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

Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation

Cutler, K. J., Stringer, C., Lo, T. W., Rappez, L., Stroustrup, N., Peterson, S. B., Wiggins, P. A., & Mougous, J. D. (2022) · Nature Methods · doi:10.1038/s41592-022-01639-4 · Cited by 389

Human microbiome: an academic update on human body site specific surveillance and its possible role

Dekaboruah, E., Suryavanshi, M. V., Chettri, D., & Verma, A. K. (2020) · Archives of Microbiology · doi:10.1007/s00203-020-01931-x · Cited by 361

Open challenges for microbial network construction and analysis

Faust, K. (2021) · The ISME Journal · doi:10.1038/s41396-021-01027-4 · Cited by 316

Current understanding of the Alzheimer’s disease-associated microbiome and therapeutic strategies

Seo, D.-O., & Holtzman, D. M. (2024) · Experimental & Molecular Medicine · doi:10.1038/s12276-023-01146-2 · Cited by 259

A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data

Yang, C., Chowdhury, D., Zhang, Z., Cheung, W. K., Lü, A., Bian, Z., & Zhang, L. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.11.028 · Cited by 242

Gut microbiota in overweight and obesity: crosstalk with adipose tissue

Cani, P. D., & Hul, M. V. (2023) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-023-00867-z · Cited by 230

Nanopore sequencing and its application to the study of microbial communities

Ciuffreda, L., Rodríguez‐Pérez, H., & Flores, C. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.02.020 · Cited by 209

Maternal exposures and the infant gut microbiome: a systematic review with meta-analysis

Grech, A. M., Collins, C. E., Holmes, A. J., Lal, R., Duncanson, K., Taylor, R., & Gordon, A. (2021) · Gut Microbes · doi:10.1080/19490976.2021.1897210 · Cited by 198

New Insights Into the Cancer–Microbiome–Immune Axis: Decrypting a Decade of Discoveries

Jain, T., Sharma, P., Are, A. C., Vickers, S. M., & Dudeja, V. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.622064 · Cited by 187

Guidelines for preventing and reporting contamination in low-biomass microbiome studies

Fierer, N., Leung, P. M., Lappan, R. J., Eisenhofer, R., Ricci, F., Holland, S. I., Dragone, N. B., Blackall, L. L., Dong, X., Dorador, C., et al. (2025) · Nature Microbiology · doi:10.1038/s41564-025-02035-2 · Cited by 191

Centennial Review: Factors affecting the chicken gastrointestinal microbial composition and their association with gut health and productive performance

Bindari, Y. R., & Gerber, P. F. (2021) · Poultry Science · doi:10.1016/j.psj.2021.101612 · Cited by 162

Advantages and Limitations of 16S rRNA Next-Generation Sequencing for Pathogen Identification in the Diagnostic Microbiology Laboratory: Perspectives from a Middle-Income Country

Rizal, N. S. M., Neoh, H., Ramli, R., Periyasamy, P. R., Hanafiah, A., Samat, M. N. A., Tan, T. L., Wong, K. K., Nathan, S., Chieng, S., et al. (2020) · Diagnostics · doi:10.3390/diagnostics10100816 · Cited by 142

The Association between Vitamin D and Gut Microbiota: A Systematic Review of Human Studies

Bellerba, F., Muzio, V., Gnagnarella, P., Facciotti, F., Chiocca, S., Bossi, P., Cortinovis, D. L., Chiaradonna, F., Serrano, D., Raimondi, S., et al. (2021) · Nutrients · doi:10.3390/nu13103378 · Cited by 137

Understanding dysbiosis and resilience in the human gut microbiome: biomarkers, interventions, and challenges

Safarchi, A., Al-Qadami, G. H., Tran, C. D., & Conlon, M. A. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1559521 · Cited by 145

Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis

Regueira‐Iglesias, A., Balsa‐Castro, C., Blanco‐Pintos, T., & Tomás, I. (2023) · Molecular Oral Microbiology · doi:10.1111/omi.12434 · Cited by 146

Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1–V2 and V3–V4 primer sets

Kameoka, S., Motooka, D., Watanabe, S., Kubo, R., Jung, N., Midorikawa, Y., Shinozaki, N. O., Sawai, Y., Takeda, A., & Nakamura, S. (2021) · BMC Genomics · doi:10.1186/s12864-021-07746-4 · Cited by 124

Machine Learning and Artificial Intelligence in the Multi-Omics Approach to Gut Microbiota

Rozera, T., Pasolli, E., Segata, N., & Ianiro, G. (2025) · Gastroenterology · doi:10.1053/j.gastro.2025.02.035 · Cited by 112

Plant–Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

Nadarajah, K. K., & Rahman, N. S. N. A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms221910388 · Cited by 114

Untapping the potential of plant mycobiomes for applications in agriculture

Pozo, M. J., Zabalgogeazcoa, Í., de Aldana, B. R. V., & Martínez‐Medina, A. (2021) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2021.102034 · Cited by 105

The emerging role of the gut microbiota and its application in inflammatory bowel disease

Xiu, W., Peng, J., Cai, P., Xia, Y., Yi, C., Shang, A., Akanyibah, F. A., & Mao, F. (2024) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2024.117302 · Cited by 117

Advancing Gut Microbiome Research: The Shift from Metagenomics to Multi-Omics and Future Perspectives

Yang, S.-Y., Han, S. M., Lee, J., Kim, K. S., Lee, J. E., & Lee, D. (2025) · Journal of Microbiology and Biotechnology · doi:10.4014/jmb.2412.12001 · Cited by 124

Unraveling the Gut Microbiota: Implications for Precision Nutrition and Personalized Medicine

Abeltino, A., Hatem, D., Serantoni, C., Riente, A., Giulio, M. M. D., Spirito, M. D., Maio, F. D., & Maulucci, G. (2024) · Nutrients · doi:10.3390/nu16223806 · Cited by 121

Data Analytics for Environmental Science and Engineering Research

Gupta, S., Aga, D. S., Pruden, A. J., Zhang, L., & Vikesland, P. J. (2021) · Environmental Science & Technology · doi:10.1021/acs.est.1c01026 · Cited by 100

Differential gut microbiota and intestinal permeability between frail and healthy older adults: A systematic review

Rashidah, N. H., Lim, S. M., Neoh, C. F., Majeed, A. B. A., Tan, M. P., Khor, H. M., Tan, A. H., Rehiman, S. H., & Ramasamy, K. (2022) · Ageing Research Reviews · doi:10.1016/j.arr.2022.101744 · Cited by 100

Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis

Li, S., Lian, W., Han, J.-R., Ali, M., Lin, Z., Liu, Y., Li, L., Zhang, D., Jiang, X., Li, W., et al. (2023) · npj Biofilms and Microbiomes · doi:10.1038/s41522-023-00439-8 · Cited by 95

Current Methods, Common Practices, and Perspectives in Tracking and Monitoring Bioinoculants in Soil

Manfredini, A., Malusà, E., Costa, C., Pallottino, F., Mocali, S., Pinzari, F., & Canfora, L. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.698491 · Cited by 95

Gut microbiota and metabolic biomarkers in metabolic dysfunction–associated steatotic liver disease

Long, Q., Luo, F., Li, B., Li, Z., Guo, Z., Chen, Z., Wu, W., & Hu, M. (2024) · Hepatology Communications · doi:10.1097/hc9.0000000000000310 · Cited by 99

Gut microbiota development across the lifespan: Disease links and health‐promoting interventions

Schoultz, I., Claesson, M. J., Domínguez-Bello, M. G., Hållenius, F. F., Konturek, P. C., Korpela, K., Laursen, M. F., Penders, J., Roager, H. M., Vatanen, T., et al. (2025) · Journal of Internal Medicine · doi:10.1111/joim.20089 · Cited by 108

Experimental temperatures shape host microbiome diversity and composition

Li, J., Bates, K. A., Hoang, K. L., Hector, T. E., Knowles, S. C. L., & King, K. C. (2022) · Global Change Biology · doi:10.1111/gcb.16429 · Cited by 101

The Human Respiratory Microbiome: Current Understandings and Future Directions

Zhao, L., Luo, J., Ali, M. K., Spiekerkoetter, E. F., & Nicolls, M. R. (2022) · American Journal of Respiratory Cell and Molecular Biology · doi:10.1165/rcmb.2022-0208tr · Cited by 96

The microbiome in cancer

Lin, A., Xiong, M., Jiang, A., Huang, L., Wong, H. Z. H., Feng, S., Zhang, C., Yu, H., Chen, L., Chi, H., et al. (2025) · iMeta · doi:10.1002/imt2.70070 · Cited by 99

Recommendations for the use of metagenomics for routine monitoring of antibiotic resistance in wastewater and impacted aquatic environments

Davis, B. C., Brown, C., Gupta, S., Calarco, J., Liguori, K., Milligan, E., Harwood, V. J., Pruden, A. J., & Keenum, I. M. (2023) · Critical Reviews in Environmental Science and Technology · doi:10.1080/10643389.2023.2181620 · Cited by 83

In situ identification of environmental microorganisms with Raman spectroscopy

Cui, D., Kong, L., Wang, Y., Zhu, Y., & Zhang, C. (2022) · Environmental Science and Ecotechnology · doi:10.1016/j.ese.2022.100187 · Cited by 90

Effects of a low FODMAP diet on the colonic microbiome in irritable bowel syndrome: a systematic review with meta-analysis

So, D., Loughman, A., & Staudacher, H. M. (2022) · American Journal of Clinical Nutrition · doi:10.1093/ajcn/nqac176 · Cited by 85

The connection between aging, cellular senescence and gut microbiome alterations: A comprehensive review

Jang, D., Shin, J., Shim, E., Ohtani, N., & Jeon, O. H. (2024) · Aging Cell · doi:10.1111/acel.14315 · Cited by 84

Multi-omics approaches to studying gastrointestinal microbiome in the context of precision medicine and machine learning

Wu, J., Singleton, S. S., Bhuiyan, U., Krammer, L., & Mazumder, R. (2024) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2023.1337373 · Cited by 85

The role of the microbiome in gastrointestinal inflammation

Sanders, D. J., Inniss, S., Sebepos‐Rogers, G., Rahman, F. Z., & Smith, A. M. (2021) · Bioscience Reports · doi:10.1042/bsr20203850 · Cited by 82

Next-Generation Sequencing Supports Targeted Antibiotic Treatment for Culture Negative Orthopedic Infections

Kullar, R., Chisari, E., Snyder, J. W., Cooper, C., Parvizi, J., & Sniffen, J. C. (2022) · Clinical Infectious Diseases · doi:10.1093/cid/ciac733 · Cited by 76

Genome-Scale Metabolic Modeling of the Human Microbiome in the Era of Personalized Medicine

Heinken, A., Basile, A., Hertel, J., Thinnes, C. C., & Thiele, I. (2021) · Annual Review of Microbiology · doi:10.1146/annurev-micro-060221-012134 · Cited by 76

Artificial intelligence and synthetic biology approaches for human gut microbiome

Kumar, P., Sinha, R., & Shukla, P. (2020) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2020.1850415 · Cited by 78

Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy

Liu, L., Wang, Y., Yu, Y., Wang, D., Cheng, S. H., Zheng, C., & Zhang, T. (2021) · Microbiome · doi:10.1186/s40168-021-01155-1 · Cited by 67

coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies

Calle, M. L., Pujolassos, M., & Susín, A. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05205-3 · Cited by 74

Fiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential

Penumutchu, S., Korry, B. J., Hewlett, K. K., & Belenky, P. A. (2023) · Nature Communications · doi:10.1038/s41467-023-40553-x · Cited by 73

A review of gut failure as a cause and consequence of critical illness

Soranno, D. E., Coopersmith, C. M., Brinkworth, J. F., Factora, F. N., Muntean, J. H., Mythen, M. G., Raphael, J., Shaw, A., Vachharajani, V., & Messer, J. S. (2025) · Critical Care · doi:10.1186/s13054-025-05309-7 · Cited by 77

Application of Microbiome in Forensics

Zhang, J., Liu, W., Simayijiang, H., Hu, P., & Yan, J. (2022) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2022.07.007 · Cited by 75

Discovering untapped microbial communities through metagenomics for microplastic remediation: recent advances, challenges, and way forward

Wani, A. K., Akhtar, N., Naqash, N., Rahayu, F., Djajadi, D., Chopra, C., Singh, R., Mulla, S. I., Sher, F., & Américo‐Pinheiro, J. H. P. (2023) · Environmental Science and Pollution Research · doi:10.1007/s11356-023-25192-5 · Cited by 68

A systematic review on the effects of exercise on gut microbial diversity, taxonomic composition, and microbial metabolites: identifying research gaps and future directions

Cullen, J. M. A., Shahzad, S., & Dhillon, J. (2023) · Frontiers in Physiology · doi:10.3389/fphys.2023.1292673 · Cited by 76

Recent advances in bivalve-microbiota interactions for disease prevention in aquaculture

Christine Paillard, A., Gueguen, Y., Wegner, K. M., Bass, D., Pallavicini, A., Vezzulli, L., & Arzul, I. (2021) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2021.07.026 · Cited by 66

Mechanisms, therapeutic implications, and methodological challenges of gut microbiota and cardiovascular diseases: a position paper by the ESC Working Group on Coronary Pathophysiology and Microcirculation

Tousoulis, D., Guzik, T. J., Padró, T., Duncker, D. J., Luca, G. D., Eringa, E. C., Vavlukis, M., Antonopoulos, A. S., Katsimichas, T., Cenko, E., et al. (2022) · Cardiovascular Research · doi:10.1093/cvr/cvac057 · Cited by 67

Bugs as features (part 1): concepts and foundations for the compositional data analysis of the microbiome–gut–brain axis

Bastiaanssen, T. F. S., Quinn, T. P., & Loughman, A. (2023) · Nature Mental Health · doi:10.1038/s44220-023-00148-3 · Cited by 71

The intratumoral microbiome: Characterization methods and functional impact

Heymann, C. J. F., Bard, J., Heymann, M., Heymann, D., & Bobin‐Dubigeon, C. (2021) · Cancer Letters · doi:10.1016/j.canlet.2021.09.009 · Cited by 60

Phage-inclusive profiling of human gut microbiomes with Phanta

Pinto, Y., Chakraborty, M., Jain, N., & Bhatt, A. S. (2023) · Nature Biotechnology · doi:10.1038/s41587-023-01799-4 · Cited by 57

Nanotechnology-driven gene silencing: advancements in SIGS–dsRNA technology for sustainable disease management

Imran, M., Feng, X., Sun, Z., AlOmari, H., Zhang, G., Zhu, J., Aldayel, M. F., & Li, C. (2025) · Chemical and Biological Technologies in Agriculture · doi:10.1186/s40538-025-00738-6 · Cited by 62

Phage therapeutics: from promises to practices and prospectives

Bhargava, K., Nath, G., Bhargava, A., Aseri, G. K., & Jain, N. (2021) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-021-11695-z · Cited by 58

High-throughput qPCR and 16S rRNA gene amplicon sequencing as complementary methods for the investigation of the cheese microbiota

Dreier, M., Meola, M., Berthoud, H., Shani, N., Wechsler, D., & Junier, P. (2022) · BMC Microbiology · doi:10.1186/s12866-022-02451-y · Cited by 58

Type 2 diabetes, gut microbiome, and systems biology: A novel perspective for a new era

