The need for an integrated multi-OMICs approach in microbiome science in the food system

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

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BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

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Plant–microbiome interactions: from community assembly to plant health

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Gut microbiota, metabolites and host immunity

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Metabolite profiles and the risk of developing diabetes

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Role of the normal gut microbiota

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A communal catalogue reveals Earth's multiscale microbial diversity

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Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

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Microbiome definition re-visited: old concepts and new challenges

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The importance of the microbiome of the plant holobiont

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Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

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Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data

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Wisdom of crowds for robust gene network inference

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A review on the plant microbiome: Ecology, functions, and emerging trends in microbial application

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Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota

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Rhizosphere microbiome assemblage is affected by plant development

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Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

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Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

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Non-lethal Inhibition of Gut Microbial Trimethylamine Production for the Treatment of Atherosclerosis

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Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

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Linking Plant Secondary Metabolites and Plant Microbiomes: A Review

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Systems biology and multi-omics integration: viewpoints from the metabolomics research community

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Molecular phenomics and metagenomics of hepatic steatosis in non-diabetic obese women

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Gut microbiota profiling of pediatric nonalcoholic fatty liver disease and obese patients unveiled by an integrated meta-omics-based approach

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Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria

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Plant–microbiome interactions under a changing world: responses, consequences and perspectives

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Qiita: rapid, web-enabled microbiome meta-analysis

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Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

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Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

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Intestine farnesoid X receptor agonist and the gut microbiota activate G‐protein bile acid receptor‐1 signaling to improve metabolism

Pathak, P., Xie, C., Nichols, R. G., Ferrell, J. M., Boehme, S., Krausz, K. W., Patterson, A. D., Gonzalez, F. J., & Chiang, J. Y. L. (2018) · Hepatology · doi:10.1002/hep.29857 · Cited by 567 · see citing works

A human gut bacterial genome and culture collection for improved metagenomic analyses

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Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella Pneumoniae

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Multi-omics of permafrost, active layer and thermokarst bog soil microbiomes

Hultman, J., Waldrop, M. P., Mackelprang, R., David, M. M., McFarland, J. W., Blazewicz, S. J., Harden, J. W., Turetsky, M. R., McGuire, A. D., Shah, M. B., et al. (2015) · Nature · doi:10.1038/nature14238 · Cited by 547 · see citing works

Drought Stress Results in a Compartment-Specific Restructuring of the Rice Root-Associated Microbiomes

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Let the Core Microbiota Be Functional

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The soil microbiome — from metagenomics to metaphenomics

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Genome-wide association study of Arabidopsis thaliana leaf microbial community

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A metabolomics pipeline for the mechanistic interrogation of the gut microbiome

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Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

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Enabling sustainable agriculture through understanding and enhancement of microbiomes

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Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage

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Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data

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Hypothesis Testing and Power Calculations for Taxonomic-Based Human Microbiome Data

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From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency

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Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online

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Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils

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Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

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Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure

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A parts list for fungal cellulosomes revealed by comparative genomics

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Bacterial ClpB heat-shock protein, an antigen-mimetic of the anorexigenic peptide α-MSH, at the origin of eating disorders

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“Guilt by Association” Is the Exception Rather Than the Rule in Gene Networks

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The effects of soil phosphorus content on plant microbiota are driven by the plant phosphate starvation response

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Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil

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EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies

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Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate.

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Does Soil Contribute to the Human Gut Microbiome?

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The Chemistry of Stress: Understanding the ‘Cry for Help’ of Plant Roots

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Overcoming barriers to early disease intervention

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Specific modulation of the root immune system by a community of commensal bacteria

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Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities

Jiang, D., Armour, C. R., Hu, C., Meng, M., Tian, C., Sharpton, T. J., & Jiang, Y. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00995 · Cited by 164 · see citing works

Recent Past, Present, and Future of the Food Microbiome

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Causes and consequences of a conserved bacterial root microbiome response to drought stress

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Metabolic Influences of Gut Microbiota Dysbiosis on Inflammatory Bowel Disease

