Literature cited in proposal 2022NN28ZZ

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Here is a complete list of references for proposal 2022NN28ZZ.

  1. Tamang J.P., Cotter P.D., Endo A., Han S.N., Kort R., Liu S.Q., Mayo B., Westerik N., Hutkins R. Fermented foods in a global age: East meets West. Compr Rev Food Sci Food Saf 19, 184–217 (2020). 1111/1541-4337.12520 
  2. Marco M.L., Heeney D., Binda S., Cifelli C.J., Cotter P.D., Foligné B., Gänzle M., Kort R., Pasin G., Pihlanto A., Smid E.J., Hutkins R. Health benefits of fermented foods: microbiota and beyond. Curr Opin Biotechnol 44, 94–102 (2017). 1016/j.copbio.2016.11.010
  3. Tamang J.P., Watanabe K., Holzapfel, W.H. Review: Diversity of Microorganisms in Global Fermented Foods and Beverages. Front Microbiol 7, 377 (2016). DOI: 3389/fmicb.2016.00377
  4. Pasolli E.; De Filippis F., Mauriello I.E., Cumbo F., Walsh A.M., Leech J., Cotter P.D., Segata N., Ercolini D. Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome. Nat Commun 11, 2610 (2020). 1038/s41467-020-16438-8
  5. Dimidi E., Cox S. R., Rossi, M., Whelan, K. Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease. Nutrients 11, 1806 (2019). 3390/nu11081806
  6. Kårlund A., Gómez –Gallego C., Korhonen J., Palo-oja O-M., Kolehmainen M. Harnessing Microbes for Sustainable Development: Food Fermentation as a Tool for Improving the Nutritional Quality of Alternative Protein Sources. Nutrients 12, 1020 (2020). 3390/nu12041020
  7. Timmis K., de Vos W.M., Ramos J.L., Vlaeminck S.E., Prieto A., Danchin A., Verstraete W., de Lorenzo V., Lee S.Y., Brüssow H., Timmis J.K., Singh B.K. The contribution of microbial biotechnology to sustainable development goals. Microb Biotechnol 10, 984–987 (2017). 1111/1751-7915.12818
  8. Capozzi V., Fragasso M. , Bimbo, F. Microbial Resources, Fermentation and Reduction of Negative Externalities in Food Systems: Patterns toward Sustainability and Resilience. Fermentation 7, 54 (2021). 3390/fermentation7020054
  9. De Filippis F., Parente E., Ercolini, D. Metagenomics insights into food fermentations. Microb Biotechnol 10, 91–102 (2017). 1111/1751-7915.12421
  10. De Filippis F., Parente E., Ercolini D. Recent Past, Present, and Future of the Food Microbiome. Annu Rev Food Sci Technol 9, 589–608 (2018). 1146/annurev-food-030117-012312
  11. Jonnala B.R.Y., McSweeney P.L.H., Sheehan J.J., Cotter, P.D. Sequencing of the Cheese Microbiome and Its Relevance to Industry. Front Microbiol 9, 1020 (2018). 3389/fmicb.2018.01020
  12. Wolfe B. E., Dutton, R. J. Fermented Foods as Experimentally Tractable Microbial Ecosystems. Cell 161, 49–55 (2015). 1016/j.cell.2015.02.034
  13. Zotta T., Ricciardi A., Condelli N., Parente, E. Metataxonomic and metagenomic approaches for the study of undefined strain starters for cheese manufacture. Crit Rev Food Sci 1–15 (2021). 1080/10408398.2020.1870927
  14. Poirier , Rué O., Peguilhan R., Coeuret G., Zagorec M., Champomier-Vergè M.-C., Loux V., Chaillou S.. Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing. PLoS One 13, e0204629 (2018). 10.1371/journal.pone.0204629
  15. Kaehler B.D., Bokulich N.A.,McDonald D., Knight R., Caporaso J.G., Huttley G.A. Species abundance information improves sequence taxonomy classification accuracy. Nat Commun 10, 4643 (2019). 1038/s41467-019-12669-6
  16. Parente E., Zotta T., Ricciardi, A. FoodMicrobionet v4: a large, integrated, open and transparent database for food bacterial communities. Biorxiv01.19.476946 (2022). 10.1101/2022.01.19.476946
  17. Springmann M., Wiebe K.,Mason-D’Croz D., Sulser T.B., Rayner M., Scarborough P. Health and nutritional aspects of sustainable diet strategies and their association with environmental impacts: a global modelling analysis with country-level detail. Lancet Planet Health 2, e451–e461 (2018). 1016/S2542-5196(18)30206-7
