FoodMicrobionet: A Database for the Visualisation and Exploration of Food Bacterial Communities Based on Network Analysis
Open accessAbstract
Amplicon targeted high-throughput sequencing has become a popular tool for the culture-independent analysis of microbial communities. Although the data obtained with this approach are portable and the number of sequences available in public databases is increasing, no tool has been developed yet for the analysis and presentation of data obtained in different studies. This work describes an approach for the development of a database for the rapid exploration and analysis of data on food microbial communities. Data from seventeen studies investigating the structure of bacterial communities in dairy, meat, sourdough and fermented vegetable products, obtained by 16S rRNA gene targeted high-throughput sequencing, were collated and analysed using Gephi, a network analysis software. The resulting database, which we named FoodMicrobionet, was used to analyse nodes and network properties and to build an interactive web-based visualisation. The latter allows the visual exploration of the relationships between Operational Taxonomic Units (OTUs) and samples and the identification of core- and sample-specific bacterial communities. It also provides additional search tools and hyperlinks for the rapid selection of food groups and OTUs and for rapid access to external resources (NCBI taxonomy, digital versions of the original articles). Microbial interaction network analysis was carried out using CoNet on datasets extracted from FoodMicrobionet: the complexity of interaction networks was much lower than that found for other bacterial communities (human microbiome, soil and other environments). This may reflect both a bias in the dataset (which was dominated by fermented foods and starter cultures) and the lower complexity of food bacterial communities. Although some technical challenges exist, and are discussed here, the net result is a valuable tool for the exploration of food bacterial communities by the scientific community and food industry.
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Specific cheese microbes or consortia are adapted to various abiotic stresses, including changes in pH, salinity, temperature, and moisture, as well as biotic stresses like competition and invasion resistance, both at the individual and community levels.
“Specific cheese microbes or consortia are adapted to various abiotic stresses, including changes in pH, salinity, temperature, and moisture, as well as biotic stresses like competition and invasion resistance, both at the individual and community levels [46,53,59,61,65,71,73,75,76,77,78].”
From Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking (2025) · cites this paper as [76]
Split into 2 atoms — 0 confirmed, 2 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredThe whey left after manufacturing has a unique temperature, chemical composition, and microflora, varying by species and biotypes depending on the chosen technology and type of milk.
“The whey left after manufacturing has a unique temperature, chemical composition, and microflora, varying by species and biotypes depending on the chosen technology and type of milk [21,59,73,76,80,109,110,111,112].”
From Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking (2025) · cites this paper as [76]
The Introduction (page unavailable) says that food microbiota can reflect the raw material and processing conditions. It does not address whey left after manufacturing or establish that its temperature, chemical composition, and microbial species or biotypes vary with the technology and type of milk. (LLM, conf=0.75)
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Cites
QIIME allows analysis of high-throughput community sequencing data
Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887 · see citing works
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 20,966 · see citing works
Gephi: An Open Source Software for Exploring and Manipulating Networks
Bastian, M., Heymann, S., & Jacomy, M. (2009) · Proceedings of the International AAAI Conference on Web and Social Media · doi:10.1609/icwsm.v3i1.13937 · Cited by 11,675 · see citing works
Microbial interactions: from networks to models
Faust, K., & Raes, J. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2832 · Cited by 4,138 · see citing works
Molecular ecological network analyses
Deng, Y., Jiang, Y., Yang, Y., He, Z., Luo, F., & Zhou, J. Z. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-113 · Cited by 3,223 · see citing works
The Structure and Dynamics of Networks