Sultan, S., El‐Mowafy, M., Elgaml, A., Ahmed, T. A., Hassan, H., & Mottawea, W. (2021) · Frontiers in Physiology · doi:10.3389/fphys.2021.715506 · Cited by 161 · see citing works

Quantitative Genetics of the Maize Leaf Microbiome

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Gut Microbiota Modulation on Intestinal Mucosal Adaptive Immunity

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Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes

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Causal integration of multi‐omics data with prior knowledge to generate mechanistic hypotheses

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Inferring Interaction Networks From Multi-Omics Data

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Overview of a Surface-Ripened Cheese Community Functioning by Meta-Omics Analyses

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Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota

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The microbiota of dairy milk: A review

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The impact of sequence database choice on metaproteomic results in gut microbiota studies

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Multi ‘omic data integration: A review of concepts, considerations, and approaches

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Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a Novel Oenococcus Species

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Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil

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The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach

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Unveiling the Mechanisms for the Plant Volatile Organic Compound Linalool To Control Gray Mold on Strawberry Fruits

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Metatranscriptome analysis of fungal strains Penicillium camemberti and Geotrichum candidumreveal cheese matrix breakdown and potential development of sensory properties of ripened Camembert-type cheese

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Composition and Metabolic Functions of the Microbiome in Fermented Grain during Light-Flavor Baijiu Fermentation

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Healthy soils for healthy plants for healthy humans

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Elucidating the role of the gut microbiota in the physiological effects of dietary fiber

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How drought and salinity affect arbuscular mycorrhizal symbiosis and strigolactone biosynthesis?

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Metabolic profile of main organic acids and its regulatory mechanism in solid-state fermentation of Chinese cereal vinegar

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Mesophilic Sporeformers Identified in Whey Powder by Using Shotgun Metagenomic Sequencing

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Multi-omic data integration in food science and analysis

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Unveiling the metabolic heterogeneity and formation mechanism in Chinese typical Daqu based on Qu-omics

Mu, Y., Yao, S., Huang, Y., Zhu, Z., Li, D., Song, Y., Liu, Z., Zhang, C., & Yu, S. (2025) · Food Research International · doi:10.1016/j.foodres.2025.115735 · Cited by 27 · see citing works

Adaptation of bacterial starter cultures from dairy to plant-based substrates: challenges and opportunities

Lavelle, K., Mahony, J., & van Sinderen, D. (2025) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2025.111304 · Cited by 20 · see citing works

Machine learning-powered multi-omics for food microbiology and smarter food safety

Bansal, S., Rodriguez, C. Z., Thompson‐Witrick, K. A., Wang, Y., Taft, D. H., & Zhang, B. (2025) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2025.105145 · Cited by 21 · see citing works

Roadmap for the integration of environmental microbiomes in risk assessments under EFSA's remit

Debode, F., Caulier, S., Demeter, S., Dubois, B., Gelhay, V., Hulin, J., Muhovski, Y., Ninane, V., Rousseau, G., & Bragard, C. (2024) · EFSA Supporting Publications · doi:10.2903/sp.efsa.2024.en-8602 · Cited by 22 · see citing works

Harnessing nanotechnology for abiotic stress mitigation in agriculture: a sustainable approach to crop resilience

Jassim, A. Y., Karnwal, A., Pant, G., Gaur, A., Selvaraj, M., Dutta, J., Sachan, R. S. K., Kumar, M., & Nesterova, N. (2025) · Journal of Plant Interactions · doi:10.1080/17429145.2025.2586338 · Cited by 18 · see citing works

Next-generation sequencing applications in food science: fundamentals and recent advances

Tigrero-Vaca, J., Díaz, B., Gu, G., & Cevallos‐Cevallos, J. M. (2025) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2025.1638957 · Cited by 16 · see citing works

Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry

Wang, A. Y., Fekete, E. E. F., Creskey, M., Cheng, K., Ning, Z., Pfeifle, A., Li, X., Figeys, D., & Zhang, X. (2024) · Microbiome Research Reports · doi:10.20517/mrr.2024.21 · Cited by 16 · see citing works

