Galli, B. D. Sustainability implications and relevance of using omics sciences to investigate cheeses with protected designation of origin. J. Sci. Food Agric. 104, 6388–6396 (2024).

CAS 
PubMed 

Google Scholar 

Masotti, F., Hogenboom, J. A., Rosi, V., De Noni, I. & Pellegrino, L. Proteolysis indices related to cheese ripening and typicalness in PDO Grana Padano cheese. Int. Dairy J. 20, 352–359 (2010).

CAS 

Google Scholar 

Ercolini, D. High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology. Appl. Environ. Microbiol. 79, 3148–3155 (2013).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Giraffa, G. The Microbiota of Grana Padano cheese. A review. Foods 10, 2632 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

De Filippis, F. et al. Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities. npj Biofilms Microbiomes 10, 67 (2024).

PubMed 
PubMed Central 

Google Scholar 

Afshari, R., Pillidge, C. J., Dias, D. A., Osborn, A. M. & Gill, H. Cheesomics: the future pathway to understanding cheese flavour and quality. Crit. Rev. Food Sci. Nutr. 60, 33–47 (2020).

CAS 
PubMed 

Google Scholar 

De Filippis, F., Genovese, A., Ferranti, P., Gilbert, J. A. & Ercolini, D. Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. Sci. Rep. 6, 21871 (2016).

PubMed 
PubMed Central 

Google Scholar 

Bertuzzi, A. S., McSweeney, P. L. H., Rea, M. C. & Kilcawley, K. N. Detection of volatile compounds of cheese and their contribution to the flavor profile of surface-ripened cheese. Compr. Rev. Food Sci. Food Saf. 17, 371–390 (2018).

CAS 
PubMed 

Google Scholar 

Anastasiou, R. et al. Omics approaches to assess flavor development in cheese. Foods 11, 188 (2022).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Neviani, E., Bottari, B., Lazzi, C. & Gatti, M. New developments in the study of the microbiota of raw-milk, long-ripened cheeses by molecular methods: the case of Grana Padano and Parmigiano Reggiano. Front. Microbiol. 4, 36 (2013).

PubMed 
PubMed Central 

Google Scholar 

Qian, M. & Reineccius, G. Potent aroma compounds in Parmigiano Reggiano cheese studied using a dynamic headspace (purge-trap) method. Flavour Fragr. J. 18, 252–259 (2003).

CAS 

Google Scholar 

Hayaloglu, A. A. Volatile composition and proteolysis in traditionally produced mature Kashar cheese. Int. J. Food Sci. Technol. 44, 1388–1394 (2009).

CAS 

Google Scholar 

Bottari, B. et al. The interrelationship between microbiota and peptides during ripening as a driver for Parmigiano Reggiano cheese quality. Front. Microbiol. 11, 581658 (2020).

PubMed 
PubMed Central 

Google Scholar 

Sforza, S., Ferroni, L., Galaverna, G., Dossena, A. & Marchelli, R. Extraction, semi-quantification, and fast on-line identification of oligopeptides in Grana Padano cheese by HPLC-MS. J. Agric. Food Chem. 51, 2130–2135 (2003).

CAS 
PubMed 

Google Scholar 

Summer, A. et al. Cheese as functional food: the example of Parmigiano Reggiano and Grana Padano. Food Technol. Biotechnol. 55, 277–289 (2017).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Rangel, A. H. D. N. et al. An overview of the occurrence of bioactive peptides in different types of cheeses. Foods 12, 4261 (2023).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Dinan, T. G., Stanton, C. & Cryan, J. F. Psychobiotics: a novel class of psychotropic. Biol. Psychiatry 74, 720–726 (2013).

CAS 
PubMed 

Google Scholar 

Balasubramanian, R., Schneider, E., Gunnigle, E., Cotter, P. D. & Cryan, J. F. Fermented foods: Harnessing their potential to modulate the microbiota-gut-brain axis for mental health. Neurosci. Biobehav. Rev. 158, 105562 (2024).

CAS 
PubMed 

Google Scholar 

Ijaz, M. U. et al. Microbiome and neurological disorders. in Human Microbiome 273–301. https://doi.org/10.1007/978-981-97-3790-1_9 (Springer Nature Singapore, 2024).

Magliulo, R. et al. Microbiome signatures associated with flavor development differentiate Protected Designation of origin water Buffalo Mozzarella cheese from different production areas. Food Res. Int. 192, 114798 (2024).

CAS 
PubMed 

Google Scholar 

Afshari, R. et al. New insights into cheddar cheese microbiota-metabolome relationships revealed by integrative analysis of multi-omics data. Sci. Rep. 10, 3164 (2020).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Bottari, B., Levante, A., Neviani, E. & Gatti, M. How the fewest become the greatest. L. casei’s impact on long ripened cheeses. Front. Microbiol. 9, 2866 (2018).

PubMed 
PubMed Central 

Google Scholar 

Kim, E., Yang, S.-M. & Kim, H.-Y. Differentiation of Lacticaseibacillus zeae using pan-genome analysis and real-time PCR method targeting a unique gene. Foods 10, 2112 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

da Silva Duarte, V., Lombardi, A., Corich, V. & Giacomini, A. Assessment of the microbiological origin of blowing defects in Grana Padano Protected Designation of Origin cheese. J. Dairy Sci. 105, 2858–2867 (2022).

