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

An insight into the fecal microbiota composition in Romanian patients with ankylosing spondylitis using high-throughput 16S rRNA gene amplicon sequencing

Oprea, M. M., Cristea, D., Dinu, S., Ciontea, S. A., Bojinca, V. C., Predețeanu, D., Balanescu, A. R., & Usein, C. R. (2022) · Revista română de medicină de laborator · doi:10.2478/rrlm-2022-0004 · Cited by 1

Assessing microbiota composition in the context of aging

Campos-Iglesias, D., Freije, J. M. P., & López-Otı́n, C. (2023) · Methods in cell biology · doi:10.1016/bs.mcb.2022.12.007 · Cited by 1

Microbiomes of native Aotearoa New Zealand animals

Ayriss, N., & Taylor, M. W. (2023) · New Zealand Journal of Ecology · doi:10.20417/nzjecol.47.3518 · Cited by 1

Whole genome sequencing approaches for taxonomic profiling and evaluation of wastewater quality

Behl, S., Kusuma, V., Cardoso, T. H. S., Hamed, A., Almheiri, G., Kazi, S., Shanmugam, B., Brudecki, G. P., Vaylombran, D., Quilez, J., et al. (2024) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2024.107051 · Cited by 1

Applications and importance of metagenomic studies for exploring rhizomicrobiome dynamics

Kour, S., Avatsingh, A. U., Sharma, S., & Singh, N. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-23691-4.00017-8 · Cited by 1

Disentangling the metabolic profile of rumen ciliates: A historical perspective and future directions

Lima, V. D. S., Cedrola, F., Morales, M. J. A., & Solferini, V. N. (2024) · European Journal of Protistology · doi:10.1016/j.ejop.2024.126126 · Cited by 1

Perspectiva biosemiótica del eje microbiota-intestino-cerebro

Méndez-Veras, R. (2025) · Metatheoria – Revista de Filosofía e Historia de la Ciencia · doi:10.48160/18532330me14.362 · Cited by 1

MetaComBin: combining abundances and overlaps for binning metagenomics reads

Tomasella, F., & Pizzi, C. (2025) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2025.1504728 · Cited by 1

Regulating Intratumoral Fungi With Hydrogels: A Novel Approach to Modulating the Tumor Microbiome for Cancer Therapy

Chen, P., Tian, W., Zeng, A., Gu, H., & Zeng, J. (2025) · Cancer Medicine · doi:10.1002/cam4.70900 · Cited by 1

Human DNA hijacking microbiota surveys: causes and consequences in colon related 16s rRNA amplicon sequencing

Gloria, L. D., Casbarra, L., Bastiani, M., Memoli, G., & Ramazzotti, M. (2025) · Gut Microbiome · doi:10.1017/gmb.2025.10012 · Cited by 1

Metagenomics and Its Application in Environmental Monitoring

Panda, A., Rout, S. S., Dey, S., Parida, C. K., Jena, R., Dhar, S., Tiwari, B., Singh, R. K., & SINGH, A. K. (2025) · Springer eBooks · doi:10.1007/978-981-95-0285-1_1 · Cited by 1

Changes in the sinus microbiome in health and chronic rhinosinusitis

Burdon, I. A., & Psaltis, A. J. (2025) · Current Opinion in Otolaryngology & Head & Neck Surgery · doi:10.1097/moo.0000000000001087 · Cited by 1

AI models and metagenomics in crop breeding: Advancing soil and plant microbiome analysis through machine learning and deep learning approaches

Virk, V., Giri, S., & Giri, K. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-33633-1.00016-2 · Cited by 1

Implications of the gut microbiome in spinal cord injuries

Jeyaraman, N., Jeyaraman, M., Dhanabal, P., Ramasubramanian, S., Ambrosio, L., Vadalà, G., & Muthu, S. (2025) · Frontiers in Surgery · doi:10.3389/fsurg.2025.1668225 · Cited by 1

Challenges and Future Perspectives in Microbiota-Based Precision Medicine: Standardization of Profiling Methods, Ethical Considerations and the Potential for Pre-emptive Healthcare

Prajapati, C., Nand, S., Parmar, G. R., & Singh, S. K. (2025) · Interdisciplinary biotechnological advances · doi:10.1007/978-981-95-2104-3_14 · Cited by 1

Genomic insights into plant-microbe interactions

Gehlot, P., Yadav, J., Meena, P., Soni, P., & Jain, T. (2025) · Ecological Genetics and Genomics · doi:10.1016/j.egg.2025.100421 · Cited by 1

Advancement in rhizospheric microbial diversity analysis: an updated perspective

Roy, T., Chaudhary, A., Mishra, A., Arora, S., Kumari, A., & Singh, K. P. (2025) · Journal of Plant Biochemistry and Biotechnology · doi:10.1007/s13562-025-01013-3 · Cited by 1

MeTAline: enabling reproducible and scalable metagenomic analyses

Khannous‐Lleiffe, O., Fuentes, D., Májer, D., & Gabaldón, T. (2025) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqaf158 · Cited by 1

The Bicocca sampling days model: a participatory citizen science approach to environmental microbiome research and education

Ghisleni, G., Armanni, A., Fumagalli, S., Rosatelli, A., Bacchi, Y. M., Barillari, C., Battista, D. A., Benocci, M., Brunelli, A., Cammarano, F., et al. (2025) · ISME Communications · doi:10.1093/ismeco/ycaf220 · Cited by 1

Micronanoplastics induce dysbiosis of intestinal gut microbiota in living beings

García‐Rodríguez, A., Rocabert, A., Hernández, A., & Marcos, R. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-24782-8.00014-5 · Cited by 1

A mathematical framework to correct for compositionality in microbiome data sets

Forry, S. P., Servetas, S. L., Kralj, J. G., Hunter, M. E., Dootz, J. N., & Jackson, S. A. (2026) · Applied and Environmental Microbiology · doi:10.1128/aem.01126-25 · Cited by 1

Methodological Insights Into Gut Microbiome Profiling: A Comprehensive Review with Emphasis on Bipolar Disorder and Major Depressive Disorder

Zol, N. M. C., Hasain, Z., Shakrin, N. N. S. M., Jati, A. K. K., Chong, C. W., Loganathan, A. L., Lim, S. Y., Ling, F. Y., Mahmud, A. A., Bon, R. S., et al. (2025) · Malaysian Journal of Medicine and Health Sciences · doi:10.47836/mjmhs.v21.i6.1359 · Cited by 1

The Airway Microbiome in Chronic Obstructive Pulmonary Disease (COPD): A Guide for Clinicians

Koo, W. L. Y., Thng, K. X., Tiew, P. Y., & Chotirmall, S. H. (2026) · British Journal of Hospital Medicine · doi:10.31083/bjhm50163 · Cited by 1

Inference of drowning sites of cases in the Pearl river based on microbial community profiling and random forest algorithm

Zhang, X., Su, Q., Chen, X., Wang, S., Du, J., Chen, L., Xu, Q., Liu, C., & Zhao, J. (2026) · International Journal of Legal Medicine · doi:10.1007/s00414-026-03740-1 · Cited by 1

Towards standardization in pig microbiome research based on a comprehensive twenty-year review

Enokela, S. O., Yergaliyev, T., Flisikowski, K., Hornburg, S. C., Reyer, H., Tetens, J., Wimmers, K., Zentek, J., & Camarinha-Silva, A. (2026) · Animal Microbiome · doi:10.1186/s42523-026-00541-0 · Cited by 1

Deciphering genotype and geography dependent microbiome composition and its role in disease suppression in Ashwagandha

Bagul, S. Y., Shreedevasena, S., Saran, P. L., Khadke, G. N., & Das, M. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1786817 · Cited by 1

Comparative Analysis of the Intestinal Microbiota in Wild and Aquaculture Populations of Sparus aurata

Lanara, M., Asimakis, E. D., Mokhtar, N. B., Koutsodima, P., Batargias, C., Toskas, K., Stathopoulou, P. M., & Tsiamis, G. (2026) · Microorganisms · doi:10.3390/microorganisms14030708 · Cited by 1

Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida

King, Z., Buckley, H. L., Lear, G., Seale, R. B., Lee, K. C. Y., Schwendenmann, L., & Lacap‐Bugler, D. C. (2026) · Environmental Microbiology Reports · doi:10.1111/1758-2229.70324 · Cited by 1

Gut microbiome in sepsis: from dysbiotic biomarker to precision and palliative decision-making

Wang, L.-M., Chen, C., Danzheng, J., & Zhao, J. (2026) · Frontiers in Medicine · doi:10.3389/fmed.2026.1811304 · Cited by 1

Exploring the Tenebrio molitor gut microbiota response to LDPE and PET: putative genetic indicators and methodological insights

Biełło, K., Rodríguez-Caballero, G., Becerra-Mora, D., Dorado-Blanco, N., Sáez-Melero, L. P., Moreno‐Vivián, C., Luque‐Almagro, V. M., Olaya‐Abril, A., & Roldán, M. D. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1746922 · Cited by 1

Bioinformatics roadmap for characterizing the gut microbiome to study its interactions and associations with the gut mucosal immune system

Anwar, M. Z., Prieto, M. D., & Hsiao, W. (2026) · Mucosal Immunology · doi:10.1016/j.mucimm.2026.100375 · Cited by 1

Mechanisms of Gut Microbiota-Derived Metabolites in Treating Hyperuricemia: Natural Products as Interventions

Gu, W., Liu, J., Choi, J. B., Alim, K., Ma, S., Dawuti, D., Xu, Y., & Xu, H. (2026) · Molecules · doi:10.3390/molecules31142421 · Cited by 1

Bioinformatic tools for microbiome analysis: from raw sequences to biological insights

Poelzer, J., & Wishart David, S. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1913362 · Cited by 1

Lichen research in the omics era: a lens into the archetypal symbiosis

Cameron, E. S., & Tagirdzhanova, G. M. (2026) · The Lichenologist · doi:10.1017/s0024282926101571 · Cited by 1

CONSULT-II: Taxonomic Identification Using Locality Sensitive Hashing

Şapcı, A. O. B., Rachtman, E., & Mirarab, S. (2023) · Lecture notes in computer science · doi:10.1007/978-3-031-36911-7_13 · Cited by 1

Challenges and priorities for researching the gut microbiota in individuals living with anorexia nervosa

West, M. L., HART, S. G. E., Loughman, A., Jacka, F. N., Staudacher, H. M., Abbaspour, A., Phillipou, A., Ruusunen, A. A., & Rocks, T. (2023) · International Journal of Eating Disorders · doi:10.1002/eat.24033 · Cited by 1

Tryptophan catabolites and predicted gut flora enzyme-encoding genes

Shatova, O. P., Михайлович, Г. А., Grigoryeva, T. V., Vasilyev, I., Столетова, Л. С., Makarov, V., Yudin, S. M., Roumiantsev, S. A., & Shestopalov, A. (2023) · Bulletin of Russian State Medical University · doi:10.24075/brsmu.2023.027 · Cited by 1

Ready Reckoner for Using Bioinformatics Tools in Fish and Shellfish Microbiome Analysis

Gollapalli, P., Prithvisagar, K. S., & Kumar, B. K. (2023) · Springer eBooks · doi:10.1007/978-981-99-0852-3_5 · Cited by 1

Characterizing living ocular bacterial communities and the effects of antibiotic perturbation in house finches

Weitzman, C. L., Hawley, D. M., Rostama, B., May, M. A., & Belden, L. K. (2024) · MicrobiologyOpen · doi:10.1002/mbo3.1398 · Cited by 1

Deciphering the Microbial Dark Matter Using Metagenome-Assembled Genomes, Culturomics, and Seqcode

Sood, U., Hira, P., Garg, G., Lal, R., & Shakarad, M. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-13320-6.00004-4 · Cited by 1

DESENVOLVIMENTO DE BANCOS DE DADOS PARA ANÁLISE METAGENÔMICA DE MICROBIOMAS DE CÃES: UMA ABORDAGEM COM KRAKEN2 E BOWTIE2

Takao, P. S., MOURA, J. F., Corrêa, P. S., Barbosa, D. A., & Menegídio, F. B. (2024) · Congresso Brasileiro de Biotecnologia On-line · doi:10.51189/conbiotec2024/33826 · Cited by 1

Procedures for sampling of small and larger samples of microbiome

Adetunji, J. B., Michael, O. S., Adetunji, C. O., Ajayi, O. O., & Ogundolie, F. A. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-91190-0.00003-5 · Cited by 1

Don’t let valuable microbiome data go to waste: combined usage of merging and direct-joining of sequencing reads for low-quality paired-end amplicon data

Ramakodi, M. P. (2024) · Biotechnology Letters · doi:10.1007/s10529-024-03509-9 · Cited by 1

Metagenomics Insight Into Microbial Community Analysis During Pesticide Degradation: State of the Art, Success Stories, Challenges, and Future Outlook

Singh, S., & Shyu, D. J. H. (2024) · Royal Society of Chemistry eBooks · doi:10.1039/bk9781837673131-00481 · Cited by 1

Assessing the impact of triiodothyronine treatment on the lung microbiome of mice with pulmonary fibrosis

Guo, X., Xu, K., Wang, Q., Han, Z., & Yu, G. (2024) · BMC Pulmonary Medicine · doi:10.1186/s12890-024-03214-3 · Cited by 2

The treatment naïve microbiome of pediatric ulcerative colitis and microbial therapeutics: A humbling challenge

Kellermayer, R. (2024) · Saudi Journal of Gastroenterology · doi:10.4103/sjg.sjg_360_24 · Cited by 1

Data science to biologists: Insights into microbiomics

Meenatchi, R., Hassan, S., Priya, P. S., Karamveer, K., Prathiviraj, R., Guru, A., & Arockiaraj, J. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-91631-8.00017-2 · Cited by 1

Evaluating Various Methods Used by Direct-to-Consumer Products Promising Personalized Nutrition

Gimpfl, S., Steinle, K., & Gedrich, K. (2024) · Dietetics · doi:10.3390/dietetics3040036 · Cited by 1

Overview of microbiota gut-brain-axis

Sharma, R., Anitha, K., Mishra, N., & Kumar, A. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-21680-0.00001-8 · Cited by 1

Archaeological dental calculus: A rich bioarchive for exploring Classical Antiquity through ancient DNA methods

Wright, S. (2025) · Journal of Archaeological Science Reports · doi:10.1016/j.jasrep.2025.105038 · Cited by 1

A review on the isolation techniques and functional role of microbial endophytes from medicinal plants of India

Pednekar, S. G., & Baing, B. S. (2025) · International Journal of Plant Pathology and Microbiology · doi:10.22271/27893065.2025.v5.i1b.122 · Cited by 1

Concordance between upper and lower airway microbiota in children with cystic fibrosis

Nassirnia, S., Scherz, V., Greub, G., Caruana, G., Taffé, P., Jaton, K., Papis, S., Posfay-Barbe, K. M., Mornand, A., Rochat, I., et al. (2025) · Journal of Medical Microbiology · doi:10.1099/jmm.0.002079 · Cited by 1

Influence of sequencing depth on bacterial classification and abundance in bacterial communitiesPreprint

Sánchez, F., Jiménez, F. A., & Tenorio, A. M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.04.474922 · Cited by 1

Microbiomes of Clownfish and Their Symbiotic Host Anemone Converge Before Their First Physical Contact.Preprint

Audet‐Gilbert, É., Sylvain, F., Bouslama, S., & Derôme, N. (2021) · doi:10.21203/rs.3.rs-179538/v1 · Cited by 1

Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systemsPreprint

Rieder, J., Kapopoulou, A., Bank, C., & Adrian‐Kalchhauser, I. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.05.498813 · Cited by 1

A graph-based Gaussian Mixture Variational Autoencoder improves metagenome binning for short contigsPreprint

Zhang, L., Zhang, Z., Rao, M., & Huang, Y. (2023) · Research Square · doi:10.21203/rs.3.rs-3308172/v1 · Cited by 1

Neural differential equations enable early-stage prediction of preterm birth using vaginal microbiotaPreprint

Karambelkar, K., & Baranwal, M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.22.558954 · Cited by 1

CompleteBin: A transformer-based framework unlocks microbial dark matter through improved short contig binningPreprint

bohao, Z. O. U., Zhang, Z., Wang, X., Tao, R., Gu, N., Kristiansen, K., Li, S., Zhang, L., & Zhang, L. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.20.649691 · Cited by 2

Deep Learning Transforms Phage-Host Interaction Discovery from Metagenomic DataPreprint

Yang, Y., Wang, T., Huang, D., Wang, X., Weiss, S. T., Korzenik, J. R., & Liu, Y. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.26.656232 · Cited by 2

Bedeutung des Mikrobioms für Adipositas und Glukosestoffwechsel

Ecker, M., & Haller, D. (2021) · Der Diabetologe · doi:10.1007/s11428-021-00735-x

Correcting for Background Noise Improves Phenotype Prediction from Human Gut Microbiome DataPreprint

Briscoe, L., Balliu, B., Sankararaman, S., Halperin, E., & Garud, N. R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.19.436199

Strengthening Healthy Saudi-habits Using Ajwain (Trachyspermum ammi) Seeds by In-Vivo Experiment on Digestive-system Bacterial-quantity at High-level Region

Sabra, S. M. M., Al-Gehani, S. A. H., & Alotaibi, F. A. (2021) · Biomedical Research and Clinical Reviews · doi:10.31579/2692-9406/069

The Differences of Prokaryotic Pan-genome Analysis on Complete Genomes and Simulated Metagenome-Assembled Genomes

Tang, L. (2021) · Lincoln (University of Nebraska)

Soil Microbial Metagenomics in Agroforestry System: Tools and Techniques

Bharati, A., Anuragi, H., Rajarajan, K., Handa, A. K., & Arunachalam, A. (2022) · Springer eBooks · doi:10.1007/978-981-16-6005-4_8

Bacterial Colonization in COPD

Donnelly, L. (2021) · Elsevier eBooks · doi:10.1016/b978-0-08-102723-3.00242-0

Microbiomes of Clownfish and Their Symbiotic Host Anemone Converge Before Their First Physical Contact.Preprint

Audet‐Gilbert, É., Sylvain, F., Bouslama, S., & Derôme, N. (2021) · Research Square · doi:10.21203/rs.3.rs-25472/v3

Microbiomes of Clownfish and Their Symbiotic Host Anemone Converge Before Their First Physical ContactPreprint

Audet‐Gilbert, É., Sylvain, F., Bouslama, S., & Derôme, N. (2021) · Research Square · doi:10.21203/rs.3.rs-25472/v4

Microbiomes of clownfish and their symbiotic host anemone converge before their first physical contactPreprint

Audet‐Gilbert, É., Sylvain, F., Bouslama, S., & Derôme, N. (2020) · Research Square · doi:10.21203/rs.3.rs-25472/v2

Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systemsPreprint

Rieder, J., Kapopoulou, A., Bank, C., & Adrian‐Kalchhauser, I. (2022) · Research Square · doi:10.21203/rs.3.rs-1815876/v1

Bedeutung des Mikrobioms für Adipositas und Glukosestoffwechsel

Ecker, M., & Haller, D. (2022) · Gynäkologische Endokrinologie · doi:10.1007/s10304-022-00467-1

Pairwise ratio-based differential abundance analysis of infant microbiome 16S sequencing data

Mildau, K., Beest, D. E. T., ENGEL, B., Gort, G., Lambert, J. M., Willemsen‐Swinkels, S. H. N., & van Eeuwijk, F. A. (2023) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqad001

Plant Mycobiome in Sustainable Agriculture

Idbella, M., Mazzoleni, S., & Bonanomi, G. (2023) · Springer eBooks · doi:10.1007/978-3-031-28307-9_5

Selection of Biosurfactant‐Producing Microorganisms

Bonilla, J., Romero, L. G., & Coronel-León, J. (2023) · doi:10.1002/9781119854395.ch2

Amplicon Sequencing Pipelines in Metagenomics

Wang, D. (2023) · Methods in molecular biology · doi:10.1007/978-1-0716-3072-3_4

Disentangling ecological networks in marine microbes

Deutschmann, I. M. (2021) · UPCommons institutional repository (Universitat Politècnica de Catalunya) · doi:10.5821/dissertation-2117-369389 · Cited by 1

Avaliação dos efeitos de crescentes teores de ingestão de β- glucanos sobre parâmetros digestivos, imunológicos e microbiota de cães adultos

Marchi, P. H. (2023) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/d.10.2023.tde-27042023-091707

Gut Microbiome: Perspectives and Challenges in Human Health

Salaria, N., Neeraj, Furhan, J., & Kumar, R. (2023) · Springer eBooks · doi:10.1007/978-981-99-3126-2_3

Association of Plants and Microbes: Past, Present and Future

Akhtar, W., Fatima, I., Yasmin, A., Safdar, N., & Khan, Z. (2023) · BENTHAM SCIENCE PUBLISHERS eBooks · doi:10.2174/9789815136838123010004

Identification of mucosal microbiome-host gene interactions in ulcerative colitis patientsPreprint

Kim, N., Gim, J., Lee, B. J., Choi, B. I., Yoon, H. S., Kim, W. S., Kim, S. H., Joo, M. K., & Park, J. (2024) · Research Square · doi:10.21203/rs.3.rs-3936546/v1

The gut microbiome in the onset and progression of Inflammatory Bowel Diseases

Klaassen, M. A. Y. (2024) · University of Groningen research database (University of Groningen / Centre for Information Technology) · doi:10.33612/diss.909058157

Agricultural management effects on root-associated microbiome assemblage and implications for soil and plant health

Lee, C. (2021) · doi:10.31274/td-20240329-48

Additional file 1 of Metagenomic comparison of the faecal and environmental resistome on Irish commercial pig farms with and without zinc oxide and antimicrobial usage

Ekhlas, D., Cobo-Díaz, J. F., Cabrera‐Rubio, R., Alexa, E. A., Sanjuán, J. M. O., Manzanilla, E. G., Crispie, F., Cotter, P. D., Leonard, F. C., Argüello, H., et al. (2023) · Figshare · doi:10.6084/m9.figshare.24792222

Additional file 1 of PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data

Hu, X., Hurtado‐Gonzales, O. P., Adhikari, B. N., French-Monar, R. D., Malapi‐Wight, M., Foster, J. A., & McFarland, C. (2023) · Figshare · doi:10.6084/m9.figshare.24804211

Analysis of Gill and Skin Microbiota in Larimichthys Crocea Reveals Bacteria Associated with Cryptocaryonosis Resistance PotentialPreprint

Zhu, S., Sun, K., Liu, A., Miao, R., Yin, F., & Xie, X. (2024) · SSRN Electronic Journal · doi:10.2139/ssrn.4803803

Metagenomics or Metataxonomics: Best Practice Methods to Uncover the Sinus MicrobiomePreprint

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