Climate Cattle

Searle, A., Turnbull, J., & Oliver, C. (2024) · Environmental Humanities · doi:10.1215/22011919-11327348 · Cited by 16 · see citing works

gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes

Arıkan, M., & Muth, T. (2024) · GigaScience · doi:10.1093/gigascience/giae038 · Cited by 14 · see citing works

Exploring sub-species variation in food microbiomes: a roadmap to reveal hidden diversity and functional potential

Flörl, L., Meyer, A., & Bokulich, N. A. (2025) · Applied and Environmental Microbiology · doi:10.1128/aem.00524-25 · Cited by 15 · see citing works

Synthetic microbiomes in bioengineered rhizospheres: new frontiers for climate-resilient agriculture

Adhikary, K., Selim, S., Sarkar, R., Ganguly, K., Das, J., Almuhayawi, M. S., Alruhaili, M. H., Gattan, H. S., & Karak, P. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1780132 · Cited by 15 · see citing works

Microbial pathways of nitrous oxide emissions and mitigation approaches in drylands

Shaaban, M. (2024) · Journal of Environmental Management · doi:10.1016/j.jenvman.2024.120393 · Cited by 15 · see citing works

Understanding the interconnected roles of gut microbiota and metabolomic profiles in alcoholic liver disease pathophysiology and their potential for innovative treatment strategies

Balakrishnan, J., Kannan, S., Arivazhagan, G., Ramachandran, N., & Sundarasamy, V. G. (2025) · Medicine in Microecology · doi:10.1016/j.medmic.2025.100154 · Cited by 14 · see citing works

Microbial communities and their role in enhancing hemp fiber quality through field retting

Orm, E. B., Bergeret, A., & Malhautier, L. (2024) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-024-13323-y · Cited by 14 · see citing works

The Role of Proteomics in Identification of Key Proteins of Bacterial Cells with Focus on Probiotic Bacteria

Št́astná, M. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25168564 · Cited by 14 · see citing works

Harmony Within: Unravelling the Microbiome–Immune System Symbiosis for Health

Suchiita, A., Gupta, N., Nandi, K., Sonkar, S. C., & Chandra, L. (2025) · Advanced Gut & Microbiome Research · doi:10.1155/agm3/9927379 · Cited by 13 · see citing works

Host-microbe interactions at barrier tissues and immunomodulation: a scoping review

Chigozie, V. U., Enyi, E. O., Akwari, A. A., & Esimone, C. O. (2025) · Discover Bacteria. · doi:10.1007/s44351-025-00037-3 · Cited by 12 · see citing works

Omics approaches to aflatoxin contaminations in the agri-food supply chain: A comprehensive review of current advances, challenges, and future potential

Yohannis, E., Teka, T. A., Urugo, M. M., Tola, Y. B., & Getachew, P. (2025) · Applied Food Research · doi:10.1016/j.afres.2025.101394 · Cited by 10 · see citing works

Smart technologies enhance detection, monitoring, and traceability in global food safety

Kirubakaran, D., Meer, M. S., Jayakodi, S., Baskar, B., Latha, S., Bupesh, G., Murugeswaran, R., Rajkumar, M., Anbazhagan, G. K., Visvanathan, P., et al. (2025) · Discover Food · doi:10.1007/s44187-025-00716-9 · Cited by 9 · see citing works

Harnessing agri-food system microbiomes for sustainability and human health

Fernández-Gómez, P., Leong, D., Berg, G., Brennan, F., Caruso, T., Charles, T. C., Cocolin, L., Lange, L., McAuliffe, O. E., Maguin, E., et al. (2025) · Frontiers in Science · doi:10.3389/fsci.2025.1575468 · Cited by 8 · see citing works

Artificial intelligence in predicting personalized nanocarrier formulations for herbal drugs: Bridging phytomedicine and precision nanotechnology

Sridhar, D., Manikandan, R., Dhanapal, Y., Khute, S., & Subash, P. (2025) · Intelligent Pharmacy · doi:10.1016/j.ipha.2025.08.001 · Cited by 8 · see citing works

Probiotics, Prebiotics and Synbiotics for Combating Antimicrobial Resistance in the Food Chain

