Microbiome and -omics application in food industry

Structure, function and diversity of the healthy human microbiome

The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works

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

Manni, M., Berkeley, M. R., Seppey, M., Simão, F. A., & Zdobnov, E. M. (2021) · Molecular Biology and Evolution · doi:10.1093/molbev/msab199 · Cited by 6,187 · see citing works

A taxonomic note on the genus lactobacillus: description of 23 novel genera, emended description of the genus lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

Zheng, J., Wittouck, S., Salvetti, E., Franz, C. M. A. P., Harris, H. M. B., Mattarelli, P., O’Toole, P. W., Pot, B., Vandamme, P., Walter, J., et al. (2020) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.004107 · Cited by 3,313 · see citing works

A communal catalogue reveals Earth's multiscale microbial diversity

Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., et al. (2017) · Nature · doi:10.1038/nature24621 · Cited by 2,684 · see citing works

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

Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303 · see citing works

Microbiome definition re-visited: old concepts and new challenges

Berg, G., Rybakova, D., Fischer, D., Cernava, T., Vergès, M.-C. C., Charles, T., Chen, X., Cocolin, L., Eversole, K., Corral, G. H., et al. (2020) · Microbiome · doi:10.1186/s40168-020-00875-0 · Cited by 2,275 · see citing works

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

Berry, D., & Stefanie Widder, A. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00219 · Cited by 1,752 · see citing works

The gut mycobiome of the Human Microbiome Project healthy cohort

Nash, A. K., Auchtung, T. A., Wong, M. C., Smith, D. P., Gesell, J. R., Ross, M. C., Stewart, C. J., Metcalf, G., Muzny, D. M., Gibbs, R. A., et al. (2017) · Microbiome · doi:10.1186/s40168-017-0373-4 · Cited by 987 · see citing works

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

Ranjan, R., Rani, A., Metwally, A., McGee, H. S., & Perkins, D. L. (2016) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2015.12.083 · Cited by 981 · see citing works

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

Shade, A. L., Jones, S. E., Caporaso, J. G., Handelsman, J., Knight, R. D., Fierer, N., & Gilbert, J. A. (2014) · mBio · doi:10.1128/mbio.01371-14 · Cited by 738 · see citing works

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

Pinu, F. R., Beale, D. J., Paten, A. M., Kouremenos, K., Swarup, S., Schirra, H. J., & Wishart, D. (2019) · Metabolites · doi:10.3390/metabo9040076 · Cited by 723 · see citing works

Traditional Cheeses: Rich and Diverse Microbiota with Associated Benefits

Montel, M.-C., Buchin, S., Mallet, A., Delbes-Paus, C., Vuitton, D. A., Desmasures, N., & Berthier, F. (2014) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2014.02.019 · Cited by 665 · see citing works

Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity

Wolfe, B. E., Button, J. E., Santarelli, M., & Dutton, R. J. (2014) · Cell · doi:10.1016/j.cell.2014.05.041 · Cited by 648 · see citing works

Community Structure Follows Simple Assembly Rules in Microbial Microcosms

Friedman, J., Higgins, L. M., & Gore, J. (2017) · Nature Ecology & Evolution · doi:10.1038/s41559-017-0109 · Cited by 557 · see citing works

Evaluating the Information Content of Shallow Shotgun Metagenomics

Hillmann, B., Al-Ghalith, G. A., Shields-Cutler, R. R., Zhu, Q., Gohl, D. M., Beckman, K. B., Knight, R., & Knights, D. (2018) · mSystems · doi:10.1128/msystems.00069-18 · Cited by 474 · see citing works

A global metagenomic map of urban microbiomes and antimicrobial resistance

Danko, D., Bezdan, D., Afshin, E. E., Ahsanuddin, S., Bhattacharya, C., Butler, D., Chng, K. R., Donnellan, D., Hecht, J., Jackson, K., et al. (2021) · Cell · doi:10.1016/j.cell.2021.05.002 · Cited by 396 · see citing works

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

Pasolli, E., De Filippis, F., Mauriello, I. E., Cumbo, F., Walsh, A. M., Leech, J., Cotter, P. D., Segata, N., & Ercolini, D. (2020) · Nature Communications · doi:10.1038/s41467-020-16438-8 · Cited by 367 · see citing works

Advancing functional and translational microbiome research using meta-omics approaches

Zhang, X., Li, L., Butcher, J., Stintzi, A., & Figeys, D. (2019) · Microbiome · doi:10.1186/s40168-019-0767-6 · Cited by 343 · see citing works

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

de Souza, R. S. C., Armanhi, J. S. L., & Arruda, P. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2020.01179 · Cited by 283 · see citing works

Highly multiplexed spatial mapping of microbial communities

Shi, H., Shi, Q., Grodner, B., Lenz, J. S., Zipfel, W. R., Brito, I., & Vlaminck, I. D. (2020) · Nature · doi:10.1038/s41586-020-2983-4 · Cited by 248 · see citing works

Metagenomics unveils microbial roles involved in metabolic network of flavor development in medium-temperature daqu starter

Yang, Y., Wang, S., Lu, Z., Zhang, X., Chai, L., Shen, C., Shi, J., & Xu, Z. (2020) · Food Research International · doi:10.1016/j.foodres.2020.110037 · Cited by 220 · see citing works

The diversity and function of sourdough starter microbiomes

Landis, E. A., Oliverio, A., McKenney, E. A., Nichols, L. M., Kfoury, N., Biango‐Daniels, M. N., Shell, L., Madden, A. A., Shapiro, L. R., Sakunala, S., et al. (2021) · eLife · doi:10.7554/elife.61644 · Cited by 208 · see citing works

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

De Filippis, F., Genovese, A., Ferranti, P., Gilbert, J. A., & Ercolini, D. (2016) · Scientific Reports · doi:10.1038/srep21871 · Cited by 196 · see citing works

Overlap of Spoilage-Associated Microbiota between Meat and the Meat Processing Environment in Small-Scale and Large-Scale Retail Distributions

Stellato, G., Storia, A. L., Filippis, F. D., Borriello, G., Villani, F., & Ercolini, D. (2016) · Applied and Environmental Microbiology · doi:10.1128/aem.00793-16 · Cited by 188 · see citing works

Automated design of synthetic microbial communities

Karkaria, B. D., Fedorec, A. J. H., & Barnes, C. P. (2021) · Nature Communications · doi:10.1038/s41467-020-20756-2 · Cited by 178 · see citing works

Metatranscriptome-based investigation of flavor-producing core microbiota in different fermentation stages of dajiang, a traditional fermented soybean paste of Northeast China

An, F., Li, M., Zhao, Y., Zhang, Y., Mu, D., Hu, X., You, S., Wu, J., & Wu, R. (2020) · Food Chemistry · doi:10.1016/j.foodchem.2020.128509 · Cited by 171 · 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

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

Dugourd, A., Kuppe, C., Sciacovelli, M., Gjerga, E., Gabor, A., Emdal, K. B., Vieira, V., Bekker‐Jensen, D. B., Kranz, J., Bindels, E. M. J., et al. (2021) · Molecular Systems Biology · doi:10.15252/msb.20209730 · Cited by 149 · see citing works

The sources and transmission routes of microbial populations throughout a meat processing facility

Zwirzitz, B., Wetzels, S. U., Dixon, E. D., Stessl, B., Zaiser, A., Rabanser, I., Thalguter, S., Conrady, B., Roch, F., Strachan, C. R., et al. (2020) · npj Biofilms and Microbiomes · doi:10.1038/s41522-020-0136-z · Cited by 146 · see citing works

Shotgun Metagenomics and Volatilome Profile of the Microbiota of Fermented Sausages

Ferrocino, I., Bellio, A., Giordano, M., Macori, G., Romano, A., Rantsiou, K., Decastelli, L., & Cocolin, L. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.02120-17 · Cited by 144 · see citing works

Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality

Walsh, A. M., Macori, G., Kilcawley, K. N., & Cotter, P. D. (2020) · Nature Food · doi:10.1038/s43016-020-0129-3 · Cited by 133 · see citing works

Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system

Somerville, V., Lutz, S., Schmid, M., Frei, D., Moser, A. I., Irmler, S., Frey, J. E., & Ahrens, C. H. (2019) · BMC Microbiology · doi:10.1186/s12866-019-1500-0 · Cited by 132 · see citing works

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

Santiago-Rodríguez, T. M., & Hollister, E. B. (2021) · Seminars in Perinatology · doi:10.1016/j.semperi.2021.151456 · Cited by 124 · see citing works

To target or not to target? Definitions and nomenclature for targeted versus non-targeted analytical food authentication

Ballin, N. Z., & Laursen, K. H. (2018) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2018.09.025 · Cited by 122 · see citing works

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

Verce, M., De Vuyst, L., & Weckx, S. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00479 · Cited by 121 · 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

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

Xu, Y., Tong, Z., Zhang, X., Wang, Y.-Y., Fang, W., Li, L., & Luo, Z. (2019) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.9b03103 · Cited by 114 · see citing works