Newman, M., Barabási, A.-Ĺ., & Watts, D. J. (2011) · Princeton University Press eBooks · doi:10.1515/9781400841356 · Cited by 2,310 · see citing works
Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
Muegge, B. D., Kuczynski, J., Knights, D., Clemente, J. C., González, A., Fontana, L., Henrissat, B., Knight, R., & Gordon, J. I. (2011) · Science · doi:10.1126/science.1198719 · Cited by 1,988 · see citing works
Food-web structure and network theory: The role of connectance and size
Dunne, J. A., Williams, R. J., & Martinez, N. D. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.192407699 · Cited by 1,531 · see citing works
Microbial co-occurrence relationships in the human microbiome
Faust, K., Sathirapongsasuti, J. F., Izard, J., Segata, N., Gevers, D., Raes, J., & Huttenhower, C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002606 · Cited by 1,527 · see citing works
The Structure and Dynamics of Networks
Boguñá, M. (2007) · Journal of Statistical Physics · doi:10.1007/s10955-006-9267-8 · Cited by 1,507 · see citing works
A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures
De Filippis, F., La Storia, A., Stellato, G., Gatti, M., & Ercolini, D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0089680 · Cited by 1,398 · see citing works
Field guide to next‐generation DNA sequencers
Glenn, T. C. (2011) · Molecular Ecology Resources · doi:10.1111/j.1755-0998.2011.03024.x · Cited by 1,139 · see citing works
Food spoilage—interactions between food spoilage bacteria
Gram, L., Flodgaard, L. R., Rasch, M., Bruhn, J. B., Christensen, A. B., & Givskov, M. (2002) · International Journal of Food Microbiology · doi:10.1016/s0168-1605(02)00233-7 · Cited by 1,061 · see citing works
Phylogenetic Molecular Ecological Network of Soil Microbial Communities in Response to Elevated CO 2
Zhou, J. Z., Deng, Y., Luo, F., He, Z., & Yang, Y. (2011) · mBio · doi:10.1128/mbio.00122-11 · Cited by 943 · see citing works
Efficient, High-Quality Force-Directed Graph Drawing
Hu, Y. (2006) · The Mathematica Journal · Cited by 482 · see citing works
Ercolini, D. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.00256-13 · Cited by 479 · see citing works
Self-citationPCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
Pinto, A. J., & Raskin, L. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0043093 · Cited by 439 · see citing works
Reproducibility and quantitation of amplicon sequencing-based detection
Zhou, J. Z., Wu, L., Deng, Y., Zhi, X., Jiang, Y., Tu, Q., Xie, J., Nostrand, J. D. V., He, Z., & Yang, Y. (2011) · The ISME Journal · doi:10.1038/ismej.2011.11 · Cited by 438 · see citing works
Chaillou, S., Chaulot‐Talmon, A., Caekebeke, H., Cardinal, M., Christieans, S., Denis, C., Desmonts, M.-H., Dousset, X., Feurer, C., Hamon, E., et al. (2014) · The ISME Journal · doi:10.1038/ismej.2014.202 · Cited by 350 · see citing works
Facility-specific “house” microbiome drives microbial landscapes of artisan cheesemaking plants
Bokulich, N. A., & Mills, D. A. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.00934-13 · Cited by 295 · see citing works
Kuczynski, J., Liu, Z. Z., Lozupone, C., McDonald, D. T., Fierer, N., & Knight, R. D. (2010) · Nature Methods · doi:10.1038/nmeth.1499 · Cited by 285 · see citing works
Microbial Interactions within a Cheese Microbial Community
Mounier, J., Monnet, C., Vallaeys, T., Roger Arditi, B., Sarthou, A., Hélias, A., & Irlinger, F. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01338-07 · Cited by 248 · see citing works
de Menezes, A. B., Prendergast‐Miller, M. T., Richardson, A. E., Toscas, P., Farrell, M., Macdonald, L. M., Baker, G. H., Wark, T., & Thrall, P. H. (2014) · Environmental Microbiology · doi:10.1111/1462-2920.12559 · Cited by 222 · see citing works
Marsh, A. J., O’Sullivan, Ó., Hill, C., Ross, R. P., & Cotter, P. D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0069371 · Cited by 221 · see citing works
Microbial Ecology Dynamics during Rye and Wheat Sourdough Preparation
Ercolini, D., Pontonio, E., Filippis, F. D., Minervini, F., Storia, A. L., Gobbetti, M., & Cagno, R. D. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.02955-13 · Cited by 212 · see citing works
Filippis, F. D., Storia, A. L., Villani, F., & Ercolini, D. (2013) · PLoS ONE · doi:10.1371/journal.pone.0070222 · Cited by 203 · see citing works
Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale
Bokulich, N. A., Bamforth, C. W., & Mills, D. A. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035507 · Cited by 197 · see citing works
Impact of next generation sequencing techniques in food microbiology.
