ren, F., Xing, Z., Zhao, Y., Yang, C., Liu, J., Shang, Q., Wang, X., & Wang, X. (2023) · PubMed Central · Cited by 11

Small investments with big returns: environmental genomic bioprospecting of microbial life

Vuong, P., Wise, M. J., Whiteley, A. S., & Kaur, P. (2022) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2021.2011833 · Cited by 10

Gut Microbiome Profiling of the Endangered Southern Greater Glider (Petauroides volans) after the 2019–2020 Australian Megafire

Clough, J., Schwab, S. G., & Mikac, K. M. (2023) · Animals · doi:10.3390/ani13223583 · Cited by 9

Detecting horizontal gene transfer with metagenomics co-barcoding sequencing

Han, K., Li, J., Yang, D., Zhuang, Q., Zeng, H., Rong, C., Yue, J., Li, N., Gu, C., Chen, L., et al. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.03602-23 · Cited by 9

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

Genomics for Arbovirus Surveillance: Considerations for Routine Use in Public Health Laboratories

Patiño, L., Benítez, A. D., Carrazco-Montalvo, A., & Regato, M. (2024) · Viruses · doi:10.3390/v16081242 · Cited by 9

Precision oncology through next generation sequencing in hepatocellular carcinoma

Shinde, S. D., Bigogno, C. M., Simmons, A., Kathuria, N., Ghose, A., Apte, V., Lapitan, P., Makker, S., Caglayan, A., & Boussios, S. (2025) · Heliyon · doi:10.1016/j.heliyon.2025.e42054 · Cited by 7

Cutting-edge deep-learning based tools for metagenomic research

Karin, E. L., & Steinegger, M. (2025) · National Science Review · doi:10.1093/nsr/nwaf056 · Cited by 10

The crosstalk between host and rumen microbiome in cattle: insights from multi-omics approaches and genome-wide association studies

Ye, X., Sahana, G., Lund, M. S., & Cai, Z. (2025) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-025-04504-6 · Cited by 10

Microbiome dysbiosis and chemotherapy resistance in acute myeloid leukemia (AML)

Tian, M., Samarkhazan, H. S., Alemohammad, S. S., Fakhraei, M., Tavakoli, F., Shams, A., & Zeynalabadi, A. (2025) · npj Biofilms and Microbiomes · doi:10.1038/s41522-025-00891-8 · Cited by 9

Ten simple rules for investigating (meta)genomic data from environmental ecosystems

Vuong, P., Wise, M. J., Whiteley, A. S., & Kaur, P. (2022) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1010675 · Cited by 9

Meta-Analysis of Publicly Available Clinical and Preclinical Microbiome Data From Studies of Burn Injury

Horseman, T. S., Frank, A. M., Shupp, J. W., & Burmeister, D. M. (2023) · Journal of Burn Care & Research · doi:10.1093/jbcr/irad098 · Cited by 9

The impact of host genetics on porcine gut microbiota composition excluding maternal and postnatal environmental influences

Heras-Molina, A., Estellé, J., Vázquez-Gómez, M., López-García, A., Pacheco, J. L. P., Astiz, S., García-Contreras, C., Escudero, R., Isabel, B., Gonzalez‐Bulnes, A., et al. (2024) · PLoS ONE · doi:10.1371/journal.pone.0315199 · Cited by 9

Safety Assessment of the CP4 EPSPS and NPTII Proteins in Eucalyptus

Avisar, D., Azulay, S., Bombonato, L., Carvalho, D., Dallapiccola, H. S., de Souza, C., Santos, A. D. D., Dias, T., Galan, M. P., Galvão, M., et al. (2023) · GM crops & food · doi:10.1080/21645698.2023.2222436 · Cited by 9

Microbiome Analysis of Organic and Conventional Chickens Processed Using Whole Carcass Enrichment and Rinse Methods

Punchihewage-Don, A. J., Hasan, N. A., Rashed, S. M., & Parveen, S. (2023) · Journal of Food Protection · doi:10.1016/j.jfp.2023.100176 · Cited by 8

Research progress in isolation and identification of rumen probiotics

Wu, R., Ji, P., Hua, Y., Li, H., Zhang, W., & Wei, Y. (2024) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2024.1411482 · Cited by 8