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

Huang, X., Fan, Y., Lu, T., Kang, J., Pang, X., Han, B., & Chen, J. (2020) · Microorganisms · doi:10.3390/microorganisms8091281 · Cited by 113 · see citing works

Relationships among house, rind and core microbiotas during manufacture of traditional Italian cheeses at the same dairy plant

Calasso, M. P., Ercolini, D., Mancini, L., Stellato, G., Minervini, F., Cagno, R. D., Angelis, M. D., & Gobbetti, M. (2015) · Food Microbiology · doi:10.1016/j.fm.2015.10.008 · Cited by 107 · see citing works

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

Wu, Y., Xia, M., Zhao, N., Tu, L., Xue, D., Zhang, X., Zhao, C., Cheng, Y., Zheng, Y., & Wang, M. (2021) · Food Research International · doi:10.1016/j.foodres.2021.110400 · Cited by 106 · see citing works

MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

Zolfo, M., Tett, A., Jousson, O., Donati, C., & Segata, N. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw837 · Cited by 105 · see citing works

Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine

Sulaiman, J., Gan, H. M., Yin, W., & Chan, K. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00556 · Cited by 102 · see citing works

Characterization of the aromatic profile of purple passion fruit (Passiflora edulis Sims) during ripening by HS-SPME-GC/MS and RNA sequencing

Li, C., Xin, M., Li, L., et al. (2021) · Food Chemistry · doi:10.1016/j.foodchem.2021.129685 · Cited by 102 · see citing works

Microbiota of an Italian Grana-Like Cheese during Manufacture and Ripening, Unraveled by 16S rRNA-Based Approaches

Alessandria, V., Ferrocino, I., Filippis, F. D., Fontana, M., Rantsiou, K., Ercolini, D., & Cocolin, L. (2016) · Applied and Environmental Microbiology · doi:10.1128/aem.00999-16 · Cited by 99 · see citing works

Computational Approaches for Integrative Analysis of the Metabolome and Microbiome

Chong, J., & Xia, J. (2017) · Metabolites · doi:10.3390/metabo7040062 · Cited by 99 · see citing works

Species classifier choice is a key consideration when analysing low-complexity food microbiome data

Walsh, A. M., Crispie, F., O’Sullivan, Ó., Finnegan, L., Claesson, M. J., & Cotter, P. D. (2018) · Microbiome · doi:10.1186/s40168-018-0437-0 · Cited by 99 · see citing works

Source identification of antibiotic resistance genes in a peri-urban river using novel crAssphage marker genes and metagenomic signatures

Chen, H., Bai, X., Li, Y., Jing, L., Chen, R., & Teng, Y. (2019) · Water Research · doi:10.1016/j.watres.2019.115098 · Cited by 96 · see citing works

Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance

Bokulich, N. A., Bergsveinson, J., Ziola, B. R., & Mills, D. A. (2015) · eLife · doi:10.7554/elife.04634 · Cited by 93 · see citing works

Omics-Based Insights into Flavor Development and Microbial Succession within Surface-Ripened Cheese

Bertuzzi, A. S., Walsh, A. M., Sheehan, J. J., Cotter, P. D., Crispie, F., McSweeney, P. L. H., Kilcawley, K. N., & Rea, M. C. (2018) · mSystems · doi:10.1128/msystems.00211-17 · Cited by 90 · see citing works

Understanding the bacterial communities of hard cheese with blowing defect

Bassi, D., Puglisi, E., & Cocconcelli, P. S. (2015) · Food Microbiology · doi:10.1016/j.fm.2015.07.004 · Cited by 87 · see citing works

Strain-Level Metagenomic Analysis of the Fermented Dairy Beverage Nunu Highlights Potential Food Safety Risks

Walsh, A. M., Crispie, F., Daari, K., O’Sullivan, Ó., Martin, J. C., Arthur, C. T., Claesson, M. J., Scott, K. P., & Cotter, P. D. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.01144-17 · Cited by 86 · see citing works

The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities

Tan, X., Chung, T., Chen, Y., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0726-2 · Cited by 86 · see citing works

FoodMicrobionet: A Database for the Visualisation and Exploration of Food Bacterial Communities Based on Network Analysis

Parente, E., Cocolin, L., De Filippis, F., Zotta, T., Ferrocino, I., O'Sullivan, O., Neviani, E., De Angelis, M., Cotter, P. D., & Ercolini, D. (2016) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2015.12.001 · Cited by 82 · see citing works

Enhancing the proportion of gluconic acid with a microbial community reconstruction method to improve the taste quality of Kombucha