Mayo, B., Rachid, C., Alegria, A., Leite, A., Peixoto, R., & Delgado, S. (2014) · Current Genomics · doi:10.2174/1389202915666140616233211 · Cited by 188 · see citing works
Ercolini, D., De Filippis, F., La Storia, A., & Iacono, M. (2012) · Applied and Environmental Microbiology · doi:10.1128/aem.02218-12 · Cited by 175 · see citing works
Self-citationThe Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations
Oakley, B. B., Morales, C. A., Line, J. E., Berrang, M. E., Meinersmann, R. J., Tillman, G. E., Wise, M. G. G., Siragusa, G. R., Hiett, K. L., & Seal, B. S. (2013) · PLoS ONE · doi:10.1371/journal.pone.0057190 · Cited by 133 · see citing works
Microbial Interactions in Food Fermentations
Ivey, M. L., Massel, M., & Phister, T. G. (2012) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-022811-101219 · Cited by 116 · see citing works
Spatial distribution patterns of benthic microbial communities along the Pearl Estuary, China
Liu, J., Yang, H., Zhao, M., & Zhang, X. (2014) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2014.10.005 · Cited by 109 · see citing works
Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches
Greppi, A., Ferrocino, I., Storia, A. L., Rantsiou, K., Ercolini, D., & Cocolin, L. (2015) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2015.01.016 · Cited by 109 · see citing works
NaOH-Debittering Induces Changes in Bacterial Ecology during Table Olives Fermentation
Cocolin, L., Alessandria, V., Botta, C., Gorra, R., Filippis, F. D., Ercolini, D., & Rantsiou, K. (2013) · PLoS ONE · doi:10.1371/journal.pone.0069074 · Cited by 96 · see citing works
Zooming into food-associated microbial consortia: a “cultural” evolution
Cocolin, L., & Ercolini, D. (2015) · Current Opinion in Food Science · doi:10.1016/j.cofs.2015.01.003 · Cited by 93 · see citing works
Self-citationPasquale, I. D., Cagno, R. D., Buchin, S., Angelis, M. D., & Gobbetti, M. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.02097-14 · Cited by 89 · see citing works
Benson, A. K., David, J. R. D., Gilbreth, S. E., Smith, G., Nietfeldt, J. W., Legge, R. M., Kim, J., Sinha, R., Duncan, C. E., Ma, J., et al. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.00774-14 · Cited by 84 · see citing works
Rizzello, C. G., Cavoski, I., Turk, J., Ercolini, D., Nionelli, L., Pontonio, E., Angelis, M. D., Filippis, F. D., Gobbetti, M., & Cagno, R. D. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.04161-14 · Cited by 76 · see citing works
The microbiota of high-moisture mozzarella cheese produced with different acidification methods
Guidone, A., Zotta, T., Matera, A., Ricciardi, A., Filippis, F. D., Ercolini, D., & Parente, E. (2015) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2015.09.002 · Cited by 62 · see citing works
Pasquale, I. D., Calasso, M. P., Mancini, L., Ercolini, D., Storia, A. L., Angelis, M. D., Cagno, R. D., & Gobbetti, M. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.00757-14 · Cited by 56 · see citing works
Impact of Nisin-Activated Packaging on Microbiota of Beef Burgers during Storage
Ferrocino, I., Greppi, A., Storia, A. L., Rantsiou, K., Ercolini, D., & Cocolin, L. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.03093-15 · Cited by 56 · see citing works
Dolci, P., Filippis, F. D., Storia, A. L., Ercolini, D., & Cocolin, L. (2014) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2014.05.021 · Cited by 46 · see citing works
Microbial community dynamics in thermophilic undefined milk starter cultures
Parente, E., Guidone, A., Matera, A., Filippis, F. D., Mauriello, G., & Ricciardi, A. (2015) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2015.10.014 · Cited by 45 · see citing works
Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations
May, A., Abeln, S., Wim Crielaard, A., Heringa, J., & Brandt, B. W. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu085 · Cited by 36 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- Mendes, L. W., Kuramae, E. E, Navarrete, A. A., van Veen, J. A., Tsai, S. M., 2014. Taxonomical and functional microbial community selection in soybean rhizosphere. ISME Journal 8, 1577-1587.