  18. Di Cagno R., Coda R., De Angelis M., Gobbetti M. Exploitation of vegetables and fruits through lactic acid fermentation. Food Microbiol 33, 1–10 (2013). 1016/j.fm.2012.09.003
  19. Campus M., Değirmencioğlu N., Comunian R. Technologies and Trends to Improve Table Olive Quality and Safety. Front Microbiol 9, 617 (2018). 3389/fmicb.2018.00617
  20. Anagnostopoulos D. A., Tsaltas, D. Current Status, Recent Advances, and Main Challenges on Table Olive Fermentation: The Present Meets the Future. Front Microbiol 12, 797295 (2022). 3389/fmicb.2021.797295
  21. Galili E., Langgu D., Terral J.F., Barazani O., Dag A., Kolska Horwitz, Ogloblin Ramirez I., Rosen B., Weinstein-Evron M., Chaim S., Kremer E., Lev-Yadun S., Boaretto E., Ben-Barak-Zelas Z., Fishman A.    Early production of table olives at a mid-7th millennium BP submerged site off the Carmel coast (Israel). Sci Rep11, 2218 (2021). 10.1038/s41598-020-80772-6
  22. Perpetuini G., Prete R., Garcia-Gonzalez N., Alam M. K., Corsetti A. Table Olives More than a Fermented Food. Foods 9, 178 (2020). 3390/foods9020178
  23. Vaccalluzzo A., Pino A., Russo N., De Angelis M., Caggia C., Randazzo C.L. FoodOmics as a new frontier to reveal microbial community and metabolic processes occurring on table olives fermentation. Food Microbiol 92, 103606 (2020). 1016/j.fm.2020.103606
  24. Hurtado A., Reguant C., Bordons A., Rozès N. Lactic acid bacteria from fermented table olives. Food Microbiol 31, 1–8 (2012). 1016/j.fm.2012.01.006
  25. Arroyo-LópezN.,  Romero-Gil V., Bautista-Gallego J. ,  Rodríguez-Gómez F.,  Jiménez-Díaz R., García-GarcíaP., Querol A.,  Garrido-Fernández A. Yeasts in table olive processing: desirable or spoilage microorganisms? Int J Food Microbiol 160, 42–49 (2012). 10.1016/j.ijfoodmicro.2012.08.003
  26. Portilha-Cunha M. F., Macedo A.C. ,Malcata F. X. A Review on Adventitious Lactic Acid Bacteria from Table Olives. Foods 9, 948 (2020). DOI: 10.3390/foods9070948
  27. de Castro, Antonio Higinio SánchezA.,  López-López  A.,  Cortés-Delgado A.,  Medina  E., Alfredo Montaño  A. Microbiota and Metabolite Profiling of Spoiled Spanish-Style Green Table Olives. Metabolites 8, 73 (2018). 10.3390/metabo8040073
  28. de Castro A., Ruiz-BarbaL., Romero C., Sánchez H. , García P., Brenes M. Formation of gas pocket defect in Spanish-style green olives by the halophile Celerinatantimonas sp. Food Control 136, 108868 (2022). 10.1016/j.foodcont.2022.108868
  29. Penland,  Deutsch S.M.,  Falentin  H.,  Pawtowski A., Poirier  E., Visenti  G.,  Le Meur   C.,  Maillard  M.-B., Thierry A.,  Mounier J.,  Coton  M. Deciphering Microbial Community Dynamics and Biochemical Changes During Nyons Black Olive Natural Fermentations. Front Microbiol 11, 586614 (2020). 10.3389/fmicb.2020.586614
  30. Penland,  MounierJ., Pawtowski  A.,  Tréguer  S.,  Deutsch S.-M., Coton M. Use of metabarcoding and source tracking to identify desirable or spoilage autochthonous microorganism sources during black olive fermentations. Food Res Int 144, 110344 (2021). 10.1016/j.foodres.2021.110344
  31. Lucena-Padrós H., Ruiz-Barba J. L. Microbial biogeography of Spanish-style green olive fermentations in the province of Seville, Spain. Food Microbiol 82, 259–268 (2019). 1016/j.fm.2019.02.004
  32. Kazou M., Tzamourani A., Panagou E. Z.,Tsakalidou, E. Unraveling the Microbiota of Natural Black cv. Kalamata Fermented Olives through 16S and ITS Metataxonomic Analysis. Microorganisms 8, 672 (2020). 3390/microorganisms8050672
  33. Soto-GironJ.,  Kim J.-N.,  Schott   E.,  Tahmin   C.,  Ishoey  T., Tracy J., Mincer T.J.,  DeWalt  J.,  Toledo G. The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host. Sci Rep 11, 24017 (2021). 10.1038/s41598-021-03334-4