A Current Overview of Next-Generation Probiotics and Their Prospects in Health and Disease Management

Loo, K.-Y., Thong, J. Y. H., Tan, L. T., Letchumanan, V., Chan, K., Lee, L., & Law, J. W. (2024) · Progress In Microbes & Molecular Biology · doi:10.36877/pmmb.a0000457 · Cited by 12

The Microbiome as a Protagonist of Xylophagous Insects in Adaptation to Environmental Conditions and Climate Change

Kuprin, A., & Baklanova, V. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms262010143 · Cited by 8

The impact of dietary, surgical, and pharmacological interventions on gut microbiota in individuals with diabetes mellitus: A systematic review

Bock, P. M., Martins, A. F., Guerra, R. R., Teló, G. H., Leivas, G., Maraschin, C. K., & Schaan, B. D. (2022) · Diabetes Research and Clinical Practice · doi:10.1016/j.diabres.2022.109944 · Cited by 9

The Nonbacterial Microbiome: Fungal and Viral Contributions to the Preterm Infant Gut in Health and Disease

Wilson, A. P., Bogie, B., Chaaban, H., & Burge, K. Y. (2023) · Microorganisms · doi:10.3390/microorganisms11040909 · Cited by 10

Skin microbiome alterations in upper extremity secondary lymphedema

Campbell, A.-C., Fei, T., Baik, J. E., Park, H. J., Shin, J., Kuonqui, K. G., Brown, S., Sarker, A., Kataru, R. P., & Mehrara, B. J. (2023) · PLoS ONE · doi:10.1371/journal.pone.0283609 · Cited by 8

Considerations for the inclusion of metabarcoding data in the plant protection product risk assessment of the soil microbiome

Sweeney, C. J., Kaushik, R., & Bottoms, M. J. (2023) · Integrated Environmental Assessment and Management · doi:10.1002/ieam.4812 · Cited by 10

Polyphenols as a new class of prebiotics for gut microbiota manipulation

Bačić, A., Gavrilović, J., & Rajilić-Stojanović, M. D. (2023) · Arhiv za farmaciju · doi:10.5937/arhfarm73-46900 · Cited by 9

Domestic hot-water boilers harbour active thermophilic bacterial communities distinctly different from those in the cold-water supply

Egli, T. W., Campostrini, L., Leifels, M., Füchslin, H. P., Kolm, C., Cheng, D., Zimmermann, S., Hauss, V., Guiller, A., Grasso, L., et al. (2024) · Water Research · doi:10.1016/j.watres.2024.121109 · Cited by 8

The gut microbiome as a modulator of arterial function and age-related arterial dysfunction

Longtine, A. G., Greenberg, N., de Quirós, Y. B., & Brunt, V. E. (2024) · American Journal of Physiology-Heart and Circulatory Physiology · doi:10.1152/ajpheart.00764.2023 · Cited by 9

Fleece rot and dermatophilosis (lumpy wool) in sheep: opportunities and challenges for new vaccines

Denman, S. E., Tellam, R. L., Vuocolo, T., Ingham, A. B., Wijffels, G. L., James, P., & Colditz, I. G. (2021) · Animal Production Science · doi:10.1071/an21120 · Cited by 8

DivCom: A Tool for Systematic Partition of Groups of Microbial Profiles Into Intrinsic Subclusters and Distance-Based Subgroup Comparisons

Intze, E., & Lagkouvardos, I. (2022) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2022.864382 · Cited by 7

Microbiome and Colorectal Cancer Management

Alrahawy, M., Javed, S., Atif, H., ElSanhoury, K., Mekhaeil, K., & Eskander, G. H. (2022) · Cureus · doi:10.7759/cureus.30720 · Cited by 8

Metagenomics Databases for Bacteria

Wang, D. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3072-3_3 · Cited by 8

Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes

Adams, A. K., Kristy, B., Gorman, M., Balint-Kurti, P. J., Yencho, G. C., & Olukolu, B. A. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad351 · Cited by 8

Data-driven microbiota biomarker discovery for personalized drug therapy of cardiovascular disease

