Microbiological spoilage of cheese is one of the important reasons that render the nutritious and tasty cheese not only inedible but also a potential source of infection. The spoilage may be due to bacteria or fungi. The defect due to contamination may arise from the surface of the cheese showing visual and organoleptic changes or it may be hidden internally. 

Fungal spoilage

First, let us take up the defects caused by fungus in cheese. Although mould varieties are essential for ripening of certain cheese varieties like Roqueforte cheese, growth of other moulds is strictly undesirable.

Mould spoilage makes the cheese unpleasant in appearance, conferring it with a musty taint/odour and liquefaction of the cheese. In some cases, moulds produce mycotoxins. Moulds responsible for spoilage of cheese include Penicillium, Aspergillus, Cladosporium, Mucor, Fusarium, Monilia and Alternaria. Most of these moulds contaminate cheese during ripening and hence suitable measures have to be taken to control them by following rigorous cleaning procedures, supplying sterilized air through filtration or ultra violet treatment.

Modified atmosphere packaging may be adopted in pre packed cheese varieties but there are incidences of growth of moulds in the residual air pockets due to improper packaging or puncture. In countries where there is legal sanction, natamycin or sorbic acid may be incorporated into the packaging to prevent cheese spoilage.

Spoilage due to yeasts

Yeasts too cause spoilage of cheeses, especially that of fresh or soft varieties like cottage cheese, during storage. The defects produced are gassiness, off-flavours and odours. Yeasts are also capable of proliferating on the surface of ripened cheeses, more so, if the surface becomes wet, causing slime formation. Yeasts most frequently encountered in spoiled cheese include Candida, Pichia, Yarrowia lipolytica, Geotrichum candidum, Kluyveromyces marxianus and Debaryomyces hansenii

Bacterial spoilage

Bacterial spoilage may occur in fresh cheeses having a sufficiently high pH such as cottage cheese. The causative organisms are Gram negative, psychrotrophic species viz.  pseudomonads and certain coliforms. These organisms gain entry and infect the product through contaminated water used to wash the curd. 

Psychrotrophic bacteria like Pseudomonas, Alcaligenes, Achromobacter and Flavobacterium species are of primary concern in cheese spoilage due to bacteria. Pseudomonas fluorescens, Pseudomonas fragi and Pseudomonas putida cause bitterness, putrefaction and rancid odour, liquefaction, gelatinization of curd, and slime and mucous formation on cheese surfaces.  Alcaligenes viscolactis produces ropiness and sliminess in cottage cheese, and Alcaligenes metacaligenes flat, or poor flavour in cottage cheese. Psychrotropic Bacillus species cause bitterness and proteolytic defects.

Bacteria may also cause spoilage by producing gas internally in the cheese, resulting in formation of slits, small holes or blown packs. Gas production in fresh cheese in early ripening stage is called as “early blowing” and well into the ripening stage is known as “late blowing”. Early blowing is usually caused by members of the Enterobacteriaceae like E.coli and Enterobacter aerogenes, but other organisms, such as Bacillus species are sometimes involved. The problem of early blowing can be effectively controlled by adequate hygiene and process control measures during cheese manufacturing. Late blowing, which usually happens after 10 days in cheese varieties such as Gouda, or after several months in some Swiss cheeses, is caused by clostridia that are capable of producing butyric acid from lactate. Late blowing sometimes also occurs in Cheddar. Species frequently implicated in the spoilage are Clostridium butyricum, Clostridium tyrobutyricum and Clostridium sporogenes. Spores of these bacteria are capable of surviving pasteurization temperatures and can be present in cheese milk.

Contamination of milk with these organisms is often seasonal; Clostridium tyrobutyricum is more prevalent in winter and is related to the supplementation of silage as a feed for dairy cows. A very low level of contamination may be sufficient to cause late blowing defect in cheese. In countries where laws permit, nisin, a natural antimicrobial compound produced by strains of Lactococcus lactis subspecies lactis, has been successfully used to control late blowing, by inhibiting the growth of clostridia. Small, irregular slits may also sometimes appear in three to six weeks old Cheddar, and is referred to as “intermediate blowing” which is usually associated with the presence of non-starter gas-producing organisms such as Lactobacilli.

Yeast and enterococci have been frequently isolated from brine-salted cheeses exhibiting white spots on the surface. Surface mould growth by species such as Aspergillus niger may cause discoloration of hard cheeses. