Skip to main content

Natural Microflora of Different Types of Foods

  • Chapter
  • First Online:
Book cover Health and Safety Aspects of Food Processing Technologies

Abstract

The sources of thousands of different microorganisms in foods could be either natural or external. The microorganisms in foods are divided into three groups as molds, yeast and bacteria. Natural microflora of foods influences the quality, availability and quantity of products. Molds are generally known as spoilage microorganisms in foods. Therefore, usage of them in food processing is limited (i.e. mold ripened cheese, soybean fermented foods). Conversely, yeasts and bacteria are widely used as important microorganisms in food industry. They have ability to ferment sugars to some industrially important compounds such as ethanol, lactic acid, acetic acid and carbon dioxide. In addition, they can contribute to the texture, flavor and safety of foods. The microorganisms intrinsically existing in food play a key role in processing of numerous foods especially plant based fermented foods, milk and meat based fermented products. The aim of the present chapter is to discuss the natural microflora belonging to different foods and also to explain their functions during food processing.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abbad Andaloussi S, Talbaoui H, Marczak R, Bonaly R (1995) Isolation and characterization of exocellular polysaccharides produced by Bifidobacterium longum. Appl Microbiol Biotechnol 43(6):995–1000

    CAS  PubMed  Google Scholar 

  • Abriouel H, Franz CMAP, Omar NB, Gálvez A (2011) Diversity and applications of Bacillus bacteriocins. FEMS Microbiol Rev 35(1):201–232

    CAS  PubMed  Google Scholar 

  • Adjou ES, Metome G, Gbaguidi BA, Dahouenon-Ahoussi E, Sohounhloue D (2017) Evaluation of the fungal microflora infesting pigeon pea (Cajanus cajan L. Millspaugh) in southern Benin and associated mycological hazards. Int J Health Anim Sci Food Saf 4(1):49–58

    Google Scholar 

  • Agirman B, Erten H (2018) The influence of various chloride salts to reduce sodium content on the quality parameters of şalgam (Shalgam): a traditional Turkish beverage based on black carrot. J Food Qual 2018:3292185

    Google Scholar 

  • Ajayi AO (2013) Nature of tomatoes microflora under storage. Am J Exp Agric 3(1):89–101

    Google Scholar 

  • Albano H, van Reenen CA, Todorov SD, Cruz D, Fraga L, Hogg T, Dicks LM, Teixeira P (2009) Phenotypic and genetic heterogeneity of lactic acid bacteria isolated from “Alheria”, a traditional fermented sausage produced in Portugal. Meat Sci 82:389–398

    CAS  PubMed  Google Scholar 

  • Alvarez-Sieiro P, Montalban-Lopez M, Mu D, Kuipers OP (2016) Bacteriocins of lactic acid bacteria: extending the family. Appl Microbiol Biotechnol 100(7):2939–2951

    CAS  PubMed  PubMed Central  Google Scholar 

  • Amari M, Arango LF, Gabriel V, Robert H, Morel S, Moulis C, Gabriel B, Remaud-Simeon M, Fontagne-Faucher C (2013) Characterization of a novel dextransucrase from Weissella confusa isolated from sourdough. Appl Microbiol Biotechnol 97(12):5413–5422

    CAS  PubMed  Google Scholar 

  • Aneja KR, Dhiman R, Aggarwal NK, Kumar V, Kaur M (2014) Microbes associated with freshly prepared juices of citrus and carrots. Int J Food Sci 2014:408085

    PubMed  PubMed Central  Google Scholar 

  • Anonymous (1999) Introduction to bacteria. https://www.umsl.edu/microbes/files/pdfs/introductiontobacteria.pdf. Accessed 21 Feb 2019

  • Anonymous (2003) Factors that influence microbial growth. Compr Rev Food Sci Food Saf 2:21–32

    Google Scholar 

  • Anonymous (2019) Microorganisms and food. http://www.epralima.com/infoodquality/English_materials/Manuais/3.Microorganisms.pdf. Accessed 21 Feb 2019

  • Antinone MJ, Ledford RA (1993) Reduction of diacetyl in cottage cheese by Geotrichum candidum. Cultured Dairy Prod J 28:26–30

    CAS  Google Scholar 

  • Arias CR, Burns JK, Friedrich LM, Goodrich RM, Parish ME (2002) Yeast species associated with orange juice: evaluation of different identification methods. Appl Environ Microbiol 68(4):1955–1961

    CAS  PubMed  PubMed Central  Google Scholar 

  • Arroyo-Lopez FN, Querol A, Bautista-Gallego J, Garrido-Fernandez A (2008) Role of yeasts in table olive production. Int J Food Microbiol 128(2):189–196

    CAS  PubMed  Google Scholar 

  • Askelson TE, Campasino A, Lee JT, Duong T (2014) Evaluation of phytate-degrading Lactobacillus culture administration to broiler chickens. Appl Environ Microbiol 80(3):943–950

    PubMed  PubMed Central  Google Scholar 

  • Austin B (2002) The bacterial microflora of fish. Sci World J 2:558–572

    CAS  Google Scholar 

  • Aylward EB, Oleary J, Langlois BE (1980) Effect of milk storage on cottage cheese yield. J Dairy Sci 63(11):1819–1825

    Google Scholar 

  • Barakat RK, Griffiths MW, Harris LJ (2000) Isolation and characterization of Carnobacterium, Lactococcus, and Enterococcus spp. from cooked, modified atmosphere packaged, refrigerated, poultry meat. Int J Food Microbiol 62(1–2):83–94

    CAS  PubMed  Google Scholar 

  • Barth M, Hankinson TR, Zhuang H, Breidt F (2009) Microbiological spoilage of fruits and vegetables. In: Sperber WH, Michael PD (eds) Compendium of the microbiological spoilage of foods and beverages. Springer, New York, pp 135–183

    Google Scholar 

  • Baur C, Krewinkel M, Kranz B, von Neubeck M, Wenning M, Scherer S, Stoeckel M, Hinrichs J, Stressler T, Fischer L (2015) Quantification of the proteolytic and lipolytic activity of microorganisms isolated from raw milk. Int Dairy J 49:23–29

    CAS  Google Scholar 

  • Bjorkroth KJ, Vandamme P, Korkeala HJ (1998) Identification and characterization of Leuconostoc carnosum, associated with production and spoilage of vacuum-packaged, sliced, cooked ham. Appl Environ Microbiol 64(9):3313–3319

    CAS  PubMed  PubMed Central  Google Scholar 

  • Borch E, Molin G (1988) Numerical taxonomy of psychrotrophic lactic-acid bacteria from prepacked meat and meat-products. A Van Leeuw J Microb 54(4):301–323

    CAS  Google Scholar 

  • Borch E, KantMuermans ML, Blixt Y (1996) Bacterial spoilage of meat and cured meat products. Int J Food Microbiol 33(1):103–120

    CAS  PubMed  Google Scholar 

  • Bourdichon F, Casaregola S, Farrokh C, Frisvad JC, Gerds ML, Hammes WP, Harnett J, Huys G, Laulund S, Ouwehand A, Powell IB, Prajapati JB, Seto Y, Ter Schure E, Van Boven A, Vankerckhoven V, Zgoda A, Tuijtelaars S, Hansen EB (2012) Food fermentations: microorganisms with technological beneficial use. Int J Food Microbiol 154(3):87–97

    CAS  PubMed  Google Scholar 

  • Buck JW, Walcott RR, Beuchat LR (2003) Recent trends in microbiological safety of fruits and vegetables. Plant Health Prog. https://doi.org/10.1094/PHP-2003-0121-01-RV

  • Bullerman LB, Bianchini A (2009) Food safety issues and the microbiology of cereals and cereal products. In: Heredia N, Wesley I, Garcia S (eds) Microbiologically safe foods. Wiley, Hoboken, NJ, pp 315–335

    Google Scholar 

  • Burgess CM, Smid EJ, Rutten G, van Sinderen D (2006) A general method for selection of riboflavin-overproducing food grade micro-organisms. Microb Cell Factories 5(1):24

    Google Scholar 

  • Cahill MM (1990) Bacterial flora of fishes: a review. Microb Ecol 19:21–41

    CAS  PubMed  Google Scholar 

  • Calvo J, Calvente V, de Orellano ME, Benuzzi D, Sanz de Tosetti MI (2007) Biological control of postharvest spoilage caused by Penicillium expansum and Botrytis cinerea in apple by using the bacterium Rahnella aquatilis. Int J Food Microbiol 113(3):251–257

    PubMed  Google Scholar 

  • Campbell AW (2016) Molds and mycotoxins: a brief review. Altern Ther Health Med 22(4):8–11