Martínez-López, Y. E., Esquivel-Hernandez, D. A., Sánchez-Castañeda, J. P., Neri-Rosario, D., Guardado‐Mendoza, R., & Reséndis-Antonio, O. (2022) · Gut Microbes · doi:10.1080/19490976.2022.2111952 · Cited by 59

Gut Microbiome Analysis for Personalized Nutrition: The State of Science

Simon, M., Sina, C., Ferrario, P. G., Daniel, H., & Working Group “Personalized Nutrition” of the German Nutrition Society (2022) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.202200476 · Cited by 60

Cutting edge tools in the field of soil microbiology

Garg, D., Patel, N. S., Rawat, A., & Rosado, A. S. (2024) · Current Research in Microbial Sciences · doi:10.1016/j.crmicr.2024.100226 · Cited by 56

Role of the duodenal microbiota in functional dyspepsia

Brown, G., Hoedt, E. C., Keely, S., Shah, A., Walker, M. M., Holtmann, G., & Talley, N. J. (2022) · Neurogastroenterology & Motility · doi:10.1111/nmo.14372 · Cited by 58

The Intestinal Microbiota May Be a Potential Theranostic Tool for Personalized Medicine

Domenico, M. D., Ballini, A., Boccellino, M., Scacco, S., Lovero, R., Charitos, I. A., & Santacroce, L. (2022) · Journal of Personalized Medicine · doi:10.3390/jpm12040523 · Cited by 54

Shifts of microbiota during cheese production: Impact on production and quality

Nam, J. H., Cho, Y. S., Rackerby, B., Goddik, L., & Park, S. H. (2021) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-021-11201-5 · Cited by 53

Considerations for mosquito microbiome research from the Mosquito Microbiome Consortium

Dada, N., Jupatanakul, N., Minard, G., Short, S. M., Akorli, J., & Villegas, L. E. M. (2021) · Microbiome · doi:10.1186/s40168-020-00987-7 · Cited by 54

G ut microbiome metagenomics in clinical practice: bridging the gap between research and precision medicine

Tegegne, H. A., & Savidge, T. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2569739 · Cited by 59

Microbiome in Death and Beyond: Current Vistas and Future Trends

Roy, D., Tomo, S., Purohit, P., & Setia, P. (2021) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2021.630397 · Cited by 55

Fecal microbiome profiles of neonatal dairy calves with varying severities of gastrointestinal disease

Slanzon, G. S., Ridenhour, B. J., Moore, D. A., Sischo, W. M., Parrish, L. M., Trombetta, S. C., & McConnel, C. S. (2022) · PLoS ONE · doi:10.1371/journal.pone.0262317 · Cited by 49

Gut Microbiota and Microbial Metabolism in Early Risk of Cardiometabolic Disease

Gabriel, C. L., & Ferguson, J. F. (2023) · Circulation Research · doi:10.1161/circresaha.123.322055 · Cited by 51

HoCoRT: host contamination removal tool

Rumbavicius, I., Rounge, T. B., & Rognes, T. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05492-w · Cited by 46

The power, potential, benefits, and challenges of implementing high-throughput sequencing in food safety systems

Imanian, B., Donaghy, J., Jackson, T. C., Gummalla, S., Ganesan, B., Baker, R. C., Henderson, M., Butler, E. K., Hong, Y., Ring, B., et al. (2022) · npj Science of Food · doi:10.1038/s41538-022-00150-6 · Cited by 46

Unravelling the enigma of the human microbiome: Evolution and selection of sequencing technologies

Xin, Y., Lu, H., Liu, X., He, J., Li, B. J., Wang, Z., Zhao, Y., Zhang, X., & Yu, X. (2023) · Microbial Biotechnology · doi:10.1111/1751-7915.14364 · Cited by 47

Gut microbiota in Alzheimer’s disease: Understanding molecular pathways and potential therapeutic perspectives