Vesković-Moračanin, S. M., Danilović, B., Milijašević, M., Milijašević, J. B., Tambur, Z., & Moračanin, M. (2025) · Processes · doi:10.3390/pr13113483 · Cited by 9 · see citing works

Data-Driven Machine Learning and Deep Learning Approaches as Practical AI Models in Predictive Food Microbiology

Ilıkkan, Ö. K., Bağdat, E. Ş., Karuppuchamy, V., & Özoğul, F. (2026) · Food Reviews International · doi:10.1080/87559129.2025.2612244 · Cited by 9 · see citing works

Microbiota of foods: a comprehensive review of diversity and potential implications

Silva, F. A., Cabral, L., de Assis, B. B. T., Ferreira, D. P., Egea, M. B., Pimentel, T. C., & Magnani, M. (2026) · Food Research International · doi:10.1016/j.foodres.2026.118899 · Cited by 8 · see citing works

Harnessing Microbial Power for a Sustainable Future Food System

Bîrgovan, A. L., Lakatos, E. S., Cioca, L., Paul, N. L., Vâtcă, S. D., Kis, E., & Păcurariu, R. L. (2025) · Microorganisms · doi:10.3390/microorganisms13092217 · Cited by 8 · see citing works

Standardizing microbiome research: interlaboratory validation of SOPs for sample preparation and DNA extraction from food and environmental ecosystems

Ferrocino, I., Ferrara, M., Garello, M., Turchetti, B., Andreolli, M., Arena, M. P., Alduina, R., Aloi, F., Bevivino, A., Bruno, E., et al. (2025) · Environmental Microbiome · doi:10.1186/s40793-025-00833-z · Cited by 7 · see citing works

Food systems microbiome‐related educational needs

Olmo, R., Wetzels, S. U., Berg, G., Cocolin, L., Hartmann, M., Hugas, M., Kostić, T., Rattei, T., Ruthsatz, M., Rybakova, D., et al. (2023) · Microbial Biotechnology · doi:10.1111/1751-7915.14263 · Cited by 6 · see citing works

Database selection for shotgun metaproteomic of low-diversity dairy microbiomes

Duarte, V. D. S., Moreira, L. D. P. D., Skeie, S. B., Svalestad, F., Øyaas, J., & Porcellato, D. (2024) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2024.110706 · Cited by 7 · see citing works

Construction of Protein Sequence Databases for Metaproteomics: A Review of the Current Tools and Databases

Arıkan, M., & Atabay, B. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00665 · Cited by 6 · see citing works

The hidden diversity of food microbiomes

Pasolli, E., & Ercolini, D. (2025) · Current Opinion in Food Science · doi:10.1016/j.cofs.2025.101318 · Cited by 6 · see citing works

Innovative Systems Biology in Baijiu Fermentation: Unveiling Omics Landscapes and Microbial Synergy

Song, D., Song, L., Luo, Y., Chen, J., Zhang, C., & Yang, L. X. (2026) · Foods · doi:10.3390/foods15050871 · Cited by 6 · see citing works

Bridging Tradition and Innovation: A Systematic Review and Bibliometric Analysis of Turkish Fermented Foods

Ilıkkan, Ö. K., Bağdat, E. Ş., Yılmaz, R., Çeti̇n, B., Çon, A. H., Erten, H., Göksungur, Y., & Şimşek, Ö. (2025) · Foods · doi:10.3390/foods14244324 · Cited by 5 · see citing works

Omics‐Driven Insights Into Soil Microbial Diversity and Phytopathogen Interactions for Sustainable Agriculture and Food Security

Parveen, S., Shafi, Z., Shahid, M., Iqbal, M. Z., Naznine, F., & Ansari, M. I. (2026) · Journal of Basic Microbiology · doi:10.1002/jobm.70155 · Cited by 5 · see citing works

Opportunities of digital twin in controlling and monitoring microbial processes in food fermentation

Shukla, K., Nagpal, S., & Vyas, A. (2026) · Systems Microbiology and Biomanufacturing · doi:10.1007/s43393-026-00454-8 · Cited by 5 · see citing works

Unveiling the Ocean's Arsenal: Successful Integration of Marine Metabolites into Disease Management

Singh, A. P., Saxena, R., Saxena, S., & Maurya, N. K. (2024) · UTTAR PRADESH JOURNAL OF ZOOLOGY · doi:10.56557/upjoz/2024/v45i134146 · Cited by 5 · see citing works

Application of Saccharomyces cerevisiae var. boulardii for Biological Detoxification of Chemical Contaminants in Foods: A Comprehensive Review

Pereira, K. N., de Oliveira, A. C. D., de Souza, H. F., Ullah, S., Nasir, U., Ali, S., & de Oliveira, C. A. F. (2025) · Foods · doi:10.3390/foods14244260 · Cited by 4 · see citing works

Research Progress in Multi-Omics Analysis of Dairy Products: Nutritional Quality, Safety Evaluation, and Health Functions

Xu, M., Ma, B., Zhu, K., Tu, W., Li, C. B., Hao, P., & Zhang, M. (2026) · Foods · doi:10.3390/foods15132389 · Cited by 4 · see citing works

Machine learning in applied microbiology, from data quality to model validation and implementation

Barcan, R. A., Carradori, S., Samsing, F., Nguyen, N., He, L., Wang, Y., & Barcan, A. S. (2026) · Microbiological Research · doi:10.1016/j.micres.2026.128588 · Cited by 4 · see citing works

Mechanistic and hormetic insights into the interaction between dietary bioactive compounds and gut microbiota in modulating human health

Elumalai, A., & Natarajan, V. (2025) · Food Chemistry Advances · doi:10.1016/j.focha.2025.101190 · Cited by 3 · see citing works

From 16S rRNA to deep learning: Evolution of computational approaches in human microbiome studies

Dwivedi, J., Shukla, M. M., Upadhyay, A., Wal, A., Sharma, K. K., & Gasmi, A. (2025) · Computational Biology and Chemistry · doi:10.1016/j.compbiolchem.2025.108852 · Cited by 3 · see citing works

Integrative analysis of fungal communities in three types of Baijiu Daqu using third-generation sequencing and culturomics

Wei, Y.-H., Han, D.-Y., Song, L., Guo, L., Bai, M., Han, P., Zhu, H., & Wen, Z. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1748163 · Cited by 3 · see citing works

Water kefir as a paradigm for multi-omics and genome-scale metabolic modelling in fermented food

Khan, A., Breselge, S., O’Mahony, A. K., O’Sullivan, Ó., Cotter, P. D., McCarthy, S. N., Mahony, J., & Kenny, J. G. (2026) · npj Biofilms and Microbiomes · doi:10.1038/s41522-026-00985-x · Cited by 3 · see citing works

Quantitative tools in food safety and risk assessment to address technological innovations and climate change

Kakagianni, M. N., Cummins, E., & Valdramidis, V. (2024) · Current Opinion in Food Science · doi:10.1016/j.cofs.2024.101237 · Cited by 3 · see citing works

Microbiota of Raw Milk and Raw Milk Cheeses

Yap, M., O’Sullivan, Ó., & Cotter, P. D. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-15956-5.00032-4 · Cited by 2 · see citing works

Microbial resources for food system sustainability: Lessons from the cocoa industry

Gupta, A., & Cocolin, L. (2025) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2025.105250 · Cited by 2 · see citing works

Investigation of meat proteins in different species by sequential window acquisition of all theoretical mass spectra-based proteomics and its application in meat adulteration

Ma, S., Zhao, W., Yu, D., Yu, A., Kong, W., Zhao, L., Zhao, Y., & Yuan, H. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.147954 · Cited by 2 · see citing works

Uncovering the differentiation mechanisms of wheat Qu under different processes based on Qu-omics: from metabolic phenotypes to mechanism analysis

Xie, R., Zhang, H., Peng, J., Liu, S., & Mao, J. (2025) · Food Bioscience · doi:10.1016/j.fbio.2025.108049 · Cited by 2 · see citing works