Shen, L., Shen, K., Bai, J., Wang, J., Singla, R. K., & Shen, B. (2020) · Pharmacological Research · doi:10.1016/j.phrs.2020.105225 · Cited by 8

16S microbiome analysis of microbial communities in distribution centers handling fresh produce

Townsend, A. M., den Bakker, H. C., Mann, A., Murphy, C. M., Strawn, L. K., & Dunn, L. L. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1041936 · Cited by 7

Unveiling the microbial symphony: Next-Gen sequencing and bioinformatics insights into the human gut microbiome

Maheshwari, K., Musyuni, P., Moulick, A., Mishra, H., Ekielski, A., Mishra, P. K., & Aggarwal, G. (2024) · Health Sciences Review · doi:10.1016/j.hsr.2024.100173 · Cited by 10

Effect of the 16S rRNA Gene Hypervariable Region on the Microbiome Taxonomic Profile and Diversity in the Endangered Fish Totoaba macdonaldi

Pérez-Bustamante, I. S., Cruz‐Flores, R., López‐Carvallo, J. A., & Sánchez-Serrano, S. (2024) · Microorganisms · doi:10.3390/microorganisms12112119 · Cited by 7

Metagenomic analysis of the faecal microbiota and AMR in roe deer in Western Pomerania

Lechleiter, N., Wedemeyer, J., Schütz, A. K., Sehl‐Ewert, J., Schaufler, K., & Homeier‐Bachmann, T. (2025) · Scientific Reports · doi:10.1038/s41598-025-93602-4 · Cited by 7

Bee gut microbiota as an emerging endpoint for the environmental risk assessment of pesticides

Rosa, A. D. S., Aguado-López, D., Jabal‐Uriel, C., Abad, M. B., Higes, M., Pinto, M. A., Henriques, D., Tosi, S., Rodríguez, J. M., Alba, C., et al. (2025) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2025.179977 · Cited by 7

BugBook: How to explore and exploit the insect-associated microbiome

Auger, L., Tegtmeier, D., Caccia, S., Klammsteiner, T., & Smet, J. D. (2025) · Journal of Insects as Food and Feed · doi:10.1163/23524588-bja10256 · Cited by 11

The Role of Gut Microbiota and Its Metabolites in Mitigating Radiation Damage

Zhu, H., Yan, X., Shi, H. S., Chen, Y., Huang, C., Zhou, Y., Yan, S., Zhang, N., Wang, J., Zhang, J., et al. (2025) · Microorganisms · doi:10.3390/microorganisms13092151 · Cited by 10

Metagenomics in bioremediation of metals for environmental cleanup

Wimalasekara, R. L., Seneviratne, K. N., & Jayathilaka, N. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-96113-4.00020-2 · Cited by 7

Antibiotic resistance gene sequencing is necessary to reveal the complex dynamics of immigration from sewers to activated sludge

Gibson, C., Kraemer, S. A., Klimova, N. G., Guo, B., & Frigon, D. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1155956 · Cited by 7

Gut microbiota-derived cholic acid mediates neonatal brain immaturity and white matter injury under chronic hypoxia

Yan, Y., Zheng, X., Liu, G., Shi, G., Li, C., Chen, H., He, X., Lin, K.-N., Deng, Z., Zhang, H., et al. (2024) · iScience · doi:10.1016/j.isci.2024.109633 · Cited by 7

Integrating artificial intelligence in exploring multiscale gut microbiota and diet relations for health promotion: A comprehensive review

Yang, Z., Zhu, J., Lu, W., Tian, F., Zhang, H., & Chen, W. (2024) · Food Bioscience · doi:10.1016/j.fbio.2024.104541 · Cited by 8

Microbial communities associated with marine sponges from diverse geographic locations harbor biosynthetic novelty

Nowak, V. V., Hou, P., & Owen, J. G. (2024) · Applied and Environmental Microbiology · doi:10.1128/aem.00726-24 · Cited by 9

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data

Gorstein, E., Aghdam, R., & Solís‐Lemus, C. (2025) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012143 · Cited by 7

Order among chaos: High throughput MYCroplanters can distinguish interacting drivers of host infection in a highly stochastic system