PubMed 

Google Scholar 

Avila, M., Gómez-Torres, N., Hernández, M. & Garde, S. Inhibitory activity of reuterin, nisin, lysozyme and nitrite against vegetative cells and spores of dairy-related Clostridium species. Int. J. Food Microbiol. 172, 70–75 (2014).

CAS 
PubMed 

Google Scholar 

Kleerebezem, M. et al. The extracellular biology of the lactobacilli. FEMS Microbiol. Rev. 34, 199–230 (2010).

CAS 
PubMed 

Google Scholar 

D’Incecco, P. et al. Lysozyme affects the microbial catabolism of free arginine in raw-milk hard cheeses. Food Microbiol. 57, 16–22 (2016).

PubMed 

Google Scholar 

Dias, R., Vilas-Boas, E., Campos, F. M., Hogg, T. & Couto, J. A. Activity of lysozyme on Lactobacillus hilgardii strains isolated from Port wine. Food Microbiol. 49, 6–11 (2015).

CAS 
PubMed 

Google Scholar 

Bassi, D., Puglisi, E. & Cocconcelli, P. S. Understanding the bacterial communities of hard cheese with blowing defect. Food Microbiol. 52, 106–118 (2015).

PubMed 

Google Scholar 

Courtin, P. et al. Accelerating cheese proteolysis by enriching Lactococcus lactis proteolytic system with lactobacilli peptidases. Int. Dairy J. 12, 447–454 (2002).

CAS 

Google Scholar 

Gatti, M. et al. A model to assess lactic acid bacteria aminopeptidase activities in Parmigiano Reggiano cheese during ripening. J. Dairy Sci. 91, 4129–4137 (2008).

CAS 
PubMed 

Google Scholar 

Bancalari, E. et al. An integrated strategy to discover Lactobacillus casei group strains for their potential use as aromatic starters. Food Res. Int. 100, 682–690 (2017).

CAS 
PubMed 

Google Scholar 

Sgarbi, E. et al. Nonstarter lactic acid bacteria volatilomes produced using cheese components. J. Dairy Sci. 96, 4223–4234 (2013).

CAS 
PubMed 

Google Scholar 

Randazzo, C. L. et al. Preliminary characterization of wild lactic acid bacteria and their abilities to produce flavour compounds in ripened model cheese system. J. Appl. Microbiol. 103, 427–435 (2007).

CAS 
PubMed 

Google Scholar 

Lazzi, C. et al. Can the development and autolysis of lactic acid bacteria influence the cheese volatile fraction? The case of Grana Padano. Int. J. Food Microbiol. 233, 20–28 (2016).

CAS 
PubMed 

Google Scholar 

Illikoud, N., Mantel, M., Rolli-Derkinderen, M., Gagnaire, V. & Jan, G. Dairy starters and fermented dairy products modulate gut mucosal immunity. Immunol. Lett. 251–252, 91–102 (2022).

PubMed 

Google Scholar 

Walther, B. et al. Quantitative analysis of menaquinones (vitamin K2) in various types of cheese from Switzerland. Int. Dairy J. 112, 104853 (2021).

CAS 

Google Scholar 

Berding, K. et al. Feed your microbes to deal with stress: a psychobiotic diet impacts microbial stability and perceived stress in a healthy adult population. Mol. Psychiatry 28, 601–610 (2023).

CAS 
PubMed 

Google Scholar 

Moreira, G. M. M. et al. Effect of ripening time on proteolysis, free amino acids, bioactive amines and texture profile of Gorgonzola-type cheese. LWT 98, 583–590 (2018).

CAS 

Google Scholar 

Lacroix, N., St-Gelais, D., Champagne, C. P. & Vuillemard, J. C. Gamma-aminobutyric acid-producing abilities of lactococcal strains isolated from old-style cheese starters. Dairy Sci. Technol. 93, 315–327 (2013).

CAS 

Google Scholar 

Sousa, R. J. M., Ribeiro, S. C., Baptista, J. A. B. & Silva, C. C. G. Evaluation of gamma-aminobutyric acid content in Portuguese cheeses with protected designation of origin status. J. Dairy Res. 90, 1–4 (2023).

Google Scholar 

Park, K.-B. & Oh, S.-H. Isolation and characterization of Lactobacillus buchneri strains with high γ-aminobutyric acid producing capacity from naturally aged cheese. Food Sci. Biotechnol. 15, 86–90 (2006).

CAS 

Google Scholar 

Cho, Y. R., Chang, J. Y. & Chang, H. C. Production of gamma-aminobutyric acid (GABA) by Lactobacillus buchneri isolated from kimchi and its neuroprotective effect on neuronal cells. J. Microbiol. Biotechnol. 17, 104–109 (2007).