The bidirectional interface between oral drug and the gut microbiome: Implications for drug delivery

Zai, K. (2026) · Pharmaceutical Science Advances · doi:10.1016/j.pscia.2026.100112 · Cited by 2 · see citing works

Microbiome alterations and host-pathogen interactions in paratuberculosis: A one health perspective

Dhillon, A., Yadav, P., Gupta, S., Singh, S. V., Sohal, J. S., & Rawat, K. D. (2026) · Veterinary Microbiology · doi:10.1016/j.vetmic.2026.110940 · Cited by 2 · see citing works

Nucleic acid and multi-omics approaches for understanding plant-microbiome interactions in grassland ecosystems

Majeed, A., Javaid, M. H., Mahreen, N., Hussain, M., Kang, Y., Hussain, K., & Su, J. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2026.153356 · Cited by 2 · see citing works

Bacterial endophytes as bioinoculants: Establishment of intimate and multifunctional plant–endophyte interactions under nonstress and salt stress conditions

Walitang, D. I., Sa, T., & Niinemets, Ü. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-13193-6.00003-8 · Cited by 2 · see citing works

Quantifying the impact of workshops promoting microbiome data standards and data stewardship

Kelliher, J. M., Rodriguez, F. E., Johnson, L. Y. D., Roux, S., Smith, M. L., Clum, A., Lynch, W., Bias, C. H., Finks, S. S., Keenum, I. M., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-89991-1 · Cited by 1 · see citing works

Characterizing Gene-Level Adaptations in the Gut Microbiome During Viral Infections: The Role of a Fucoidan-Rich Extract

Garcı́a, G., Soto, J., Valenzuela, C., & Cano, R. J. (2025) · Genes · doi:10.3390/genes16070740 · Cited by 1 · see citing works

Microbiome-driven food safety enhancement through refined environmental monitoring of postharvest facilities

Wang, L., & Rantsiou, K. (2025) · Current Opinion in Food Science · doi:10.1016/j.cofs.2025.101354 · Cited by 1 · see citing works

Species sorting shapes the divergence of a traditional fermented dairy-derived bacterial community with repeatable functionality during propagation with alternative substrates

Nehanda, S., Alekseeva, A. Y., van Mastrigt, O., Chileshe, J., Zwaan, B. J., Smid, E. J., & Schoustra, S. E. (2026) · World Journal of Microbiology and Biotechnology · doi:10.1007/s11274-026-04830-3 · Cited by 1 · see citing works

Advancing Personalized Medicine With AI-Driven Microbiome and Nutrigenomics

Sah, A. K., Maurya, A. K., Mishra, P. S., Mishra, R., & Choudhary, R. K. (2026) · IGI Global eBooks · doi:10.4018/979-8-3373-4849-0.ch004 · Cited by 1 · see citing works

Ecological isolation by the Chishui River drives microecology divergence in Daqu

Song, D., Zhong, X., Mu, Y., Huang, H., & Yang, L. (2026) · Frontiers in Microbiology · doi:10.3389/fmicb.2026.1786069 · Cited by 1 · see citing works

Methods for untargeted analysis of cows’ milk – factors impacting metabolite identification

White, B., & Edwards, P. J. B. (2026) · International Dairy Journal · doi:10.1016/j.idairyj.2026.106658 · Cited by 1 · see citing works

Microbial Ecology at the Nexus of Food Safety and Biotechnology With Ecological Mechanisms, Risks, and Emerging Innovations

Tepson, J. A., & Agyirifo, D. S. (2026) · International Journal of Food Science · doi:10.1155/ijfo/6618960 · Cited by 1 · see citing works

Trends and mechanisms in Baijiu flavor: A bibliometric and multi-omics perspective

Song, D., Zhang, C., Wu, Y., & Yang, L. (2026) · LWT · doi:10.1016/j.lwt.2026.119666 · Cited by 1 · see citing works

Role of microbiome for plant nutrient homeostasis

Jakhar, A. M., Ma, J., Faqir, Y., Kaleri, A. R., Shah, S. M. M., & Umer, N. (2024) · Elsevier eBooks · doi:10.1016/b978-0-443-16082-0.00021-7