    PubMed  Google Scholar 

  • Cao J, Zhang H, Yang Q, Ren R (2013) Efficacy of Pichia caribbica in controlling blue mold rot and patulin degradation in apples. Int J Food Microbiol 162:167–173

    PubMed  Google Scholar 

  • Capozzi V, Russo P, Dueñas MT, López P, Spano G (2012) Lactic acid bacteria producing B-group vitamins: a great potential for functional cereals products. Appl Microbiol Biotechnol 96(6):1383–1394

    CAS  PubMed  Google Scholar 

  • Carraturo F, De Castro O, Troisi J, De Luca A, Masucci A, Cennamo P, Trifuoggi M, Aliberti F, Guida M (2018) Comparative assessment of the quality of commercial black and green tea using microbiology analyses. BMC Microbiol 18:4

    PubMed  PubMed Central  Google Scholar 

  • Castro-Rosas J, Lopez EMS, Gomez-Aldapa CA, Ramirez CAG, Villagomez-Iberra JR, Gordillo-Martinez AJ, Lopez AV, Torres-Vitela MDR (2010) Incidence and behavior of Salmonella and Esherichia coli on whole and sliced zucchini squash (Cucurbita pepo) fruit. J Food Protect 73(8):1423–1429

    Google Scholar 

  • Cerning J (1990) Exocellular polysaccharides produced by lactic acid bacteria. FEMS Microbiol Lett 87(1):113–130

    CAS  Google Scholar 

  • Cerning J (1995) Production of exopolysaccharides by lactic acid bacteria and dairy propionibacteria. Lait 75(4–5):463–472

    CAS  Google Scholar 

  • Chaillou S, Christieans S, Rivollier M, Lucquin I, Champomier-Verges MC, Zagorec M (2014) Quantification and efficiency of Lactobacillus sakei strain mixtures used as protective cultures in ground beef. Meat Sci 97(3):332–338

    CAS  PubMed  Google Scholar 

  • Chand-Goyal T, Spotts RA (1996) Enumeration of bacterial and yeast colonists of apple fruits and identification of epiphytic yeasts on pear fruits in the Pacific Northwest United States. Microbiol Res 151:427–432

    CAS  PubMed  Google Scholar 

  • Chaoui A, Faid M, Belhcen R (2003) Effect of natural starters used for sourdough bread in Morocco on phytate biodegradation. East Mediterr Health J 9(1–2):141–147

    CAS  PubMed  Google Scholar 

  • Chavan RS, Chavan SR (2011) Sourdough technology—a traditional way for wholesome foods: a review. Compr Rev Food Sci Food Saf 10(3):169–182

    Google Scholar 

  • Chen H, Hoover DG (2003) Bacteriocins and their food applications. Compr Rev Food Sci Food Saf 2(3):82–100

    CAS  Google Scholar 

  • Choudhery AK, Mikolajcik EM (1970) Activity of Bacillus cereus proteinases in milk. J Dairy Sci 53(3):363–366

    CAS  PubMed  Google Scholar 

  • Christensen CM, Fanse HA, Nelson GH, Bates F, Mirocha CJ (1967) Microflora of black and red pepper. Appl Microbiol 15(3):622–626

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cocolin L, Innocente N, Biasutti M, Comi G (2004) The late blowing in cheese: a new molecular approach based on PCR and DGGE to study the microbial ecology of the alteration process. Int J Food Microbiol 90(1):83–91

    CAS  PubMed  Google Scholar 

  • Cocolin L, Dolci P, Rantsiou K (2011) Biodiversity and dynamics of meat fermentations: the contribution of molecular methods for a better comprehension of a complex ecosystem. Meat Sci 89(3):296–302

    CAS  PubMed  Google Scholar 

  • Comi G, Iacumin L (2012) Identification and process origin of bacteria responsible for cavities and volatile off-flavour compounds in artisan cooked ham. Int J Food Sci Technol 47:114–121

    CAS  Google Scholar 

  • Dalton HK, Board RG, Davenport RR (1984) The yeasts of British fresh sausage and minced beef. Antonie Van Leeuwenhoek 50(3):227–248

    CAS  PubMed  Google Scholar 

  • De Angelis M, Gallo G, Corbo MR, McSweeney PL, Faccia M, Giovine M, Gobbetti M (2003) Phytase activity in sourdough lactic acid bacteria: purification and characterization of a phytase from Lactobacillus sanfranciscensis CB1. Int J Food Microbiol 87(3):259–270

    PubMed  Google Scholar 

  • De Vuyst L, Degeest B (1999) Heteropolysaccharides from lactic acid bacteria. FEMS Microbiol Rev 23(2):153–177

    PubMed  Google Scholar 

  • De Vuyst L, Neysens P (2005) The sourdough microflora: biodiversity and metabolic interactions. Trends Food Sci Technol 16:43–56

    Google Scholar 

  • De Vuyst L, Vandamme EJ (1994) Lactic acid bacteria and bacteriocins: their practical importance. In: De Vuyst L, Vandamme EJ (eds) Bacteriocins of lactic acid bacteria: microbiology, genetics and applications. Blackie Academic and Professional, Glasgow, pp 1–12

    Google Scholar 

  • Delfini C, Gaia P, Schellino R, Strano M, Pagliara A, Ambro S (2002) Fermentability of grape must after inhibition with dimethyl dicarbonate (DMDC). J Agric Food Chem 50:5605–5611

    CAS  PubMed  Google Scholar 

  • Di Cagno R, De Angelis M, Limitone A, Minervini F, Carnevali P, Corsetti A, Gaenzle M, Ciati R, Gobbetti M (2006) Glucan and fructan production by sourdough Weissella cibaria and Lactobacillus plantarum. J Agric Food Chem 54(26):9873–9881

    PubMed  Google Scholar 

  • Díez L, Rojo-Bezares B, Zaragaza M, Rodriguez JM, Torres C, Ruiz-Larrea F (2012) Antimicrobial activity of pediocin PA-1 against Oenococcus oeni and other wine bacteria. Food Microbiol 31(2):167–172

    PubMed  Google Scholar 

  • Doores S (1983) The microbiology of apples and apple products. Crit Rev Food Sci Nutr 19(2):133–149

    CAS  PubMed  Google Scholar 

  • Doyle MP, Beuchat LR (eds) (2007) Food microbiology: fundamentals and frontiers. ASM Press, Washington

    Google Scholar 

  • Egan AF, Shay BJ, Rogers PJ (1989) Factors affecting the production of hydrogen sulphide by Lactobacillus sake L13 growing on vacuum-packaged beef. J Appl Bacteriol 67(3):255–262

    CAS  Google Scholar 

  • Endo A, Dicks LMT (2014) Physiology of the LAB. In: Holzapfel WH, Wood BJB (eds) Lactic acid bacteria biodiversity and taxonomy. Wiley, West Sussex, pp 13–30

    Google Scholar 

  • Ercolini D, Russo F, Torrieri E, Masi P, Villani F (2006) Changes in the spoilage-related microbiota of beef during refrigerated storage under different packaging conditions. Appl Environ Microbiol 72(7):4663–4671

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ercolini D, Russo F, Nasi A, Ferranti P, Villani F (2009) Mesophilic and psychrotrophic bacteria from meat and their spoilage potential in vitro and in beef. Appl Environ Microbiol 75(7):1990–2001

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ercolini D, Ferrocino I, Nasi A, Ndagijimana M, Vernocchi P, La Storia A, Laghi L, Mauriello G, Guerzoni ME, Villani F (2011) Monitoring of microbial metabolites and bacterial diversity in beef stored under different packaging conditions. Appl Environ Microbiol 77(20):7372–7381

    CAS  PubMed  PubMed Central  Google Scholar 

  • Erdem O, Gultekin-Ozguven M, Berktas I, Ersan S, Tuna HE, Karadag A, Özçelik B, Güneş G, Cutting SM (2014) Development of a novel synbiotic dark chocolate enriched with Bacillus indicus HU36, maltodextrin and lemon fiber: optimization by responce surface methodology. LWT Food Sci Technol 56:187–193

    CAS  Google Scholar 

  • Erten H, Tanguler H (2016) Shalgam (Şalgam): a traditional Turkish lactic acid fermented beverage based on black carrot. In: Hui YH, Evranuz EÖ, Erten H, Bingöl G, Flores MEJ (eds) Handbook of vegetable preservation and processing, 2nd edn. CRC Press, Boca Raton, FL, pp 841–849