Cited by
Sorted by citations
The use of next generation sequencing for improving food safety: Translation into practice
Jagadeesan, B., Gerner‐Smidt, P., Allard, M. W., Leuillet, S., Winkler, A., Xiao, Y., Chaffron, S., van der Vossen, J., Tang, S., Katase, M., et al. (2018) · Food Microbiology · doi:10.1016/j.fm.2018.11.005 · Cited by 370 · see citing works
The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health
De Filippis, F., Pasolli, E., & Ercolini, D. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa015 · Cited by 303 · see citing works
Metagenomics insights into food fermentations
Filippis, F. D., Parente, E., & Ercolini, D. (2016) · Microbial Biotechnology · doi:10.1111/1751-7915.12421 · Cited by 257 · see citing works
Rybakova, D., Mancinelli, R., Wikström, M., Birch-Jensen, A.-S., Postma, J., Ehlers, R., Goertz, S., & Berg, G. (2017) · Microbiome · doi:10.1186/s40168-017-0310-6 · Cited by 206 · see citing works
Blaya, J., Barzideh, Z., & LaPointe, G. (2018) · Journal of Dairy Science · doi:10.3168/jds.2017-13345 · Cited by 200 · see citing works
Wang, S., Wu, Q. J., Nie, Y., Wu, J., & Xu, Y. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.03090-18 · Cited by 185 · see citing works
Canon, F., Nidelet, T., Guédon, É., Thierry, A., & Gagnaire, V. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.02088 · Cited by 167 · see citing works
Recent Past, Present, and Future of the Food Microbiome
De Filippis, F., Parente, E., & Ercolini, D. (2018) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-030117-012312 · Cited by 163 · see citing works
Self-citationZhao, M., Su, X. Q., Nian, B., Chen, L. J., Zhang, D. L., Duan, S., Wang, L. Y., Shi, X., Jiang, B., Jiang, W., et al. (2019) · mSystems · doi:10.1128/msystems.00680-19 · Cited by 163 · see citing works
Drivers that establish and assembly the lactic acid bacteria biota in cheeses.
Gobbetti, M., Di Cagno, R., Calasso, M., Neviani, E., Fox, P. F., & De Angelis, M. (2018) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2018.06.010 · Cited by 151 · see citing works
Mayo, B., Rodríguez, J., Vázquez, L., & Flórez, A. B. (2021) · Foods · doi:10.3390/foods10030602 · Cited by 149 · see citing works
Highlighting the microbial diversity of 12 French cheese varieties
Dugat‐Bony, É., Garnier, L., Denonfoux, J., Ferreira, S., Sarthou, A., Bonnarme, P., & Irlinger, F. (2016) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2016.09.026 · Cited by 148 · see citing works
The microbiota of dairy milk: A review
Parente, E., Ricciardi, A., & Zotta, T. (2020) · International Dairy Journal · doi:10.1016/j.idairyj.2020.104714 · Cited by 130 · see citing works
The need for an integrated multi-OMICs approach in microbiome science in the food system
Ferrocino, I., Rantsiou, K., McClure, R., Kostic, T., de Souza, R. S. C., Lange, L., FitzGerald, J., Kriaa, A., Cotter, P., Maguin, E., et al. (2023) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.13103 · Cited by 110 · see citing works
Self-citationTracking the Dairy Microbiota from Farm Bulk Tank to Skimmed Milk Powder
McHugh, A. J., Feehily, C., Fenelon, M. A., Gleeson, D. E., Hill, C., & Cotter, P. D. (2020) · mSystems · doi:10.1128/msystems.00226-20 · Cited by 81 · see citing works
Zotta, T., Parente, E., Ianniello, R. G., Filippis, F. D., & Ricciardi, A. (2019) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2019.01.008 · Cited by 80 · see citing works
Current perspectives in food-based studies exploiting multi-omics approaches