Gut Microbiota and Future Research Directions

Gayen, S., Chattopadhyay, S., Hazra, R., Mallick, A., & Roy, S. (2025) · BENTHAM SCIENCE PUBLISHERS eBooks · doi:10.2174/9789815324549125010014

Food Safety 4.0: The Future of Food Safety Leveraging Industry 4.0 Technologies

Dogo, E. M., Bokaba, T., Makun, H. A., Ahmed, A., & Kparbong, P. B. (2025) · Lecture notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering · doi:10.1007/978-3-031-94439-0_12

From probiotics to fermentation: A review of microbes in food and supplements

Ali, I. U., Fatima, S. T., Naz, H., & Waheed, A. (2025) · Bio Communications · doi:10.71320/bcs.0010

Innovations at the Interface of Biology and Computation: A New Frontier in Food Safety

Çarkci, E. D., Erarslan, A., & Yuka, S. A. (2025) · Food and Bioprocess Technology · doi:10.1007/s11947-025-04047-6

Kimchi’den Gochujang’a: Kore Fermente Yiyeceklerinin Gastronomik Değeri

Oyan, S. (2025) · İktisadi ve İdari Yaklaşımlar Dergisi · doi:10.47138/jeaa.1721223

Unlocking agricultural potential: A fusion of metabolomics and proteomics for enhanced crop yield, resilience, and sustainability

Bera, K., Ball, K., Sadhukhan, S., & Dutta, P. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-36457-0.00014-6 · Cited by 1 · see citing works

Challenges and Opportunities in Implementing Omics in Aquaculture for Food Security

Gargotra, P., Aakash, M., & Ravindra, V. (2026) · Springer eBooks · doi:10.1007/978-3-032-14971-8_9

A state-of-the-art in exploring microalgal vitamins: Advancements in production, extraction, market potential, applications, and perspectives for a sustainable future

Maity, S., & Yadav, A. K. (2026) · Preparative Biochemistry & Biotechnology · doi:10.1080/10826068.2026.2625200

Advanced multi-omics technologies in gut microbiome research

Hanafi, S., Salvamani, S., Ulaganathan, V., Augundhooa, D., Chambari, M., Devi, K., Firoz, N., & Gunasekaran, B. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-40483-2.00013-3

Advanced methods and technological advances in personalized microbiome research

Rana, S., Joshi, V., Kumar, P., Kumar, M., & Sahoo, G. C. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-40483-2.00002-9

In silico prediction of shelf-life for marinated meat products using an integrative framework of machine learning and text mining

Zhang, H., Yan, S., Zhao, D., Yang, L., Hong, X., Han, X., Huang, Q., & Xu, B. (2026) · Food Quality and Safety · doi:10.1093/fqsafe/fyag026

Plant–virus–insect interactions: Microbiome-mediated mechanisms in crop protection

Qadri, T. A., Rehman, N. U., Hussain, S., Khan, S. N., & Shah, S. T. A. (2026) · Rhizosphere · doi:10.1016/j.rhisph.2026.101340

Elucidating microbial succession and aroma-active metabolite formation in hybrid dry-fermented sausage analogues with texturized pea protein: Integrating flavoromics, metabolomics, and metagenomics

Li, Y., Liu, X., Li, C., Xu, X., Tang, C., Zhou, G., Liu, Y., & Blank, I. (2026) · Food Research International · doi:10.1016/j.foodres.2026.119324

Transcriptomics: Studying gene expression dynamics in plant-microbe interactions

John, C. K., Ajibade, F. O., Ajibade, T. F., Yusuf, A., & Guadie, A. (2026) · Methods in microbiology · doi:10.1016/bs.mim.2026.04.008

The Microbiome-Brain Axis in Neurodegenerative Disease: Emerging Insights and Therapeutic Horizons

Prasannakumar, P., Manikandan, S., Ameena, I., & Antony, A. R. (2026) · Springer eBooks · doi:10.1007/978-981-95-7494-0_14