CAS 
PubMed 

Google Scholar 

Valenzuela, J. A., Flórez, A. B., Vázquez, L., Vasek, O. M. & Mayo, B. Production of γ-aminobutyric acid (GABA) by lactic acid bacteria strains isolated from traditional, starter-free dairy products made of raw milk. Benef. Microbes 10, 579–587 (2019).

CAS 
PubMed 

Google Scholar 

Sanders, J. W. et al. A chloride-inducible acid resistance mechanism in Lactococcus lactis and its regulation. Mol. Microbiol. 27, 299–310 (1998).

CAS 
PubMed 

Google Scholar 

Chen, M. et al. Neurotransmitter and intestinal interactions: focus on the Microbiota-gut-brain axis in irritable bowel syndrome. Front. Endocrinol.13, 817100 (2022).

Google Scholar 

Laroute, V. et al. Lactococcus lactis NCDO2118 exerts visceral antinociceptive properties in rat via GABA production in the gastro-intestinal tract. eLife 11, e77100 (2022).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Liang, S. et al. Administration of Lactobacillus helveticus NS8 improves behavioral, cognitive, and biochemical aberrations caused by chronic restraint stress. Neuroscience 310, 561–577 (2015).

CAS 
PubMed 

Google Scholar 

Murru, E. et al. Conjugated linoleic acid and brain metabolism: a possible anti-neuroinflammatory role mediated by PPARα activation. Front. Pharmacol. 11, 587140 (2020).

CAS 
PubMed 

Google Scholar 

Fujita, Y. et al. Dietary cis-9, trans-11-conjugated linoleic acid reduces amyloid β-protein accumulation and upregulates anti-inflammatory cytokines in an Alzheimer’s disease mouse model. Sci. Rep. 11, 9749 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Valcarcel-Jimenez, L. & Frezza, C. Fumarate hydratase (FH) and cancer: a paradigm of oncometabolism. Br. J. Cancer 129, 1546–1557 (2023).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Wikoff, W. R. et al. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc. Natl. Acad. Sci. USA 106, 3698–3703 (2009).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Bertani, G. et al. Dynamics of a natural bacterial community under technological and environmental pressures: the case of natural whey starter for Parmigiano Reggiano cheese. Food Res. Int. 129, 108860 (2020).

CAS 
PubMed 

Google Scholar 

Neviani, E., Levante, A. & Gatti, M. The microbial community of natural whey starter: Why is it a driver for the production of the most famous Italian long-ripened cheeses?. Fermentation 10, 186 (2024).

Google Scholar 

Lazzi, C., Rossetti, L., Zago, M., Neviani, E. & Giraffa, G. Evaluation of bacterial communities belonging to natural whey starters for Grana Padano cheese by length heterogeneity-PCR. J. Appl. Microbiol. 96, 481–490 (2004).

CAS 
PubMed 

Google Scholar 

De Dea Lindner, J. et al. Parmigiano Reggiano cheese: evolution of cultivable and total lactic microflora and peptidase activities during manufacture and ripening. Dairy Sci. Technol. 88, 511–523 (2008).

Google Scholar 

Schmieder, R. & Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863–864 (2011).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Blanco-Míguez, A. et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4. Nat. Biotechnol. 41, 1633–1644 (2023).

PubMed 
PubMed Central 

Google Scholar 

Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).

CAS 
PubMed 

Google Scholar 

Wood, D. E. & Salzberg, S. L. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol. 15, R46 (2014).

PubMed 
PubMed Central 

Google Scholar 

Blin, K. et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res. 51, W46–W50 (2023).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Pasolli, E. et al. Extensive unexplored human microbiome diversity revealed by over 150,000 genomes from metagenomes spanning age, geography, and lifestyle. Cell 176, 649–662.e20 (2019).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Kang, D. D., Froula, J., Egan, R. & Wang, Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3, e1165 (2015).

PubMed 
PubMed Central 

Google Scholar 

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 36, 1925–1927 (2019).

PubMed 
PubMed Central 

Google Scholar 

Letunic, I. & Bork, P. Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool. Nucleic Acids Res. 52, W78–W82 (2024).

PubMed 
PubMed Central 

Google Scholar 

Liao, H., Ji, Y. & Sun, Y. High-resolution strain-level microbiome composition analysis from short reads. Microbiome 11, 183 (2023).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Zhu, W., Lomsadze, A. & Borodovsky, M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res. 38, e132 (2010).

PubMed 
PubMed Central 

Google Scholar 

Rawlings, N. D., Waller, M., Barrett, A. J. & Bateman, A. MEROPS: the database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res. 42, D503–D509 (2014).

CAS 
PubMed 

Google Scholar 

Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).

CAS 
PubMed 
PubMed Central 

Google Scholar 

Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L. & Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods 5, 621–628 (2008).

CAS 
PubMed 

Google Scholar 

da Silva Duarte, V. et al. Database selection for shotgun metaproteomic of low-diversity dairy microbiomes. Int. J. Food Microbiol. 418, 110706 (2024).

PubMed 

Google Scholar 

Balivo, A. et al. Can hydroponic forage affect the chemical and sensory properties of PDO buffalo Mozzarella cheese? Int. J. Dairy Technol. 78, e13147 (2025).

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