    Google Scholar 

  • Erten H, Ağirman B, Boyaci-Gündüz CP, Çarşanba E, Sert S, Bircan S, Tangüler H (2014) Importance of yeasts and lactic acid bacteria in food processing. In: Malik A, Erginkaya Z, Ahmad S, Erten H (eds) Food processing strategies for quality assessment. Springer, New York, pp 351–378

    Google Scholar 

  • Erten H, Boyacı-Gündüz CP, Agirman B, Cabaroglu T (2016) Fermentation, pickling and Turkish table olives. In: Hui YH, Evranuz Ö, Bingöl G, Erten H, Jaramillo-Flores ME (eds) Handbook of vegetable preservation and processing, 2nd edn. CRC Press, Boca Raton, FL, pp 209–230

    Google Scholar 

  • Erten H, Agirman B, Boyaci-Gunduz CP, Ben Ghorbal A (2017) Regional fermented vegetables and fruits in Europe. In: Paramithiotis S (ed) Lactic acid fermentation of fruits and vegetables. CRC Press, Boca Raton, FL, pp 205–235

    Google Scholar 

  • Ewaschuk JB, Walker JW, Diaz H, Madsen KL (2006) Bioproduction of conjugated linoleic acid by probiotic bacteria occurs in vitro and in vivo in mice. J Nutr 136(6):1483–1487

    CAS  PubMed  Google Scholar 

  • Fairbairn DJ, Law BA (1986) Proteinases of psychrotrophic bacteria - their production, properties, effects and control. J Dairy Res 53(1):139–177

    CAS  PubMed  Google Scholar 

  • FAO (1999) Fermented cereals: a global perspective. FAO Agricultural Services Bulletin, Rome

    Google Scholar 

  • FAO (2014) Sources of meat. http://www.fao.org/ag/againfo/themes/en/meat/backgr_sources.html. Accessed 20 Feb 2019

  • FAO/WHO (2002) Report of a Joint FAO/WHO Working Group on Drafting guidelines for the evaluation of probiotics in food. London, Ontario, Canada, April 30 and May 1

    Google Scholar 

  • Farhad M, Kailasapathy K, Tamang JP (2010) Health aspects of fermented foods. In: Tamang JP, Kailasapathy K (eds) Fermented foods and beverages of the world. CRC Press, New York, NY, pp 391–414

    Google Scholar 

  • Fitzgerald DJ, Stratford M, Gasson MJ, Narbad A (2004) The potential application of vanillin in preventing yeast spoilage of soft drinks and fruit juices. J Food Prot 67(2):391–395

    CAS  PubMed  Google Scholar 

  • Fleet GH (2003) Yeast interactions and wine flavour. Int J Food Microbiol 86(1–2):11–22

    CAS  PubMed  Google Scholar 

  • Forde A, Fitzgerald GF (2000) Biotechnological approaches to the understanding and improvement of mature cheese flavour. Curr Opin Biotechnol 11(5):484–489

    CAS  PubMed  Google Scholar 

  • Franco W, Johanningsmeier S, Lu J, Demo J, Wilson E, Moeller L (2017) Cucumber fermentation. In: Paramithiotis S (ed) Lactic acid fermentation of fruits and vegetables. CRC Press, Boca Raton, FL, pp 107–155

    Google Scholar 

  • Fucikovsky L, Ortega S (1997) Bacterial and fungal diseases of lettuce (Lactuca sativa L.) in the state of Mexico, Mexico. In: Rudolph K, Burr TJ, Mansfield JW, Stead D, Vivian A, von Kietzell J (eds) Pseudomonas syringae pathovars and related pathogens - developments in plant pathology. Springer, Dordrecht, pp 45–48

    Google Scholar 

  • Galanakis CM (2017) Chapter 1 - Introduction. In: Galanakis CM (ed) Nutraceutical and functional food components. Academic, London, pp 1–14

    Google Scholar 

  • Galle S, Schwab C, Arendt E, Ganzle M (2010) Exopolysaccharide-forming Weissella strains as starter cultures for sorghum and wheat sourdoughs. J Agric Food Chem 58(9):5834–5841

    CAS  PubMed  Google Scholar 

  • Gänzle M, Gobbetti M (2013) Physiology and biochemistry of lactic acid bacteria. In: Gobbetti M, Gänzle M (eds) Handbook on sourdough biotechnology. Springer, Boston, MA, pp 183–216

    Google Scholar 

  • Gänzle MG, Loponen J, Gobbetti M (2008) Proteolysis in sourdough fermentations: mechanisms and potential for improved bread quality. Trends Food Sci Technol 19(10):513–521

    Google Scholar 

  • García M, Sanz B, Garcia-Collia P, Ordónez J (1989) Activity and thermostability of the extracellular lipases and proteinases from pseudomonads isolated from raw milk. Milchwissenschaft 44:547–550

    Google Scholar 

  • Gardini F, Özogul Y, Suzzi G, Tabanelli G, Özogul F (2016) Technological factors affecting biogenic amine content in foods: a review. Front Microbiol 7:1218

    PubMed  PubMed Central  Google Scholar 

  • Garofalo C, Osimani A, Milanovic V, Aquilanti L, De Filippis F, Stellato G, Di Mauro S, Turchetti B, Buzzini P, Ercolini D, Clementi F (2015) Bacteria and yeast microbiota in milk kefir grains from different Italian regions. Food Microbiol 49:123–133

    CAS  PubMed  Google Scholar 

  • Geeraerts W, De Vuyst L, Leroy F (2019) Mapping the dominant microbial species diversity at expiration date of raw meat and processed meats from equine origin, an underexplored meat ecosystem, in the Belgian trail. Int J Food Microbiol 289:189–199

    PubMed  Google Scholar 

  • Geissler AJ, Behr J, von Kamp K, Vogel RF (2016) Metabolic strategies of beer spoilage lactic acid bacteria in beer. Int J Food Microbiol 216:60–68

    CAS  PubMed  Google Scholar 

  • Gerez CL, Rollan GC, de Valdez GF (2006) Gluten breakdown by Lactobacilli and pediococci strains isolated from sourdough. Lett Appl Microbiol 42(5):459–464

    CAS  PubMed  Google Scholar 

  • Gill CO (1996) Extending the storage life of raw chilled meats. Meat Sci 43(s1):99–109

    Google Scholar 

  • Gill CO (2003) Active packaging in practice: meat. In: Ahvenainem R (ed) Novel food packaging technology, 1st edn. Woodhead Publishing Limited and CRC Press, Boca Raton, FL, pp 378–396

    Google Scholar 

  • Gill CO, Badoni M (2004) Effects of peroxyacetic acid, acidified sodium chlorite or lactic acid solutions on the microflora of chilled beef carcasses. Int J Food Microbiol 91(1):43–50

    CAS  PubMed  Google Scholar 

  • Gobbetti M, Smacchi E, Corsetti A (1996) The proteolytic system of Lactobacillus sanfrancisco CB1: purification and characterization of a proteinase, a dipeptidase, and an aminopeptidase. Appl Environ Microbiol 62(9):3220–3226

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gobbetti M, De Angelis M, Corsetti A, Di Cagno R (2005) Biochemistry and physiology of sourdough lactic acid bacteria. Trends Food Sci Technol 16(1):57–69

    CAS  Google Scholar 

  • Gobbetti M, Cagno RD, De Angelis M (2010) Functional microorganisms for functional food quality. Crit Rev Food Sci Nutr 50(8):716–727

    CAS  PubMed  Google Scholar 

  • Gonzalez R (2006) Metabolic engineering of bacteria for food ingredients. In: Shetty K, Paliyath G, Pometto A, Levin RE (eds) Food biotechnology, 2nd edn. Taylor & Francis Group, Boca Raton, FL, pp 133–152

    Google Scholar 

  • Green PH, Cellier C (2007) Celiac disease. N Engl J Med 357(17):1731–1743

    CAS  PubMed  Google Scholar 

  • Gribble A, Brightwell G (2013) Spoilage characteristics of Brochothrix thermosphacta and campestris in chilled vacuum packaged lamb, and their detection and identification by real time PCR. Meat Sci 94(3):361–368

    CAS  PubMed  Google Scholar 

  • Gribble A, Mills J, Brightwell G (2014) The spoilage characteristics of Brochothrix thermosphacta and two psychrotolerant Enterobacteriacae in vacuum packed lamb and the comparison between high and low pH cuts. Meat Sci 97(1):83–92

    CAS  PubMed  Google Scholar 

  • Griffiths MW, Phillips JD, Muir DD (1987) Effect of low-temperature storage on the bacteriological quality of raw milk. Food Microbiol 4(4):285–291

    Google Scholar 

  • Gullo M, Giudici P (2008) Acetic acid bacteria in traditional balsamic vinegar: phenotypic traits relevant for starter cultures selection. Int J Food Microbiol 125(1):46–53

    CAS  PubMed  Google Scholar 

  • Gurung N, Ray S, Bose S, Rai V (2013) A broader view: microbial enzymes and their relevance in industries, medicine, and beyond. Biomed Res Int 2013:329121

    PubMed  PubMed Central  Google Scholar 

  • Hammes WP, Ganzle M (1998) Sourdough breads and related products. In: Woods BJB (ed) Microbiology of fermented foods. Blackie Academic and Professional, London, pp 199–216

    Google Scholar 

  • Hammes WP, Hertel C (2009) Genus I. Lactobacillus. Beijerink 1901. In: De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer K-H, Whitman WB (eds) Bergey’s manual of systematic bacteriology, The Firmicutes, vol 3, 2nd edn. Springer Science+Business Media, New York, NY, pp 465–510

    Google Scholar 

  • Hansen ÅS (2012) Sourdough bread. In: Hui EÖE YH, Arroyo-López FN, Fan L, Hansen AS, Jaramillo-Flores ME, Rakin M, Schwan RF, Zhou W (eds) Handbook of plant-based fermented food and beverage technology, 2nd edn. CRC Press, Boca Raton, FL, pp 493–515

    Google Scholar 

  • Hansen Å, Hansen B (1996) Flavour of sourdough wheat bread crumb. Z Lebensm Unters For 202(3):244–249

    CAS  Google Scholar 

  • Hardin J, Bertoni G, Kleinsmith LJ (2012) Becker’s world of the cell, 8th edn. Pearson Education, Inc., San Francisco

    Google Scholar 

  • Harding MW, Butler N, Dmytriw W, Rajput S, Burke DA, Howard RJ (2016) Characterization of microorganisms from fresh produce in Alberta, Canada reveals novel food-spoilage fungi. Res J Microbiol 12(1):20–32

    Google Scholar 

  • Harzallah D, Belhadj H (2013) Lactic acid bacteria as probiotics: characteristics, selection criteria and role in immunomodulation of human GI muccosal barrier. In: Kongo JM (ed) Lactic acid bacteria-R & D for food, health and livestock purposes. Intech, Rijeka, pp 197–216

    Google Scholar 

  • Holzapfel WH, Geisen R, Schillinger U (1995) Biological preservation of foods with reference to protective cultures, bacteriocins and food-grade enzymes. Int J Food Microbiol 24(3):343–362

    CAS  PubMed  Google Scholar 

  • Hou Z, Fink RC, Radtke C, Sadowsky MJ, Diez-Gonzalez F (2013) Incidence of naturally internalized bacteria in lettuce leaves. Int J Food Microbiol 162:260–265

    PubMed  Google Scholar 

  • Hozbor MC, Saiz AI, Yeannes MI, Fritz R (2006) Microbiological changes and its correlation with quality indices during aerobic iced storage of sea salmon (Pseudopercis semifasciata). LWT Food Sci Technol 39(2):99–104

    CAS  Google Scholar 

  • Hugenholtz J, Hunik J, Santos H, Smid E (2002) Nutraceutical production by propionibacteria. Lait 82(1):103–112

    CAS  Google Scholar 

  • Hutkins RW (2001) Metabolism of starter cultures. In: Marth EH, Steele J (eds) Applied dairy microbiology, 2nd edn. CRC Press, New York, NY, pp 207–241

    Google Scholar 

  • Jaiswal P, Sharma R, Sanodiya BS, Prakash S, Bisen P (2014) Microbial exopolysaccharides: natural modulators of dairy products. J Appl Pharm Sci 4(10):105–109

    Google Scholar 

  • Jay JM (2000) Modern food microbiology. Aspen Publishers, Gaithersburg

    Google Scholar 

  • Johnson ME (2001) Cheese products. In: Marth EH, Steele J (eds) Applied dairy microbiology, 2nd edn. CRC Press, New York, NY, pp 345–384

    Google Scholar 

  • Jolly L, Vincent SJF, Duboc P, Neeser J-R (2002) Exploiting exopolysaccharides from lactic acid bacteria. Antonie Van Leeuwenhoek 82(1):367–374

    CAS  PubMed  Google Scholar 

  • Kantor A, Kocaniova M, Kluz M (2015) Natural microflora of wine grape berries. J Microbiol Biotechnol Food Sci 4(SI1):32–36

    Google Scholar 

  • Kasfi K, Parissa T, Jafarpour B, Tarighi S (2018a) Identification of epiphytic yeasts and bacteria with potential for biocontrol of grey mold disease on table grapes caused by Botrytis cinerea. Span J Agric Res 16(1):e1002

    Google Scholar 

  • Kasfi K, Taheri P, Jafarpour B, Tarighi S (2018b) Identification of epiphytic yeasts and bacteria with potential for biocontrol of grey mold disease on table grapes caused by Botrytis cinerea. Span J Agric Res 16(1):e1002

    Google Scholar 

  • Katina K, Poutanen K (2013) Nutritional aspects of cereal fermentation with lactic acid bacteria and yeast. In: Gobbetti M, Gänzle M (eds) Handbook on sourdough biotechnology. Springer, Boston, MA, pp 229–244

    Google Scholar 

  • Katina K, Maina NH, Juvonen R, Flander L, Johansson L, Virkki L, Tenkanen M, Laitila A (2009) In situ production and analysis of Weissella confusa dextran in wheat sourdough. Food Microbiol 26(7):734–743

    CAS  PubMed  Google Scholar 

  • Khade PJ, Phirke NV (2015) Isolation and characterization of microbial flora associated with traditional wheat fermentation in submerged condition. Int J Res Stud Biosci 3(8):86–90

    Google Scholar 

  • Khalid NM, Marth EH (1990) Lactobacilli-their enzymes and role in ripening and spoilage of cheese: a review. J Dairy Sci 73(10):2669–2684

    CAS  Google Scholar 

  • Kim SW, Kim S, Lee HJ, Park JW, Ro HS (2013) Isolation of fungal pathogens to an edible mushroom, Pleurotus eryngii, and development of spesific ITS Primers. Mycobiology 41(4):252–255

    CAS  PubMed  PubMed Central  Google Scholar 

  • Klaenhammer TR (1988) Bacteriocins of lactic acid bacteria. Biochimie 70(3):337–349

    CAS  PubMed  Google Scholar 

  • Kleerebezem M, Hugenholtz J (2003) Metabolic pathway engineering in lactic acid bacteria. Curr Opin Biotechnol 14(2):232–237

    CAS  PubMed  Google Scholar 

  • Klijn N, Nieuwenhof FF, Hoolwerf JD, van der Waals CB, Weerkamp AH (1995) Identification of Clostridium tyrobutyricum as the causative agent of late blowing in cheese by species-specific PCR amplification. Appl Environ Microbiol 61(8):2919–2924

    CAS  PubMed  PubMed Central  Google Scholar 

  • Komesu A, Oliveira JAR, Martins LHS, Wolf Maciel MR, Maciel Filho R (2017) Lactic acid production to purification: a review. Bioresources 12(2):4364–4383

    CAS  Google Scholar 

  • Konar N, Toker OS, Oba S, Sagdic O (2016) Improving functionality of chocolate: a review on probiotic, prebiotic, and/or synbiotic characteristics. Trends Food Sci Technol 49:35–44

    CAS  Google Scholar 

  • König H, Fröhlich J, Unden G (eds) (2009) Biology of microorganisms on grapes, in must and in wine. Springer, Berlin

    Google Scholar 

  • Korakli M, Rossmann A, Ganzle MG, Vogel RF (2001) Sucrose metabolism and exopolysaccharide production in wheat and rye sourdoughs by Lactobacillus sanfranciscensis. J Agric Food Chem 49(11):5194–5200

    CAS  PubMed  Google Scholar 

  • Kris-Etherton PM, Hecker KD, Bonanome A, Coval SM, Binkoski AE, Hilpert KF, Griel AE, Etherton TD (2002) Bioactive compounds in foods: their role in the prevention of cardiovascular disease and cancer. Am J Med 113(9, Supplement 2):71–88

    Google Scholar 

  • Kröckel L (2013) The role of lactic acid bacteria in safety and flavour development of meat and meat products. In: Kongo M (ed) Lactic acid bacteria - R & D for food, health and livestock purposes. InTech, Rijeka, pp 129–152

    Google Scholar 

  • Kwon JH, Jee HJ (2005) Soft rot eggplant (Solanum melongena) caused by Choanephora cucurbitarum in Korea. Mycobiology 33(3):163–165