Ferrocino, I., & Cocolin, L. (2017) · Current Opinion in Food Science · doi:10.1016/j.cofs.2017.01.002 · Cited by 77 · see citing works
Detection and Enumeration of Spore-Forming Bacteria in Powdered Dairy Products
McHugh, A. J., Feehily, C., Hill, C., & Cotter, P. D. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00109 · Cited by 75 · see citing works
Comparison of complex network analysis software: Citespace, SCI2 and Gephi
Yang, J., Cheng, C., Shen, S., & Yang, S. (2017) · IEEE International Conference on Big Data Analysis (ICBDA) · doi:10.1109/icbda.2017.8078800 · Cited by 69 · see citing works
Omics approaches to understand sourdough fermentation processes
Weckx, S., Kerrebroeck, S. V., & Vuyst, L. D. (2018) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2018.05.029 · Cited by 67 · see citing works
Bortolini, C., Patrone, V., Puglisi, E., & Morelli, L. (2016) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2016.07.004 · Cited by 65 · see citing works
Nikoloudaki, O., Aheto, F., Cagno, R. D., & Gobbetti, M. (2024) · Food Research International · doi:10.1016/j.foodres.2024.114780 · Cited by 66 · see citing works
Yu, X., Kang, X., Li, Y., Cui, Y., Tu, W., Shen, T., Yan, M., Gu, Y., Zou, L., Ma, M., et al. (2019) · Environmental Pollution · doi:10.1016/j.envpol.2019.113167 · Cited by 64 · see citing works
Zhang, Y., Zhu, X. M., Wang, N., Liu, X., Wang, L., & Ning, K. (2025) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2025.104891 · Cited by 67 · see citing works
Cauchie, E., Delhalle, L., Taminiau, B., Tahiri, A., Korsak, N., Burteau, S., Fall, P. A., Farnir, F., Baré, G., & Daube, G. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.03074 · Cited by 56 · see citing works
Zheng, X., Liu, F., Kai-xiong, L., Shi, X., Ni, Y., Li, B., & Zhuge, B. (2018) · Food Research International · doi:10.1016/j.foodres.2018.05.019 · Cited by 56 · see citing works
Sequino, G., Valentino, V., Villani, F., & Filippis, F. D. (2022) · Food Research International · doi:10.1016/j.foodres.2022.111242 · Cited by 53 · see citing works
Huang, X., Du, H., Deng, X., Chen, Y., Xiang, L., Li, Y.-W., Li, H., Mo, C.-H., Cai, Q.-Y., & Zhao, H.-M. (2021) · Journal of Cleaner Production · doi:10.1016/j.jclepro.2021.127064 · Cited by 50 · see citing works
Jiao, W., Xie, F., Gao, L., Du, L., Wei, Y., Zhou, J., & He, G. (2022) · LWT · doi:10.1016/j.lwt.2022.113140 · Cited by 49 · see citing works
Lactic acid bacteria in cow raw milk for cheese production: Which and how many?
Bettera, L., Levante, A., Bancalari, E., Bottari, B., & Gatti, M. (2023) · Frontiers in microbiology · doi:10.3389/fmicb.2022.1092224 · Cited by 47 · see citing works
A comparison of bioinformatic approaches for 16S rRNA gene profiling of food bacterial microbiota
Filippis, F. D., Parente, E., Zotta, T., & Ercolini, D. (2017) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2017.10.028 · Cited by 45 · see citing works
Investigating dairy microbiome: an opportunity to ensure quality, safety and typicity
Ferrocino, I., Rantsiou, K., & Cocolin, L. (2021) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2021.08.009 · Cited by 46 · see citing works
Microbiota of Cheese Ecosystems: A Perspective on Cheesemaking
Neviani, E., Gatti, M., Gardini, F., & Levante, A. (2025) · Foods · doi:10.3390/foods14050830 · Cited by 39 · see citing works
“The whey left after manufacturing has a unique temperature, chemical composition, and microflora, varying by species and biotypes depending on the chosen technology and type of milk [21,59,73,76,80,109–112].”
Parente, E., Filippis, F. D., Ercolini, D., Ricciardi, A., & Zotta, T. (2019) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2019.108249 · Cited by 37 · see citing works
Sarkar, S., Sha, S. P., & Ghatani, K. (2023) · Frontiers in Sustainable Food Systems · doi:10.3389/fsufs.2023.1040567 · Cited by 40 · see citing works
Microbiome and -omics application in food industry
Ferrocino, I., Rantsiou, K., & Cocolin, L. (2022) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2022.109781 · Cited by 34 · see citing works
Parente, E., Zotta, T., & Ricciardi, A. (2022) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2022.109618 · Cited by 39 · see citing works
Structure of association networks in food bacterial communities
Parente, E., Zotta, T., Faust, K., Filippis, F. D., & Ercolini, D. (2017) · Food Microbiology · doi:10.1016/j.fm.2017.12.010 · Cited by 28 · see citing works
Tracking bacteriome variation over time in Listeria monocytogenes-positive foci in food industry
Rodríguez-López, P., Rodríguez-Herrera, J. J., & Cabo, M. L. (2019) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2019.108439 · Cited by 26 · see citing works
Kang, X., Cui, Y., Shen, T., Yan, M., Tu, W., Shoaib, M., Xiang, Q., Zhao, K., Gu, Y., Chen, Q., et al. (2020) · Ecotoxicology and Environmental Safety · doi:10.1016/j.ecoenv.2020.110816 · Cited by 25 · see citing works
Lin, W., He, Y., Shi, C., Mu, C., Wang, C., Li, R., & Ye, Y. (2022) · Food Research International · doi:10.1016/j.foodres.2022.110992 · Cited by 24 · see citing works
Chao, H., Zheng, X., Xia, R., Sun, M., & Hu, F. (2021) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2021.149337 · Cited by 23 · see citing works
Wu, L., Zhao, L., Tao, Y., Zhang, D., He, A., Ma, X., Zhang, H., Li, G., Rong, L., & Li, R. (2023) · Journal of Food Science · doi:10.1111/1750-3841.16764 · Cited by 23 · see citing works
Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments
Parente, E., Zotta, T., Giavalisco, M., & Ricciardi, A. (2023) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2023.110124 · Cited by 21 · see citing works
del Árbol, J. T., Pulido, R. P., Storia, A. L., Burgos, M. J. G., Lucas, R., Ercolini, D., & Gálvez, A. (2016) · Food Research International · doi:10.1016/j.foodres.2016.10.014 · Cited by 21 · see citing works
Somerville, V., Schowing, T., Chabas, H., Schmidt, R. S., von Ah, U., Bruggmann, R., & Engel, P. (2022) · Microbiome · doi:10.1186/s40168-022-01328-6 · Cited by 20 · see citing works
Ruvalcaba-Gómez, J. M., Delgado-Macuil, R. J., Zelaya-Molina, L. X., Maya, O., Ruesga-Gutiérrez, E., Esparza, L. M. A., Villagrán, Z., la Mora, D. A. L.-D., & Arteaga-Garibay, R. I. (2020) · Microorganisms · doi:10.3390/microorganisms9010024 · Cited by 19 · see citing works
Yuan, M., Zhang, D., Wang, Z., Zhu, Z., Sun, H., Wang, W., Han, D., Qu, Z., Ma, B., Wang, J., et al. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1142780 · Cited by 19 · see citing works
Parente, E., Zotta, T., & Ricciardi, A. (2022) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2022.109696 · Cited by 15 · see citing works
Exciting strain‐level resolution studies of the food microbiome
Ercolini, D. (2017) · Microbial Biotechnology · doi:10.1111/1751-7915.12593 · Cited by 15 · see citing works
FDF-DB: A Database of Traditional Fermented Dairy Foods and Their Associated Microbiota
Zinno, P., Calabrese, F. M., Schifano, E., Sorino, P., Cagno, R. D., Gobbetti, M., Parente, E., Angelis, M. D., & Devirgiliis, C. (2022) · Nutrients · doi:10.3390/nu14214581 · Cited by 14 · see citing works
Effect of storage temperature on bacterial diversity in chicken skin
Meng, J., Huang, X., Song, L., Hou, B., Qiao, M., Zhang, P., Zhao, Q., Zhang, B., & Liu, F. (2018) · Journal of Applied Microbiology · doi:10.1111/jam.14183 · Cited by 13 · see citing works
