Zooming into food-associated microbial consortia: a “cultural” evolution

QIIME allows analysis of high-throughput community sequencing data

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Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

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The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

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A Selected Core Microbiome Drives the Early Stages of Three Popular Italian Cheese Manufactures

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Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

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

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PCR-DGGE fingerprinting: novel strategies for detection of microbes in food

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Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food

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Sequence-based analysis of the bacterial and fungal compositions of multiple kombucha (tea fungus) samples

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High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

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A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

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Facility-specific “house” microbiome drives microbial landscapes of artisan cheesemaking plants

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Microbial terroir for wine grapes

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High-Throughput Sequencing for Detection of Subpopulations of Bacteria Not Previously Associated with Artisanal Cheeses

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Culture independent methods to assess the diversity and dynamics of microbiota during food fermentation

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Diversity, distribution and sources of bacteria in residential kitchens

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Multifactorial Diversity Sustains Microbial Community Stability

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Microbial Ecology Dynamics during Rye and Wheat Sourdough Preparation

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Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons

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Exploring the Sources of Bacterial Spoilers in Beefsteaks by Culture-Independent High-Throughput Sequencing

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Culture dependent and independent analysis of bacterial communities associated with commercial salad leaf vegetables

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Brewhouse-Resident Microbiota Are Responsible for Multi-Stage Fermentation of American Coolship Ale

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Monitoring Seasonal Changes in Winery-Resident Microbiota

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“Remake” by high-throughput sequencing of the microbiota involved in the production of water buffalo mozzarella cheese

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Microbial community dynamics during fermentation of doenjang-meju, traditional Korean fermented soybean

Jung, J. Y., Lee, S. H., & Jeon, C. O. (2014) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2014.06.003 · Cited by 155 · see citing works

Metagenomic Analysis of the Viral Communities in Fermented Foods

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Comparison of microbial communities in marinated and unmarinated broiler meat by metagenomics

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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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Comparative Transcriptomic and Phenotypic Analysis of the Responses ofBacillus cereusto Various Disinfectant Treatments

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Dynamics of Bacterial Communities during the Ripening Process of Different Croatian Cheese Types Derived from Raw Ewe's Milk Cheeses

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Transcriptome analysis of Listeria monocytogenes exposed to biocide stress reveals a multi-system response involving cell wall synthesis, sugar uptake, and motility

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Tool for Quantification of Staphylococcal Enterotoxin Gene Expression in Cheese

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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

Exploiting the explosion of information associated with whole genome sequencing to tackle Shiga toxin-producing Escherichia coli (STEC) in global food production systems

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Staphylococcus aureus virulence and metabolism are dramatically affected by Lactococcus lactis in cheese matrix

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Strain dependent expression of stress response and virulence genes of Listeria monocytogenes in meat juices as determined by microarray

Rantsiou, K., Greppi, A., Garosi, M., Acquadro, A., Mataragas, M., & Cocolin, L. (2011) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2011.08.009 · Cited by 66 · see citing works

Global Gene Expression of Listeria monocytogenes to Salt Stress

Bae, D., Liu, C. S., ZHANG, T., Jones, M. B., Peterson, S. N., & Wang, C. (2012) · Journal of Food Protection · doi:10.4315/0362-028x.jfp-11-282 · Cited by 60 · see citing works

Relative transcription of Listeria monocytogenes virulence genes in liver pâtés with varying NaCl content

Olesen, I., Thorsen, L., & Jespersen, L. (2010) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2010.01.042 · Cited by 58 · see citing works

Short- and Long-Term Biomarkers for Bacterial Robustness: A Framework for Quantifying Correlations between Cellular Indicators and Adaptive Behavior

den Besten, H. M. W., Arvind, A., Gaballo, H. M. S., Moezelaar, R., Zwietering, M. H., & Abee, T. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013746 · Cited by 57 · see citing works

Causal Relationship between Microbial Ecology Dynamics and Proteolysis during Manufacture and Ripening of Protected Designation of Origin (PDO) Cheese Canestrato Pugliese

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

Influence of storage temperature on gene expression and virulence potential of Listeria monocytogenes strains grown in a salmon matrix

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Animal Rennets as Sources of Dairy Lactic Acid Bacteria

Cruciata, M., Sannino, C., Ercolini, D., Scatassa, M. L., Filippis, F. D., Mancuso, I., Storia, A. L., Moschetti, G., & Settanni, L. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.03837-13 · Cited by 54 · see citing works

rRNA-based monitoring of the microbiota involved in Fontina PDO cheese production in relation to different stages of cow lactation

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

Transcriptomic and Phenotypic Responses ofListeria monocytogenesStrains Possessing Different Growth Efficiencies under Acidic Conditions

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Understanding the behavior of foodborne pathogens in the food chain: New information for risk assessment analysis

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Differential gene expression profiling of Listeria monocytogenes in Cacciatore and Felino salami to reveal potential stress resistance biomarkers

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How many16S-based studies should be included in a metagenomic conference? It may be a matter of etymology

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Microarray-based transcriptome ofListeria monocytogenesadapted to sublethal concentrations of acetic acid, lactic acid, and hydrochloric acid

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Differential Gene Expression of E. coli O157:H7 in Ground Beef Extract Compared to Tryptic Soy Broth

Fratamico, P. M., Wang, S., Yan, X., Zhang, W., & Li, Y. (2011) · Journal of Food Science · doi:10.1111/j.1750-3841.2010.01952.x · Cited by 29 · see citing works

Microbiome definition re-visited: old concepts and new challenges

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Residential Bacteria on Surfaces in the Food Industry and Their Implications for Food Safety and Quality

Møretrø, T., & Langsrud, S. (2017) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.12283 · Cited by 369 · see citing works

Metagenomics insights into food fermentations

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Fermentation for tailoring the technological and health related functionality of food products

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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

Microbial consortia: a critical look at microalgae co-cultures for enhanced biomanufacturing

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Metagenomics reveals flavour metabolic network of cereal vinegar microbiota

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Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.