    PubMed  PubMed Central  Google Scholar 

  • Labadie J (1999) Consequences of packaging on bacterial growth. Meat is an ecological niche. Meat Sci 52(3):299–305

    CAS  PubMed  Google Scholar 

  • Laiño JE, LeBlanc JG, Savoy de Giori G (2012) Production of natural folates by lactic acid bacteria starter cultures isolated from artisanal Argentinean yogurts. Can J Microbiol 58(5):581–588

    PubMed  Google Scholar 

  • Lambrechts MG, Pretorius IS (2000) Yeast and its importance to wine aroma—a review. S Afr J Enol Vitic 21:97–129

    CAS  Google Scholar 

  • Landete JM, Ferrer S, Pardo I (2007) Biogenic amine production by lactic acid bacteria, acetic bacteria and yeast isolated from wine. Food Control 18(12):1569–1574

    CAS  Google Scholar 

  • Lasztity R (2004) Micro-organisms important in food microbiology, Food quality and standards, vol 3. Department of Biochemistry and Food Technology, Budapest University of Technology and Economics, Budapest, Hungary

    Google Scholar 

  • LeBlanc JG, Burgess C, Sesma F, de Giori GS, van Sinderen D (2005) Ingestion of milk fermented by genetically modified Lactococcus lactis improves the riboflavin status of deficient rats. J Dairy Sci 88(10):3435–3442

    CAS  PubMed  Google Scholar 

  • LeBlanc JG, Rutten G, Bruinenberg P, Sesma F, de Giori GS, Smid EJ (2006) A novel dairy product fermented with Propionibacterium freudenreichii improves the riboflavin status of deficient rats. Nutrition 22(6):645–651

    CAS  PubMed  Google Scholar 

  • Ledenbach LH, Marshall RT (2009) Microbiological spoilage of dairy products. In: Sperber WH, Doyle MP (eds) Compendium of the microbiological spoilage of foods and beverages. Springer, New York, pp 41–67

    Google Scholar 

  • Lee LW, Cheong MW, Curran P, Yu B, Liu SQ (2015) Coffee fermentation and flavor – an intricate and delicate relationship. Food Chem 185:182–191

    CAS  PubMed  Google Scholar 

  • Leff JW, Fierer N (2013) Bacterial communities associated with surfaces of fresh fruits and vegetables. PLoS One 8(3):e59310

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liao CH (2006) Pseudomonas and related genera. In: Blackburn CD (ed) Food spoilage microorganisms, 1st edn. Woodhead Publishing, Cambridge, pp 507–540

    Google Scholar 

  • Lim Y, Ryu JS, Shi S, Noh W, Kim E, Le QV, Lee HS, Ro HS (2008) Isolation of bacteria associated with the king oyster mushroom, Pleurotus eryngii. Mycobiology 36(1):13–18

    CAS  PubMed  PubMed Central  Google Scholar 

  • Linares DM, Gómez C, Renes E, Fresno JM, Tornadijo ME, Ross RP, Stanton C (2017) Lactic acid bacteria and Bifidobacteria with potential to design natural biofunctional health-promoting dairy foods. Front Microbiol 8:846

    PubMed  PubMed Central  Google Scholar 

  • Lopes FC, Lade S, Tichota DM, Daroit DJ, Velho RV, Pereira JQ, Corrêa APF, Brandelli A (2011) Production of proteolytic enzymes by a keratin-degrading Aspergillus niger. Enzyme Res 2011:487093

    PubMed  PubMed Central  Google Scholar 

  • Lopez HW, Leenhardt F, Coudray C, Remesy C (2002) Minerals and phytic acid interactions: is it a real problem for human nutrition? Int J Food Sci Technol 37(7):727–739

    CAS  Google Scholar 

  • Loponen J (2006) Prolamin degradation in sourdoughs. Doctoral dissertation, University of Helsinki, Helsinki

    Google Scholar 

  • Loss CR, Hotchkiss JH (2002) Inhibition of microbial growth by low-pressure and ambient pressure gasses. In: Juneja VK, Sofos JN (eds) Control of foodborne microorganisms. Marcel Dekker, New York, pp 245–279

    Google Scholar 

  • Lövgren A, Zhang M, Engström A, Dalhammar G, Landén R (1990) Molecular characterization of immune inhibitor A, a secreted virulence protease from Bacillus thuringiensis. Mol Microbiol 4(12):2137–2146

    PubMed  Google Scholar 

  • Loving AL, Perz J (2007) Microbialflora on restaurant beverage lemon slices. Features 70(5):18–22

    Google Scholar 

  • Maggiora M, Bologna M, Ceru MP, Possati L, Angelucci A, Cimini A, Miglietta A, Bozzo F, Margiotta C, Muzio G, Canuto RA (2004) An overview of the effect of linoleic and conjugated-linoleic acids on the growth of several human tumor cell lines. Int J Cancer 112(6):909–919

    CAS  PubMed  Google Scholar 

  • Makela P, Schillinger U, Korkeala H, Holzapfel WH (1992) Classification of ropy slime-producing lactic-acid bacteria based on DNA-DNA homology, and identification of Lactobacillus sake and Leuconostoc amelibiosum as dominant spoilage organisms in meat-products. Int J Food Microbiol 16(2):167–172

    CAS  PubMed  Google Scholar 

  • Manani TA, Collison EK, Mpuchane S (2006) Microflora of minimally processed frozen vegetables sold in Gaborone, Bostwana. J Food Protect 69(11):2581–2586

    Google Scholar 

  • Mangia NP, Murgia MA, Garau G, Sanna MG, Deiana P (2008) Influence of selected lab cultures on the evolution of free amino acids, free fatty acids and Fiore Sardo cheese microflora during the ripening. Food Microbiol 25(2):366–377

    CAS  PubMed  Google Scholar 

  • Martins G, Lauga B, Miot-Sertier C, Mercier A, Lonvaud A, Soulas ML, Soulas G, Masneuf-Pomarede I (2013) Characterization of epiphytic bacterial communities from grapes, leaves, bark and soil of grapevine plants grown, and their relations. PLoS One 8(8):e73013

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mas A, Guillamon JM, Torija MJ, Beltran G, Cerezo AB, Troncoso AM, Garcia-Parrilla MC (2014) Bioactive compounds derived from the yeast metabolism of aromatic amino acids during alcoholic fermentation. Biomed Res Int 898045:7

    Google Scholar 

  • Masoud W, Cesar LB, Jespersen L, Jakobsen M (2004) Yeast involved in fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturating gradient gel electrophoresis. Yeast 21(7):549–556

    CAS  PubMed  Google Scholar 

  • Maulani S, Hosseini SM, Elikaie A, Mirnurollahi SM (2012) Isolated microorganisms from Iranian grapes and its derivatives. Iran J Microbiol 4(1):25–29

    CAS  PubMed  PubMed Central  Google Scholar 

  • Mayo B, Aleksandrzak-Piekarczyk T, Fernández M, Kowalczyk M, Álvarez-Martín P, Bardowski J (2010) Updates in the metabolism of lactic acid bacteria. In: Biotechnology of lactic acid bacteria. Wiley-Blackwell, Hoboken, NJ, pp 3–33

    Google Scholar 

  • Mercanoglu Taban B, Saichana N (2017) Physiology and biochemistry of acetic acid bacteria. In: Yucel Sengun I (ed) Acetic acid bacteria fundamentals and food applications. CRC Press, Boca Raton, FL, pp 71–91

    Google Scholar 

  • Milesi MM, McSweeney PL, Hynes ER (2008) Viability and contribution to proteolysis of an adjunct culture of Lactobacillus plantarum in two model cheese systems: cheddar cheese-type and soft-cheese type. J Appl Microbiol 105(3):884–892

    CAS  PubMed  Google Scholar 

  • Mohamed FO, Bassette R (1979) Quality and yield of cottage cheese influenced by psychrotrophic microorganisms in milk. J Dairy Sci 62(2):222–226

    Google Scholar 

  • Molin G, Ternstrom A (1982) Numerical taxonomy of psychrotrophic Pseudomonads. J Gen Microbiol 128(6):1249–1264

    CAS  PubMed  Google Scholar 

  • Molin G, Ternstrom A (1986) Phenotypically based taxonomy of psychrotrophic Pseudomonas isolated from spoiled meat, water, and soil. Int J Syst Bacteriol 36(2):257–274

    Google Scholar 

  • Moral U, Nagar P, Maan S, Kaur K (2017) A growth of different types of microorganism, intrinsic and extrinsic factors of microorganism and their affects in food. Int J Curr Microbiol Appl Sci 6(1):290–298

    CAS  Google Scholar 

  • Mossel DAA, Corry JEL, Struijk CB, Baird RM (1995) Essentials of the microbiology of foods: a textbook for advanced studies. Wiley, Chichester