Microbial association networks in cheese: a meta-analysisPreprint
Parente, E., Zotta, T., & Ricciardi, A. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.07.21.453196 · Cited by 13 · see citing works
Yeast Ecology of Fermented Table Olives: A Tool for Biotechnological Applications
Anagnostopoulos, D. A., Bozoudi, D., & Tsaltas, D. (2017) · InTech eBooks · doi:10.5772/intechopen.70760 · Cited by 10 · see citing works
Determining the core bacterial and fungal genera in table olive fermentations
Ricciardi, A., López, F. N. A., Giavalisco, M., Pietrafesa, R., & Parente, E. (2025) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2025.111344 · Cited by 9 · see citing works
A Comprehensive View of Food Microbiota: Introducing FoodMicrobionet v5
Parente, E., & Ricciardi, A. (2024) · Foods · doi:10.3390/foods13111689 · Cited by 9 · see citing works
Impact of Electrolyzed Water on the Microbial Spoilage Profile of Piedmontese Steak Tartare
Botta, C., Coïsson, J. D., Ferrocino, I., Colasanto, A., Pessione, A., Cocolin, L., Arlorio, M., & Rantsiou, K. (2021) · Microbiology Spectrum · doi:10.1128/spectrum.01751-21 · Cited by 9 · see citing works
Garcia‐Garcia, L. A., & Rodríguez-Salvador, M. (2020) · Journal of Biomedical Semantics · doi:10.1186/s13326-020-0219-z · Cited by 8 · see citing works
Fermented Beverages Produced by Mixed Cultures, Pure Cultures, and Defined Cocultures
Bader, J., Brigham, C. J., Ståhl, U., & Popović, M. (2019) · Elsevier eBooks · doi:10.1016/b978-0-12-815271-3.00003-8 · Cited by 6 · see citing works
Aspri, M., & Tsaltas, D. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-816449-5.00004-7 · Cited by 6 · see citing works
Luo, L., Dai, F., Xu, Z., Guan, J., Fei, G., Qu, J., Yao, M., Xue, Y., Zhou, Y., & Zou, X. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.01053-24 · Cited by 5 · see citing works
Omics Approaches in Food and Environmental Analysis
Farré, M. (2022) · The handbook of environmental chemistry · doi:10.1007/698_2022_893 · Cited by 4 · see citing works
Microbiota of Milk and Dairy Foods: Structure and Function by -omics Approaches
Ferrocino, I., Rantsiou, K., & Cocolin, L. (2020) · Elsevier eBooks · doi:10.1016/b978-0-08-100596-5.22973-9 · Cited by 4 · see citing works
Fermented food microbiome: influence on oral and gut microbiota, and human health
Kim, D., Joe, H.-I., Bae, J., Wu, G. D., Compher, C. W., & Koo, H. (2026) · Nature Reviews Microbiology · doi:10.1038/s41579-026-01333-8 · Cited by 4 · see citing works
Bader, J., Brigham, C. J., Ståhl, U., & Popović, M. (2018) · Elsevier eBooks · doi:10.1016/b978-0-12-811443-8.00005-0 · Cited by 3 · see citing works
The Phyllosphere Microbial Community Structure of Three Camellia Species upon Anthracnose
Peng, X., Wang, H., & Zhou, X. (2024) · Forests · doi:10.3390/f15122080 · Cited by 3 · see citing works
New Insights Into Lactic Acid Bacteria Fermentation of Plant Foods Through Complementary Omics
Cagno, R. D., Filannino, P., Albiac, M. A., & Gobbetti, M. (2020) · Elsevier eBooks · doi:10.1016/b978-0-08-100596-5.23043-6 · Cited by 3 · see citing works
Botta, C., Spada, D., Buzzanca, D., Zadeh, N. S., Tsoureki, D., Biolcati, F., Ferrocino, I., Zeppa, G., & Dolci, P. (2025) · Food Research International · doi:10.1016/j.foodres.2025.117039 · Cited by 3 · see citing works
Somerville, V., Schowing, T., Chabas, H., Schmidt, R. S., von Ah, U., Bruggmann, R., & Engel, P. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.13.488139 · Cited by 2 · see citing works
Parente, E., Zotta, T., & Ricciardi, A. (2022) · doi:10.1101/2022.01.19.476946 · Cited by 15 · see citing works