Li, R., Xu, Y., Chen, M., Wang, F., Zou, C., & Yin, J. (2021) · LWT · doi:10.1016/j.lwt.2021.112937 · Cited by 82 · see citing works

Next generation of microbiological risk assessment: Potential of omics data for exposure assessment

den Besten, H. M. W., Amézquita, A., Bover‐Cid, S., et al. (2017) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2017.10.006 · Cited by 78 · see citing works

Colonization of the human gut by bovine bacteria present in Parmesan cheese

Milani, C., Duranti, S., Napoli, S., Alessandri, G., Mancabelli, L., Anzalone, R., Longhi, G., Viappiani, A., Mangifesta, M., Lugli, G. A., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-09303-w · Cited by 78 · see citing works

Novel approaches for the identification of microbial communities in kimchi: MALDI-TOF MS analysis and high-throughput sequencing

Kim, E., Cho, E.-J., Yang, S.-M., Kim, M., & Kim, H. (2020) · Food Microbiology · doi:10.1016/j.fm.2020.103641 · Cited by 76 · see citing works

Genomic and metabolic features of Lactobacillus sakei as revealed by its pan-genome and the metatranscriptome of kimchi fermentation

Kim, K. H., Chun, B. H., Baek, J. H., Roh, S. W., Lee, S. H., & Jeon, C. O. (2019) · Food Microbiology · doi:10.1016/j.fm.2019.103341 · Cited by 72 · see citing works

Counteracting the effect of reducing nitrate/nitrite levels on dry fermented sausage aroma by Debaryomyces hansenii inoculation

Perea-Sanz, L., López-Díez, J. J., Belloch, C., et al. (2020) · Meat Science · doi:10.1016/j.meatsci.2020.108103 · Cited by 72 · see citing works

Co-Occurrence of Listeria spp. and Spoilage Associated Microbiota During Meat Processing Due to Cross-Contamination Events

Zwirzitz, B., Wetzels, S. U., Dixon, E. D., et al. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.632935 · Cited by 69 · see citing works

Development of Microbiome Biobanks – Challenges and Opportunities

Ryan, M. J., Schloter, M., Berg, G., KOSTIC, T. M., Kinkel, L. L., Eversole, K., Macklin, J., Schelkle, B., Κάζου, Μ., Sarand, I., et al. (2020) · Trends in Microbiology · doi:10.1016/j.tim.2020.06.009 · Cited by 67 · see citing works

Construction of a synthetic microbial community for the biosynthesis of volatile sulfur compound by multi-module division of labor

Du, R., Liu, J., Jiang, J. G., Wang, Y., Ji, X., Yang, N., Wu, Q. J., & Xu, Y. (2021) · Food Chemistry · doi:10.1016/j.foodchem.2021.129036 · Cited by 65 · see citing works

Population Genetics of Lactobacillus sakei Reveals Three Lineages with Distinct Evolutionary Histories

Chaillou, S., Lucquin, I., Najjari, A., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0073253 · Cited by 64 · see citing works

Effect of synthetic microbial community on nutraceutical and sensory qualities of kombucha

Wang, S., Zhang, L., Qi, L., et al. (2020) · International Journal of Food Science & Technology · doi:10.1111/ijfs.14596 · Cited by 61 · see citing works

Metagenome‐based surveillance and diagnostic approaches to studying the microbial ecology of food production and processing environments

Doyle, C. J., O’Toole, P. W., & Cotter, P. D. (2017) · Environmental Microbiology · doi:10.1111/1462-2920.13859 · Cited by 60 · see citing works

Processing Environment and Ingredients Are Both Sources of Leuconostoc gelidum, Which Emerges as a Major Spoiler in Ready-To-Eat Meals

Pothakos, V., Stellato, G., Ercolini, D., & Devlieghere, F. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.03941-14 · Cited by 59 · see citing works

Potential of yeasts isolated from dry-cured ham to control ochratoxin A production in meat models

Peromingo, B., Núñez, F., Rodríguez, A., Alía, A., & Andrade, M. J. (2018) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2018.01.006 · Cited by 56 · see citing works

Spatiotemporal Distribution of the Environmental Microbiota in Food Processing Plants as Impacted by Cleaning and Sanitizing Procedures: the Case of Slaughterhouses and Gaseous Ozone

Botta, C., Ferrocino, I., Pessione, A., Cocolin, L., & Rantsiou, K. (2020) · Applied and Environmental Microbiology · doi:10.1128/aem.01861-20 · Cited by 54 · see citing works