Computational and multi-omics systems biology for precision microbiome therapeutics

Dewan, A., & Mascellino, M. T. (2026) · Frontiers in Microbiomes · doi:10.3389/frmbi.2026.1842701

AI-Driven Personalized Nutrition System: Predicting Nutrient Bioavailability Using Deep Learning Models for Optimal Dietary Recommendations

Meng, X. (2026) · International Conference on Computer, Artificial Intelligence and Control Engineering (CAICE) · doi:10.1145/3804601.3804664

Microbial and enzymatic synergy in fermented fish: impacts on flavor, texture, and safety with multi-omics and AI insights

Dai, L. L., Chen, L., Xiao, Y., Zheng, S., Hou, G., Zheng, B., & Zhang, L. (2026) · Food Chemistry X · doi:10.1016/j.fochx.2026.104119

AI Technologies for Advancing Probiotic Applications

Ogidi, O. I., Timi-Johnson, E., Alagha, E. W., & Gupta, R. K. (2026) · Advances in computational intelligence and robotics book series · doi:10.4018/979-8-3373-8172-5.ch007

Multi-omics insights into microbial community and functional expression in medium-temperature Daqu following mung bean substitutionPreprint

Wang, R. T., Yan, L., Wang, R. T., Zhou, H., Xu, B., Xu, S., Yuan, Y., Wu, X., & Li, X. (2026) · SSRN Electronic Journal · doi:10.2139/ssrn.7027972

Fermentation for Personalized Nutrition—AI-Driven Approaches to Tailor Fermented Foods to Individual Needs

Muthuvel, I., Priyadharshini, D., Ponnaiah, S. K., Kavitha, P. S., & Selvaraj, K. V. (2026) · Springer eBooks · doi:10.1007/978-3-032-29927-7_7

Beyond protein source: The structure–gut microbiome axis in alternative protein digestion, fermentation, and health

Shafi, Z., Waheed, A., Shahid, M., Rasool, A., & Ali, S. (2026) · Food Research International · doi:10.1016/j.foodres.2026.119983

Nonconventional feed ingredients in aquaculture: Effects on fish health, gene expression, and metagenomic insights into the alteration of fish gut microbiome

Ghosh, K., Acharya, D., Sukul, T., Mukhopadhyay, A., & Hoseinifar, S. H. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-41728-3.00005-8

Microbiome Research and the Advent of Next-Generation Sequencing

Ferrocino, I., & Cocolin, L. (2026) · Elsevier eBooks · doi:10.1016/b978-0-443-40344-6.00277-5

Analytical Capabilities and Future Perspectives of Chemometrics in Omics for Food Microbial Investigation

Sun, F., Zhang, Y., Tan, C. P., Gu, Y., Liu, Y., & Xu, Y. (2025) · Critical Reviews in Analytical Chemistry · doi:10.1080/10408347.2025.2463430 · Cited by 3 · see citing works

Next generation microbiological risk assessment meta-omics: The next need for integration

Cocolin, L., Mataragas, M., Bourdichon, F., Doulgeraki, A. I., Pilet, M.-F., Jagadeesan, B., Rantsiou, K., & Phister, T. G. (2017) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2017.11.008 · Cited by 120 · see citing works

Multi-omic data integration in food science and analysis

Herráiz-Gil, S., de Arriba, M. D. C., Escamez, M. J., & León, C. (2023) · Current Opinion in Food Science · doi:10.1016/j.cofs.2023.101049 · Cited by 32 · see citing works

Microbial Bioinformatics Approach in Food Science

Jan, I., Sharma, P., & Bansal, A. (2023) · Springer eBooks · doi:10.1007/978-981-99-4784-3_13 · Cited by 2 · see citing works

Integrating multi-omics technologies to decipher microbiome functions

Bossche, T. V. D., Lazau, E., Aho, V. T. E., Blakeley‐Ruiz, J. A., Wolf, M., Kunath, B. J., Valentin-Alvarado, L. E., Hellwig, P., Verschaffelt, P., Rajczewski, A. T., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-77539-4 · Cited by 1 · see citing works