    Google Scholar 

  • Mritunjay SK, Kumar V (2017) A study on prevalence of microbial contamination on the surface of raw salad vegetables. 3Biotech 7(13):1–9

    Google Scholar 

  • Nath KR, Kostak BJ (1986) Etiology of white spot defect in Swiss cheese made from pasteurized milk. J Food Protect 49(9):718–723

    CAS  Google Scholar 

  • Nelson PJ, Marshall RT (1977) Microbial proteolysis sometimes decreases yield of cheese curd. J Dairy Sci 60:35–36

    Google Scholar 

  • Nguyen H, Elegado F, Librojo-Basilio N, Mabesa R, Dizon E (2011) Isolation and characterisation of selected lactic acid bacteria for improved processing of nem chua, a traditional fermented meat from Vietnam. Benef Microbes 1(1):67–74

    Google Scholar 

  • Nguyen DTL, Van Hoorde K, Cnockaert M, de Bradt E, de Bruyne K, Le BT, Vandamme P (2013) A culture-dependent and -independent approach for the identification of lactic acid acteria associated with the production of nem chua, a Vietnamese fermented meat product. Food Res Int 50(1):232–240

    CAS  Google Scholar 

  • Nieminen TT, Vihavainen E, Paloranta A, Lehto J, Paulin L, Auvinen P, Solismaa M, Bjorkroth KJ (2011) Characterization of psychrotrophic bacterial communities in modified atmosphere-packed meat with terminal restriction fragment length polymorphism. Int J Food Microbiol 144(3):360–366

    CAS  PubMed  Google Scholar 

  • Nigam PS (2013) Microbial enzymes with special characteristics for biotechnological applications. Biomol Ther 3(3):597–611

    Google Scholar 

  • Nychas GJE, Skandamis PN, Tassou CC, Koutsoumanis KP (2008) Meat spoilage during distribution. Meat Sci 78(1–2):77–89

    PubMed  Google Scholar 

  • Ojinnaka C, Jay AJ, Colquhoun IJ, Brownsey GJ, Morris ER, Morris VJ (1996) Structure and conformation of acetan polysaccharide. Int J Biol Macromol 19(3):149–156

    CAS  PubMed  Google Scholar 

  • Oladele, Olakunle O (2011) Microorganisms associated with the deterioration of fresh leafy Indian spinach in storage. J Plant Pathol Microbiol 2:110

    Google Scholar 

  • Oranusi S, Obioha TU, Adekeye BT (2014) Investigation on the microbial profile of frozen foods: fish and meat. Int J Adv Res Biol Sci 1(2):71–78

    Google Scholar 

  • Osburn K, Amaral J, Metcalf SR, Nickens DM, Rogers CM, Sausen C, Caputo R, Miller J, Li H, Tennessen JM, Bochman ML (2018) Primary souring: a novel bacteria-free method for sour beer production. Food Microbiol 70:76–84

    CAS  PubMed  Google Scholar 

  • Ouattara HD, Ouattara HG, Droux M, Reverchon S, Nasser W, Niamke SL (2017) Lactic acid bactria involved in cocoa beans fermentation from Ivory Coas: species diversity and citrate lypase production. Int J Food Microbiol 256:11–19

    CAS  PubMed  Google Scholar 

  • Öz E, Kaban G, Barış Ö, Kaya M (2017) Isolation and identification of lactic acid bacteria from pastırma. Food Control 77:158–162

    Google Scholar 

  • Özdemir N, Yazıcı G, Şimşek Ö, Özkal SG, Çon AH (2018) The effect of lactic acid bacteria and yeast usage on aroma development during tarhana fermentation. Food Biosci 26:30–37

    Google Scholar 

  • Paola B, Marco CL (2015) OTA-Grapes: a mechanistic model to predict ochratoxin A risk in grapes, a step beyond the system approach. Toxins 7:3012–3019

    CAS  PubMed  Google Scholar 

  • Papagianni M (2012) Metabolic engineering of lactic acid bacteria for the production of industrially important compounds. Comput Struct Biotechnol J 3:e201210003

    PubMed  PubMed Central  Google Scholar 

  • Pastink MI, Sieuwerts S, de Bok FAM, Janssen PWM, Teusink B, Vlieg JETV, Hugenholtz J (2008) Genomics and high-throughput screening approaches for optimal flavour production in dairy fermentation. Int Dairy J 18(8):781–789

    CAS  Google Scholar 

  • Patel A, Shah N, Prajapati J (2013) Biosynthesis of vitamins and enzymes in fermented foods by lactic acid bacteria and related genera - a promising approach. Croat J Food Sci Technol 5(2):85–91

    Google Scholar 

  • Patra JK, Das G, Paramithiotis S (2017) Kimchii: a well-known Korean traditional fermented food. In: Paramithiotis S (ed) Lactic acid fermentation of fruits and vegetables. CRC Press, Boca Raton, FL, pp 83–105

    Google Scholar 

  • Perez Chabela ML, Rodriguez Serrano GM, Lara Calderon P, Guerrero I (1999) Microbial spoilage of meats offered for retail sale in Mexico City. Meat Sci 51(4):279–282

    CAS  PubMed  Google Scholar 

  • Pessione E, Cirrincione S (2016) Bioactive molecules released in food by lactic acid bacteria: encrypted peptides and biogenic amines. Front Microbiol 7:876

    PubMed  PubMed Central  Google Scholar 

  • Pothakos V, Devlieghere F, Villani F, Bjorkroth J, Ercolini D (2015) Lactic acid bacteria and their controversial role in fresh meat spoilage. Meat Sci 109:66–74

    CAS  PubMed  Google Scholar 

  • Pusey PL, Stockwell VO, Mazzola M (2009) Epiphytic bacteria and yeasts on apple blossoms and their potential as antagonists of Erwinia amylovora. Biol Control 99(5):571–581

    Google Scholar 

  • Pylypenko I, Pylypenko L, Sevastyanova E, Kotlyar E, Kruchek R (2016) Epiphytic and regulated microbial contaminants of food vegetable raw materials and products. Ukrainian Food J 5(2):272–280

    CAS  Google Scholar 

  • Quigley L, O’Sullivan O, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD (2011) Molecular approaches to analysing the microbial composition of raw milk and raw milk cheese. Int J Food Microbiol 150:81–94

    CAS  PubMed  Google Scholar 

  • Quigley L, O’Sullivan O, Stanton C, Beresford TP, Ross RP, Fitzgerald GF, Cotter PD (2013) The complex microbiota of raw milk. FEMS Microbiol Rev 37:664–698

    CAS  PubMed  Google Scholar 

  • Rai AK, Tamang JP, Palni U (2010) Nutritional value of lesser-known ethnic meat products of the Himalayas. J Hill Res 23(1–2):22–25

    Google Scholar 

  • Rathi J, Dhiman A (2016) Characterization of microbes in contaminated fruits and vegetables. J Pharm Sci Innov 5(2):51–53

    CAS  Google Scholar 

  • Rattanasomboon N, Bellara SR, Harding CL, Fryer PJ, Thomas CR, Al-Rubeai M, McFarlane CM (1999) Growth and enumeration of the meat spoilage bacterium Brochothrix thermosphacta. Int J Food Microbiol 51(2–3):145–158

    CAS  PubMed  Google Scholar 

  • Rauch M, Lynch SV (2012) The potential for probiotic manipulation of the gastrointestinal microbiome. Curr Opin Biotechnol 23(2):192–201

    CAS  PubMed  Google Scholar 

  • Rawat S (2015) Food spoilage: microorganisms and their prevention. Asian J Plant Sci Res 5(4):47–56

    CAS  Google Scholar 

  • Ray B, Bhunia A (2013) Fundamental food microbiology. CRC Press, Boca Raton, FL

    Google Scholar 

  • Ray RC, Joshi VK (2015) Fermented foods: past, present and future. In: Ray RC, Montet D (eds) Microorganisms and fermentation of traditional foods. CRC Press, Boca Raton, FL, p 392

    Google Scholar 

  • Raybaudi-Massilia RM, Mosqueda-Melgar J, Soliva-Fortuny R, Martin-Belloso O (2009) Control of pathogenic and spoilage microorganisms in fresh-cut fruits and fruit juices by traditional and alternative natural antimicrobials. Compr Rev Food Sci Food Saf 8:157–180

    CAS  PubMed  Google Scholar 

  • Reale A, Mannina L, Tremonte P, Sobolev AP, Succi M, Sorrentino E, Coppola R (2004) Phytate degradation by lactic acid bacteria and yeasts during the wholemeal dough fermentation: a 31P NMR study. J Agric Food Chem 52(20):6300–6305