Self-citationYan, M., Chen, N., Liu, T., Gao, D., Ye, Z., Xiao, J., Cai, W., Farooq, A., & Yan, W. (2026) · Plant and Soil · doi:10.1007/s11104-026-08564-x · Cited by 1 · see citing works
Jaba, A., Dagher, F., Oskouei, A. M. H., Guertin, C., & Constant, P. (2019) · Canadian Journal of Microbiology · doi:10.1139/cjm-2019-0052
Jin, Y., Jiao, S., & Lu, Y. (2020) · doi:10.21203/rs.3.rs-23525/v1
Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environmentsPreprint
Parente, E., Zotta, T., Giavalisco, M., & Ricciardi, A. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.09.09.507241
Gatti, M., Bettera, L., Levante, A., Bancalari, E., Bottari, B., & Neviani, E. (2022) · Scienza e Tecnica Lattiero Casearia · doi:10.36138/stlc.05.2022.01
Somerville, V., Schowing, T., Chabas, H., Schmidt, R. S., von Ah, U., Bruggmann, R., & Engel, P. (2022) · Figshare · doi:10.6084/m9.figshare.20677973
Luo, Y., Lu, Z., Yang, J., Liu, S., Zhao, W., & Jiang, X. (2025) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm66473.2025.11357039
Xia, Z., Chen, Y., Wang, S., Wang, S., Gou, M., Zhang, S., TANG, Y., & Xiao, H. (2026) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.5c12295
Analysis of Phage-Bacteria-Food Association and its Relation to Human Health Using Knowledge Graphs
Verma, V., Pokhrel, V., Kuntal, B. K., & Ghosh, P. (2025) · IEEE Pune Section International Conference (PuneCon) · doi:10.1109/punecon67554.2025.11377613
Medouni‐Haroune, L., Medouni‐Adrar, S., Messaoudene, L., Negrichi, S., Bouiche, C., Sahraoui-Remini, Y., Allam, A., Meghlaoui, Z., Mouhoubi, K., Abbou, A., et al. (2026) · Food & Function · doi:10.1039/d6fo00371k
Chen, W., Wang, J., Jia, R., Wu, S. S., Yuan, H., Li, X. Y., & Zuo, X. (2026) · Sustainability · doi:10.3390/su18126166
Shen, S., Shao, Z., Atta-Delgado, M. X., Chen, X., Ding, T., & Jiang, J. (2026) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.70630
- Authors
- Parente, E., Cocolin, L., De Filippis, F., Zotta, T., Ferrocino, I., O'Sullivan, O., Neviani, E., De Angelis, M., Cotter, P. D., & Ercolini, D.
- Affiliations
- University of Basilicata (IT)
- University of Turin (IT)
- Institute of Food Science (IT)
- University of Parma (IT)
- Teagasc - The Irish Agriculture and Food Development Authority (IE)
- University of Naples Federico II (IT)
- Corresponding author
- Parente, Eugenio
- ORCID
- Venue
- International Journal of Food Microbiology
- Publisher
- Elsevier BV
- Published
- 2016-02
- Volume
- 219
- Pages
- 28-37
- ISSN
- 0168-1605 (ISSN-L)
- OpenAlex
- W2192338192
- Cited by
- 82
- References
- 44
- Citations by year
- 2026: 6 · 2025: 6 · 2024: 4 · 2023: 6 · 2022: 13 · 2021: 7 · 2020: 12 · 2019: 8 · 2018: 7 · 2017: 9 · 2016: 4
- FWCI
- 8.92
- Type
- journal article
- Language
- en
- Open access
- green
- hdl.handle.net
- Licence
- Locations
- International Journal of Food Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Institutional Research Information System University of Turin (University of Turin) (submittedVersion, other-oa)
- CINECA IRIS Institutional Research Information System (University of Basilicata) (submittedVersion)
- CINECA IRIS Institutional Research Information System (University of Bari Aldo Moro) (submittedVersion)
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- network analysis, 16S rRNA gene sequencing, microbial interaction networks, fermented foods, dairy products, meat products, sourdough, fermented vegetables, starter cultures, core microbiome, web-based visualization
- MeSH terms
- Vegetable Products, Animals, DNA, Bacterial, Food Microbiology, Foodborne Diseases, Humans, Meat, Milk, RNA, Ribosomal, 16S, Sensitivity and Specificity, Software, DNA Primers, Databases, Genetic, Limit of Detection, Real-Time Polymerase Chain Reaction, Microbiota
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