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

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The human gastrointestinal tract and oral microbiota in inflammatory bowel disease: a state of the science review

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The challenges and perspectives of the selection of starter cultures for fermented cocoa beans

Figueroa-Hernández, C. Y., Gutierrez, J. M., Ferrocino, I., Hernández‐Estrada, Z. J., González-Ríos, Ó., Cocolin, L., & Suárez-Quiroz, M. L. (2019) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2019.05.002 · Cited by 114 · see citing works

Microbial co-culturing strategies for the production high value compounds, a reliable framework towards sustainable biorefinery implementation – an overview

Rosero-Chasoy, G., Rodríguez-Jasso, R. M., Aguilar, C. N., Buitrón, G., Chairez, I., & Ruiz, H. A. (2021) · Bioresource Technology · doi:10.1016/j.biortech.2020.124458 · Cited by 111 · see citing works

Translating Omics to Food Microbiology

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Food Safety, a Global Challenge

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Sausage fermentation and starter cultures in the era of molecular biology methods

Franciosa, I., Alessandria, V., Dolci, P., Rantsiou, K., & Cocolin, L. (2018) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2018.04.038 · Cited by 99 · 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

Occurrence and Importance of Yeasts in Indigenous Fermented Food and Beverages Produced in Sub-Saharan Africa

Johansen, P. G., Owusu‐Kwarteng, J., Parkouda, C., Padonou, S. W., & Jespersen, L. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01789 · Cited by 99 · see citing works

The Significance of Mesophilic Aeromonas spp. in Minimally Processed Ready-to-Eat Seafood

Hoel, S., Vadstein, Ô., & Jakobsen, A. N. (2019) · Microorganisms · doi:10.3390/microorganisms7030091 · Cited by 94 · see citing works

Minced meat-like products from mealworm larvae (Tenebrio molitor and Alphitobius diaperinus): microbial dynamics during production and storage

Stoops, J., Vandeweyer, D., Crauwels, S., Verreth, C., Boeckx, H., Borght, M. V. D., CLAES, J. E., Lievens, B., & Campenhout, L. V. (2017) · Innovative Food Science & Emerging Technologies · doi:10.1016/j.ifset.2017.02.001 · Cited by 92 · 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

Next-Generation Food Research: Use of Meta-Omic Approaches for Characterizing Microbial Communities Along the Food Chain

Yap, M., Ercolini, D., Álvarez‐Ordóñez, A., O’Toole, P. W., O’Sullivan, Ó., & Cotter, P. D. (2021) · Annual Review of Food Science and Technology · doi:10.1146/annurev-food-052720-010751 · Cited by 75 · see citing works

Omics approaches to understand sourdough fermentation processes

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Investigation of the Activity of the Microorganisms in a Reblochon-Style Cheese by Metatranscriptomic Analysis

Monnet, C., Dugat‐Bony, É., Swennen, D., Beckerich, J.-M., Irlinger, F., Fraud, S., & Bonnarme, P. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00536 · Cited by 64 · 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

High-Throughput Sequence Analyses of Bacterial Communities and Multi-Mycotoxin Profiling During Processing of Different Formulations of Kunu, a Traditional Fermented Beverage

Ezekiel, C. N., Ayeni, K. I., Ezeokoli, O. T., Sulyok, M., van Wyk, D. A. B., Oyedele, O. A., Akinyemi, M. O., Chibuzor‐Onyema, I. E., Adeleke, R. A., Nwangburuka, C. C., et al. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.03282 · Cited by 59 · see citing works

Different Lactobacillus populations dominate in “Chorizo de León” manufacturing performed in different production plants

Quijada, N. M., Filippis, F. D., Sanz, J. J., Fernández, M. D. C. G., Rodrı́guez-Làzaro, D., Ercolini, D., & Hernández, M. (2017) · Food Microbiology · doi:10.1016/j.fm.2017.09.009 · Cited by 57 · see citing works

From DNA barcoding to personalized nutrition: the evolution of food traceability

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Impact of Nisin-Activated Packaging on Microbiota of Beef Burgers during Storage

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Microbial ecology involved in the ripening of naturally fermented llama meat sausages. A focus on lactobacilli diversity

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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

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A continuously changing selective context on microbial communities associated with fish, from egg to fork

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Production and Conservation of Starter Cultures: From “Backslopping” to Controlled Fermentations

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Bioactive Compounds Produced by the Accompanying Microflora in Bulgarian Yoghurt

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Exploiting Beneficial Pseudomonas spp. for Cannabis Production

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Yeasts are essential for mucilage degradation of coffee beans during wet fermentation

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Next Generation Sequencing: problems and opportunities for next generation studies of microbial communities in food and food industry

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Implementation of omics tools for infant food microbial safety

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Advances in the Application of FISH in Food Microbiology

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Microbial Ecology and Fermentation Dynamics of Moroccan Lben

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