Is there any still undisclosed biodiversity in Ciauscolo salami? A new glance into the microbiota of an artisan production as revealed by high-throughput sequencing

Belleggia, L., Milanović, V., Ferrocino, I., Cocolin, L., Haouet, M. N., Scuota, S., Maoloni, A., Garofalo, C., Cardinali, F., Aquilanti, L., et al. (2020) · Meat Science · doi:10.1016/j.meatsci.2020.108128 · Cited by 53 · see citing works

Integrative Metagenomics–Metabolomics for Analyzing the Relationship Between Microorganisms and Non-volatile Profiles of Traditional Xiaoqu

Zhao, C. G., Su, W., Mu, Y., Mu, Y., & Jiang, L. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.617030 · Cited by 53 · see citing works

Shotgun metagenomics approach reveals the bacterial community and metabolic pathways in commercial hongeo product, a traditional Korean fermented skate product

Zhao, C., & Eun, J. (2020) · Food Research International · doi:10.1016/j.foodres.2020.109030 · Cited by 52 · see citing works

Composition, Succession, and Source Tracking of Microbial Communities throughout the Traditional Production of a Farmstead Cheese

Sun, L., & D’Amico, D. J. (2021) · mSystems · doi:10.1128/msystems.00830-21 · Cited by 52 · see citing works

Is it useful to use several “omics” for obtaining valuable results?

Sozoniuk, M., Chrobak, L., Kowalczyk, K., & Kankofer, M. (2019) · Molecular Biology Reports · doi:10.1007/s11033-019-04793-9 · Cited by 51 · see citing works

Strain-Level Diversity Analysis of Pseudomonas fragi after <i>In Situ</i> Pangenome Reconstruction Shows Distinctive Spoilage-Associated Metabolic Traits Clearly Selected by Different Storage Conditions

De Filippis, F., La Storia, A., Villani, F., & Ercolini, D. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.02212-18 · Cited by 47 · 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

Efficacy of the Combined Protective Cultures of Penicillium chrysogenum and Debaryomyces hansenii for the Control of Ochratoxin A Hazard in Dry-Cured Ham

Cebrián, E., Rodrı́guez, M., Peromingo, B., Bermúdez, E., & Núñez, F. (2019) · Toxins · doi:10.3390/toxins11120710 · Cited by 44 · see citing works

Culture-enriched human gut microbiomes reveal core and accessory resistance genes

Raymond, F., Boissinot, M., Ouameur, A. A., Déraspe, M., Plante, P.-L., Kpanou, S., Bérubé, È., Huletsky, A., Roy, P. H., Ouellette, M., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0669-7 · Cited by 43 · see citing works

A Vegetable Fermentation Facility Hosts Distinct Microbiomes Reflecting the Production Environment

Einson, J. E., Rani, A., You, X., Rodriguez, A. A., Randell, C. L., Barnaba, T. J., Mammel, M. K., Kotewicz, M. L., Elkins, C. A., & Sela, D. A. (2018) · Applied and Environmental Microbiology · doi:10.1128/aem.01680-18 · Cited by 41 · see citing works

In vitro antifungal effects of spices on ochratoxin A production and related gene expression in Penicillium nordicum on a dry-cured fermented sausage medium

Álvarez, M., Rodríguez, A., Núñez, F., Silva, A., & Andrade, M. J. (2020) · Food Control · doi:10.1016/j.foodcont.2020.107222 · Cited by 40 · see citing works

Advancing integration of data on food microbiome studies: FoodMicrobionet 3.1, a major upgrade of the FoodMicrobionet database

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

Editorial: Exploring the need to include microbiomes into EFSA's scientific assessments

Merten, C., Schoonjans, R., Gioia, D. D., Peláez, C., Sanz, Y., Maurici, D., & Robinson, T. P. (2020) · EFSA Journal · doi:10.2903/j.efsa.2020.e18061 · Cited by 36 · see citing works

Specific metagenomic asset drives the spontaneous fermentation of Italian sausages

Franciosa, I., Ferrocino, I., Giordano, M., Mounier, J., Rantsiou, K., & Cocolin, L. (2021) · Food Research International · doi:10.1016/j.foodres.2021.110379 · Cited by 36 · see citing works

Toward a Global Ecology of Fermented Foods

Dunn, R. R., Wilson, J. B., Nichols, L. M., & Gavin, M. C. (2021) · Current Anthropology · doi:10.1086/716014 · Cited by 36 · see citing works

Calling for a systems approach in microbiome research and innovation

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Are microbiome studies ready for hypothesis-driven research?

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