    CAS  PubMed  Google Scholar 

  • Richards GM, Beuchat LR (2005) Metabiotic associations of molds and Salmonella Poona on intact and wounded cantaloupe rind. Int J Food Microbiol 97:327–339

    PubMed  Google Scholar 

  • Rieder G, Krisch L, Fischer H, Kaufmann M, Maringer A, Wessler S (2012) Carnobacterium divergens - a dominating bacterium of pork meat juice. FEMS Microbiol Lett 332(2):122–130

    CAS  PubMed  Google Scholar 

  • Rizzello CG, De Angelis M, Di Cagno R, Camarca A, Silano M, Losito I, De Vincenzi M, De Bari MD, Palmisano F, Maurano F, Gianfrani C, Gobbetti M (2007) Highly efficient gluten degradation by Lactobacilli and fungal proteases during food processing: new perspectives for celiac disease. Appl Environ Microbiol 73(14):4499–4507

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rizzello CG, Coda R, Gobbetti M (2017) Chapter 18 - Use of sourdough fermentation and nonwheat flours for enhancing nutritional and healthy properties of wheat-based foods A2 - Frias, Juana. In: Martinez-Villaluenga C, Peñas E (eds) Fermented foods in health and disease prevention. Academic, Boston, MA, pp 433–452

    Google Scholar 

  • Rollan G, De Angelis M, Gobbetti M, de Valdez GF (2005) Proteolytic activity and reduction of gliadin-like fractions by sourdough Lactobacilli. J Appl Microbiol 99(6):1495–1502

    CAS  PubMed  Google Scholar 

  • Sahu L, Panda S, Paramithiotis S, Zdolec N, Ray R (2015) Biogenic amines in fermented foods: overview. In: Montet D, Ray RC (eds) Fermented foods. Part 1: Biochemistry and technology. CRC Press, Boca Raton, FL, pp 318–332

    Google Scholar 

  • Sajur SA, Saguir FM, Manca de Nadra MC (2007) Effect of dominant slecie of lactic acid bacteria from tomato on natural microflora development in tomato puree. Food Control 18:594–600

    Google Scholar 

  • Salovaara H, Gänzle M (2012) Lactic acid bacteria in cereal-based products. In: Lahtinen S, Ouwehand AC, Salminen S, von Wright A (eds) Lactic acid bacteria microbiological and functional aspects, 4th edn. Taylor & Francis Group, LLC, Boca Raton, FL, pp 227–245

    Google Scholar 

  • Scardovi V (1986) Genus Bifidobacterium Orla-Jensen 1924, 472AL. In: Sneath PHA, Mair NS, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 2. Williams & Wilkins, Baltimore, MD, pp 1418–1434

    Google Scholar 

  • Schwenninger SM, Meile L, Lacroix C (2011) 2 - Antifungal lactic acid bacteria and propionibacteria for food biopreservation. In: Lacroix C (ed) Protective cultures, antimicrobial metabolites and bacteriophages for food and beverage biopreservation. Woodhead Publishing, Cambridge, UK, pp 27–62

    Google Scholar 

  • Sengun IY, Karabiyikli S (2011) Importance of acetic acid bacteria in food industry. Food Control 22:647–665

    CAS  Google Scholar 

  • Shaw BG, Latty JB (1982) A numerical taxonomic study of Pseudomonas strains from spoiled meat. J Appl Bacteriol 52(2):219–228

    CAS  PubMed  Google Scholar 

  • Shobha S (2014) Bacteriological analysis of fresh vegetables and fruits of local market and effect of pretreatment by antimicrobial agents on their quality. Int Res J Biol Sci 3(11):15–17

    Google Scholar 

  • Simova E, Simov Z, Beshkova D, Frengova G, Dimitrov Z, Spasov Z (2006) Amino acid profiles of lactic acid bacteria, isolated from kefir grains and kefir starter made from them. Int J Food Microbiol 107(2):112–123

    CAS  PubMed  Google Scholar 

  • Şimşek Ö, Özel S, Çon AH (2017) Comparison of lactic acid bacteria diversity during the fermentation of Tarhana produced at home and on a commercial scale. Food Sci Biotechnol 26(1):181–187

    PubMed  PubMed Central  Google Scholar 

  • Sivieri K, Bedani R, Cardoso D, Cavallini U, Rossi EA (2013) Probiotics and intestinal microbiota: implications in colon cancer prevention. In: Kongo JM (ed) Lactic acid bacteria-R & D for food, Health and Livestock Purposes. InTech, Rijeka, pp 217–242

    Google Scholar 

  • Solieri L, Giudici P (2008) Yeasts associated to traditional balsamic vinegar: ecological and technological features. Int J Food Microbiol 125:36–45

    CAS  PubMed  Google Scholar 

  • Spano G, Russo P, Lonvaud-Funel A, Lucas P, Alexandre H, Grandvalet C, Coton E, Coton M, Barnavon L, Bach B, Rattray F, Bunte A, Magni C, Ladero V, Alvarez M, Fernández M, Lopez P, de Palencia PF, Corbi A, Trip H, Lolkema JS (2010) Biogenic amines in fermented foods. Eur J Clin Nutr 64(Suppl 3):S95–S100

    CAS  PubMed  Google Scholar 

  • Stanton C, Ross RP, Fitzgerald GF, Van Sinderen D (2005) Fermented functional foods based on probiotics and their biogenic metabolites. Curr Opin Biotechnol 16(2):198–203

    CAS  PubMed  Google Scholar 

  • Sun SY, Gong HS, Jiang XM, Zhao YP (2014) Selected non-Saccharomyces wine yeasts in controlled multistarter fermentations with S. cerevisiae on alcoholic fermentation behaviour and wine aroma of cherry wines. Food Microbiol 44:15–23

    CAS  PubMed  Google Scholar 

  • Sutherland IW (1972) Bacterial exopolysaccharides. Adv Microbiol Physiol 8:143–213

    CAS  Google Scholar 

  • Svoboda A, Shaw A, Wilson L, Mendonca A, Nair A, Daraba A (2016) The effects of produce washes on the quality and shelf life of “cantaloupe” (Cucumis melo var. cantalupensis) and “watermelon” (Citrullus lantus var. lanatus). J Food Qual 39:773–779

    CAS  Google Scholar 

  • Swain MR, Ananadharaj M (2017) Regional fermented vegetavles and fruits in Asia-Pacific. In: Paramithiotis S (ed) Lactic acid fermentation of fruits and vegetables. CRC Press, Boca Raton, FL, pp 181–203

    Google Scholar 

  • Szkaradkiewicz AK, Karpiński TM (2013) Probiotics and prebiotics. J Biol Earth Sci 3(1):42–47

    Google Scholar 

  • Tamang JP, Tamang B, Schillinger U, Guigas C, Holzapfel WH (2009) Functional properties of lactic acid bacteria isolated from ethnic fermented vegetables of the Himalayas. Int J Food Microbiol 135(1):28–33

    CAS  PubMed  Google Scholar 

  • Tamang JP, Thapa N, Tamang B, Rai A, Chettri R (2015) Microorganisms in fermented foods and beverages. In: Tamang JP (ed) Health benefits of fermented foods and beverages. CRC Press, Boca Raton, FL, pp 1–110

    Google Scholar 

  • Tamang JP, Shin D-H, Jung S-J, Chae S-W (2016a) Functional properties of microorganisms in fermented foods. Front Microbiol 7:578

    PubMed  PubMed Central  Google Scholar 

  • Tamang JP, Watanabe K, Holzapfel WH (2016b) Review: Diversity of microorganisms in global fermented foods and beverages. Front Microbiol 7:377

    PubMed  PubMed Central  Google Scholar 

  • Tamime AY, Robinson RK (2007) Yoghurt: science and technology. Woodhead Publishing Ltd, Cambridge

    Google Scholar 

  • Tamine AY, Skriver A, Nilsson LE (2006) Starter cultures. In: Tamime A (ed) Fermented milk. Blackwell Publishing, Oxford, pp 11–52

    Google Scholar 

  • Taniwaki MH, Hocking AD, Pitt JI, Fleet GH (2010) Growth and mycotoxin production by fungi in atmospheres containing 80% carbon dioxide and 20% oxygen. Int J Food Microbiol 143(3):218–225

    CAS  PubMed  Google Scholar 

  • Taranto MP, Vera JL, Hugenholtz J, De Valdez GF, Sesma F (2003) Lactobacillus reuteri CRL1098 produces cobalamin. J Bacteriol 185(18):5643–5647