Lista, S., Munafò, A., Caraci, F., Imbimbo, C., Emanuele, E., Minoretti, P., Pinto-Fraga, J., Merino-País, M., Crespo‐Escobar, P., López‐Ortiz, S., et al. (2025) · Ageing Research Reviews · doi:10.1016/j.arr.2025.102659 · Cited by 50

Reconstruction of the personal information from human genome reads in gut metagenome sequencing data

Tomofuji, Y., Sonehara, K., Kishikawa, T., Maeda, Y., Ogawa, K., Kawabata, S., Nii, T., Okuno, T., Oguro-Igashira, E., Kinoshita, M., et al. (2023) · Nature Microbiology · doi:10.1038/s41564-023-01381-3 · Cited by 45

Gut microbiome and amyotrophic lateral sclerosis: a systematic review of current evidence

Sun, J., Huang, T., Debelius, J. W., & Fang, F. (2021) · Journal of Internal Medicine · doi:10.1111/joim.13336 · Cited by 43

Metagenomics study in aquatic resource management: Recent trends, applied methodologies and future needs

Behera, B. K., Dehury, B., Rout, A. K., Patra, B., Mantri, N. L., Chakraborty, H. J., Sarkar, D. J., Kaushik, N. K., Bansal, V., Singh, I., et al. (2021) · Gene Reports · doi:10.1016/j.genrep.2021.101372 · Cited by 45

Correlation between Targeted qPCR Assays and Untargeted DNA Shotgun Metagenomic Sequencing for Assessing the Fecal Microbiota in Dogs

Sung, C., Pilla, R., Chen, C.-C., Ishii, P. E., Toresson, L., Allenspach‐Jorn, K., Jergens, A. E., Summers, S., Swanson, K. S., Volk, H. A., et al. (2023) · Animals · doi:10.3390/ani13162597 · Cited by 52

Integrating Omics Technologies for a Comprehensive Understanding of the Microbiome and Its Impact on Cattle Production

Kaur, H., Kaur, G., Gupta, T., Mittal, D., & Ali, S. A. (2023) · Biology · doi:10.3390/biology12091200 · Cited by 47

From hype to hope: Considerations in conducting robust microbiome science

McGuinness, A. J., Stinson, L. F., Snelson, M., Loughman, A., Stringer, A. M., Hannan, A. J., Cowan, C. S. M., Jama, H. A., Caparros-Martin, J. A., West, M. L., et al. (2023) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2023.09.022 · Cited by 44

Evidence for the contribution of the gut microbiome to obesity and its reversal

de Wit, D. F., Hanssen, N. M. J., Wortelboer, K., Herrema, H., Rampanelli, E., & Nieuwdorp, M. (2023) · Science Translational Medicine · doi:10.1126/scitranslmed.adg2773 · Cited by 50

Unlocking the Potential of Metagenomics with the PacBio High-Fidelity Sequencing Technology

Han, Y., He, J., Li, M., Peng, Y., Jiang, H., Zhao, J., Li, Y., & Deng, F. (2024) · Microorganisms · doi:10.3390/microorganisms12122482 · Cited by 43

Vaginal microbiome of women with adenomyosis: A case-control study

Kunaseth, J., Waiyaput, W., Chanchaem, P., Sawaswong, V., Permpech, R., Payungporn, S., & Sophonsritsuk, A. (2022) · PLoS ONE · doi:10.1371/journal.pone.0263283 · Cited by 41

The Microbiome as a Maternal Effect: A Systematic Review on Vertical Transmission of Microbiota

Murphy, K., Le, S. M., Wilson, A. E., & Warner, D. A. (2023) · Integrative and Comparative Biology · doi:10.1093/icb/icad031 · Cited by 40

Cyanobacterial blooms in wastewater treatment facilities: Significance and emerging monitoring strategies

Romanis, C. S., Pearson, L. A., & Neilan, B. A. (2020) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2020.106123 · Cited by 43

Benchmarking genome assembly methods on metagenomic sequencing data

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Application of emerging technologies for gut microbiome research

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