Chen, M. Y., Fulton, L., Huang, I., Liman, A., Hossain, S. S., Hamilton, C. D., Song, S., Geissmann, Q., King, K. C., & Haney, C. H. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1012894 · Cited by 7

Genome-resolved metagenomics from short-read sequencing data in the era of artificial intelligence

Qayyum, H., Ishaq, Z., Ali, A. H., Kayani, M. U. R., & Huang, L. (2025) · Functional & Integrative Genomics · doi:10.1007/s10142-025-01625-x · Cited by 9

First dynamics of bacterial community during development of Acropora humilis larvae in aquaculture

Kullapanich, C., Jandang, S., Palasuk, M., Viyakarn, V., Chavanich, S. A., & Somboonna, N. (2021) · Scientific Reports · doi:10.1038/s41598-021-91379-w · Cited by 8

Microbial Forensics: A Present to Future Perspective on Genomic Targets, Bioinformatic Challenges, and Applications

Shadoff, R., Panoyan, M. A., & Novroski, N. M. M. (2022) · Forensic Genomics · doi:10.1089/forensic.2022.0007 · Cited by 7

Gut microbial ecology of Xenopus tadpoles across life stagesPreprint

Scalvenzi, T., Clavereau, I., Bourge, M., & Pollet, N. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.05.25.110734 · Cited by 7

Metagenomics: a powerful lens viewing the microbial world

Tiwari, N., Bansal, M., & Sharma, J. (2021) · Wastewater Treatment Reactors · doi:10.1016/b978-0-12-823991-9.00007-1 · Cited by 11

The buzz about honey-based biosurveys

Vuong, P., Griffiths, A. P., Barbour, E., & Kaur, P. (2024) · npj Biodiversity · doi:10.1038/s44185-024-00040-y · Cited by 6

Next-Generation Sequencing in Periprosthetic Joint Infections

Kullar, R., Tipton, C. D., File, T. M., Shahi, A., Sniffen, J. C., & Goldstein, E. J. C. (2025) · Infectious Diseases in Clinical Practice · doi:10.1097/ipc.0000000000001448 · Cited by 7

Higher-order microbial interactions revealed by comparative metabolic modeling of synthetic communities with varying species composition

Wang, D., Hunt, K. A., Abrahamson, B., Flinkstrom, Z., Tao, X., Tanner, R. S., León, K. B. D., Zhou, A., Zhou, J. Z., McInerney, M. J., et al. (2025) · ISME Communications · doi:10.1093/ismeco/ycaf142 · Cited by 7

Oral Microbiome in Oral Cancer Research from Sampling to Analysis: Strategies, Challenges, and Recommendations

Liu, K. Y. P., Huang, A., Pepin, C., Shen, Y., Tsang, P., & Poh, C. F.-Y. (2025) · Cancers · doi:10.3390/cancers18010145 · Cited by 6

Multiomics: the intersection of personalized nutrition in cardiometabolic diseases

Çelik, E., Koçyiğit, E., Bingöl, F. G., Karaçolak, C., Cemali, Ö., Simonelli, M., Ağagündüz, D., & Capasso, R. (2026) · Journal of Translational Medicine · doi:10.1186/s12967-026-07836-5 · Cited by 8

Getting off tract: contributions of intraorgan microbiota to cancer in extraintestinal organs

Thomas, S. C., Miller, G., Li, X., & Saxena, D. (2023) · Gut · doi:10.1136/gutjnl-2022-328834 · Cited by 6

Special series on the role of the microbiome in reproduction and fertility

O’Mahony, S. M., & Comizzoli, P. (2023) · Reproduction and Fertility · doi:10.1530/raf-23-0080 · Cited by 6

The lower airway microbiome in paediatric health and chronic disease

Campbell, S., Gerasimidis, K., Milling, S. W. F., Dicker, A., Hansen, R., & Langley, R. (2024) · Paediatric Respiratory Reviews · doi:10.1016/j.prrv.2024.02.001 · Cited by 8

Overview on Multi-omics Research in Microbiome Analysis

Mathuria, A., Ali, N., Mani, I., & Singh, V. (2024) · Springer eBooks · doi:10.1007/978-981-97-1844-3_1 · Cited by 8

Experimental models for peri-implant diseases: a narrative review

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