    CAS  PubMed  PubMed Central  Google Scholar 

  • Thanigaivel G, Anandhan AS (2015) Isolation and characterization of microorganisms from raw meat obtained from different market places in and around Chennai. J Pharm Chem Biol Sci 3(2):295–301

    Google Scholar 

  • Thapa N, Tamang JP (2015) Functionality and therapeutic values of fermented foods. In: Tamang JP (ed) Health benefits of fermented foods, vol 111–168. CRC Press, New York, NY, pp 111–151

    Google Scholar 

  • Thiele C, Gänzle MG, Vogel RF (2002) Contribution of sourdough Lactobacilli, yeast, and cereal enzymes to the generation of amino acids in dough relevant for bread flavor. Cereal Chem 79(1):45–51

    CAS  Google Scholar 

  • Thomas DS, Davenport RR (1985) Zygosaccharomyces bailii—a profile of characteristics and spoilage activities. Food Microbiol 2(2):157–169

    Google Scholar 

  • Thuy Ho VT, Zhao J, Fleet G (2014) Yeasts are essential for cocoa bean fermentation. Int J Food Microbiol 174:72–87

    Google Scholar 

  • Tieking M, Korakli M, Ehrmann MA, Gänzle MG, Vogel RF (2003) In situ production of exopolysaccharides during sourdough fermentation by cereal and intestinal isolates of lactic acid bacteria. Appl Environ Microbiol 69(2):945–952

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tjwan Tan PS, Poolman B, Konings WN (1993) Proteolytic enzymes of Lactococcus lactis. J Dairy Res 60(2):269–286

    PubMed  Google Scholar 

  • Tortora G, Funke B, Case C (2010a) Microbiology: an introduction. Pearson Benjamin Cummings, San Francisco

    Google Scholar 

  • Tortora GJ, Funke BR, Case CL (2010b) Microbiology: an introduction, 10th edn. Pearson Education, San Francisco, CA, 960 p

    Google Scholar 

  • Tournas VH (2005a) Spoilage of vegetable crops by bacteria and fungi and related health hazards. Crit Rev Microbiol 31:33–44

    CAS  PubMed  Google Scholar 

  • Tournas VH (2005b) Moulds and yeasts in fresh and minimally processed vegetables, and sprouts. Int J Food Microbiol 99(1):71–77

    CAS  PubMed  Google Scholar 

  • Tournas VH, Katsoudas E (2005) Mould and yeast flora in fresh berries, grapes and citrus fruits. Int J Food Microbiol 105:11–17

    CAS  PubMed  Google Scholar 

  • Tournas V, Stack ME, Mislivec PB, Koch HA, Bandler R (2000) Yeasts, molds and mycotoxins. https://wwwfdagov/food/foodscienceresearch/laboratorymethods/ucm071435.htm. Accessed 21 Feb 2019

  • Tye-Din J, Anderson R (2008) Immunopathogenesis of celiac disease. Curr Gastroenterol Rep 10(5):458–465

    PubMed  Google Scholar 

  • Us O, Wesley B, Ga O (2012) Investigation on the microbial profile of canned foods. J Biol Food Sci Res 1(1):15–18

    Google Scholar 

  • Van Hoorde K, Van Landschoot A (2014) Application of adjunct-cultures and their influence on the sensory properties of hard and semi-hard cheese varieties. In: Ravishankar Rai V, Bai JA (eds) Beneficial microbes in fermented and functional foods. CRC Press, Boca Raton, FL, pp 531–550

    Google Scholar 

  • Varela J, Varela C (2019) Microbiological strategies to produce beer and wine with reduced ethanol concentration. Curr Opin Biotechnol 56:88–96

    CAS  PubMed  Google Scholar 

  • Vicente AR, Manganaris GA, Sozzi GO, Crisosto CH (2009) Nutritional quality of fruits and vegetables. In: Florkowski WJ, Shewfelt RL, Brueckner B, Prussia E (eds) Postharvest handling: a system approach, 2nd edn. Academic, New York, NY, pp 58–106

    Google Scholar 

  • Vieira DAP, Cabral L, Noronha MF, Junior GVL, Sant’ana AS (2019) Microbiota of eggs revealed by 16S Rrna-based sequencing: from raw materials produced by different suppliers to chilled pasteurized liquid products. Food Control 96:194–204

    CAS  Google Scholar 

  • von Holy A, Cloete TE, Holzapfel WH (1991) Quantification and characterization of microbial populations associated with spoiled, vacuum-packed Vienna sausages. Food Microbiol 8(2):95–104

    Google Scholar 

  • von Wright A, Axelsson L (2012) Lactic acid bacteria: an introduction. In: Lahtinen S, Ouwehand AC, Salminen S, von Wright A (eds) Lactic acid bacteria microbiological and functional aspects, 4th edn. CRC Press, Boca Raton, FL, pp 1–16

    Google Scholar 

  • Walker GM (1999) Yeast physiology and biotechnology. Wiley, Chichester

    Google Scholar 

  • Walker M, Phillips CA (2007) The growth of Propionibacterium cyclohexanicum in fruit juices and its survival following elevated temperature treatments. Food Microbiol 24(4):313–318

    CAS  PubMed  Google Scholar 

  • Wang JJ, Frank JF (1981) Characterization of psychrotrophic bacterial-contamination in commercial Buttermilk. J Dairy Sci 64(11):2154–2160

    Google Scholar 

  • Wang JF, Chen NC, Li HM (1998) Resistance sources to bacterial wilt in eggplant (Solanum melongena). In: Prior P, Allen C, Elphinstone J (eds) Bacterial wilt disease. Springer, Berlin, pp 284–289

    Google Scholar 

  • Wareing P, Stuart F, Fernandes R (2011) Factors affecting the growth of microorganisms in foods. RSC Adv 2011:437

    Google Scholar 

  • Wiander B (2017) Sauerkraut fermentation. In: Paramithiotis S (ed) Lactic acid fermentation of fruits and vegetables. CRC Press, Boca Raton, FL, pp 65–81

    Google Scholar 

  • Wohlrab Y, Bockelmann W (1992) Purification and characterization of a dipeptidase from Lactobacillus delbrueckii subsp. bulgaricus. Int Dairy J 2(6):345–361

    CAS  Google Scholar 

  • Yalcin S, Bozdemir MT, Ozbas Y (2010) Citric acid production by yeasts: fermentation conditions, process optimization and strain improvement. In: Mendez-Vilas A (ed) Current research, technology and education topics in applied microbiology and microbial biotechnology, vol 2. Formatex Research Center, Badajoz, Spain, pp 1374–1382

    Google Scholar 

  • Yu JH (2015) Fresh seminar: Molds, mycotoxins, and concerns of the food industry. Madison, Food Research Institute, Department of Bacteriology, University of Wisconsin–Madison

    Google Scholar 

  • Zahavi T, Droby S, Cohen L, Weiss B, Ben-Arie R (2002) Characterization of the yeast flora on the surface of grape berries in Israel. Vitis 41(4):203–208

    Google Scholar 

  • Zajsek K, Kolar M, Gorsek A (2011) Characterisation of the exopolysaccharide kefiran produced by lactic acid bacteria entrapped within natural kefir grains. Int J Dairy Technol 64(4):544–548

    CAS  Google Scholar 

  • Zakpaa HD, Imbeah CM, Mak-Mensah EE (2009) Microbial characterization of fermented meat products on some selected markets in the Kumasi metropolis, Ghana. Afr J Food Sci 3(11):340–346

    Google Scholar 

  • Zhang W, Zhang Y (2017) Spoilage microorganisms in meat products. In: Wang Y, Zhang W, Fu L (eds) Food spoilage microorganisms: ecology and control, 1st edn. CRC Press, Boca Raton, FL, pp 77–93

    Google Scholar 

  • Zhang YM, Mao YW, Li K, Dong PC, Liang RR, Luo X (2011) Models of Pseudomonas growth kinetics and shelf life in chilled Longissimus dorsi muscles of beef. Asian Austral J Anim 24(5):713–722

    Google Scholar 

  • Zoon P, Allersma D (1996) Eye and crack formation in cheese by carbon dioxide from decarboxylation of glutamic acid. Neth Milk Dairy J 50(2):309–318

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Hüseyin Erten .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2019 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Erten, H., Agirman, B., Boyaci-Gunduz, C.P., Carsanba, E., Leventdurur, S. (2019). Natural Microflora of Different Types of Foods. In: Malik, A., Erginkaya, Z., Erten, H. (eds) Health and Safety Aspects of Food Processing Technologies. Springer, Cham. https://doi.org/10.1007/978-3-030-24903-8_4

Download citation

Publish with us

Policies and ethics