  34. Martín-Vertedor,  SchaideT.,  Boselli  E.,  Martínez  M.,  Arias-Calderón  R., Francisco Pérez-Nevado  F.Effects of Different Controlled Temperatures on Spanish-Style Fermentation Processes of Olives. Foods 10, 666 (2021). 10.3390/foods10030666
  35. Romero-Gil V., Bautista-Gallego J., Rodríguez-Gómez F., García-García P., Jiménez-Díaz R., Garrido-Fernández A., Arroyo-López F.N. Evaluating the individual effects of temperature and salt on table olive related microorganisms. Food Microbiol 33, 178–184 (2013). 1016/j.fm.2012.09.015
  36. Cosetta C.M., Wolfe B. E. Causes and consequences of biotic interactions within microbiomes. Curr Opin Microbiol 50, 35–41 (2019). 1016/j.mib.2019.09.004
  37. Wolfe B. E., Button J. E., Santarelli M., Dutton R. J. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. Cell 158, 422–433 (2014). 1016/j.cell.2014.05.041
  38. Layeghifard M., Hwang D. M., Guttman D. S. Disentangling Interactions in the Microbiome: A Network Perspective. Trends Microbiol 25, 217–228 (2017). 1016/j.tim.2016.11.008
  39. Jiang,  Armour   C.R.,  Hu C.,  Mei M.,  Tian  C.,  Sharpton T.J., Yuan Jiang Y. Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities. Front Genet 10, 995 (2019). 10.3389/fgene.2019.00995
  40. Lanza B., Zago M., Carminati D., Rossetti L., Meucci A., Marfisi P. Russi F., Iannucci F., Di Serio M.G., Giraffa G. Isolation and preliminary characterization of Lactobacillus plantarum bacteriophages from table olive fermentation. Ann Microbiol 62, 1467–1472 (2012). 1007/s13213-011-0400-9
  41. Canon F., Nidelet T., Guédon E., Thierry A., Gagnaire V. Understanding the Mechanisms of Positive Microbial Interactions That Benefit Lactic Acid Bacteria Co-cultures. Front Microbiol 11, 2088 (2020). 3389/fmicb.2020.02088
  42. Pollock, J., Glendinning, L., Wisedchanwet, T. & Watson, M. The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies. Appl Environl Microbiol 84, 3225 (2018). 1128/AEM.02627-17
  43. Bokulich N. A., Ziemski M., Robeson M.S. Kaehler B.D. Measuring the microbiome: Best practices for developing and benchmarking microbiomics methods. Comput Struct Biotechnol J 18, 4048–4062 (2020). 1016/j.csbj.2020.11.049
  44. Davis N.M., Proctor D.M., Holmes S.P., Relman D.A., Callahan, B.J. Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome 6, 226 (2018). 1186/s40168-018-0605-2
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  46. Pasolli,  Asnicar F. ,  Manara  S.,  Zolfo M.,  Karcher N.,  Armanini F.,  Beghini  F. ,  Manghi  P.,  Tett  A. , Ghensi P., Collado M.C., Rice B.L., DuLong C., Morgan X.C., Golden C.D., Quince C., Huttenhower C., Segata N., Collado M.C.,  Rice B.L. ,  DuLong  C.,  Morgan  X.C.,  Golden C.D., Quince C.,  Huttenhower  C., Segata N. Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle. Cell 176, 649-662.e20 (2019). 10.1016/j.cell.2019.01.001
  47. De Filippis F., Pasolli E., Ercolini D. Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease. Curr Biol 30, 4932-4943.e4 (2020). 1016/j.cub.2020.09.063
  48. SánchezH. ,  López-López A.,  Cortés-Delgado  A.,  Beato  V.M., Medina  E. , Antonio de Castro A., Alfredo Montaño A. Effect of post-fermentation and packing stages on the volatile composition of Spanish-style green table olives. Food Chem 239, 343–353 (2018). 10.1016/j.foodchem.2017.06.125
  49. Salzano A., Manganiello G., Neglia G.,Vinale F., De Nicola D., D’Occhio M., Campanile G. Preliminary Study on Metabolome Profiles of Buffalo Milk and Corresponding Mozzarella Cheese: Safeguarding the Authenticity and Traceability of Protected Status Buffalo Dairy Products. Molecules 25, 304 (2020). 3390/molecules25020304
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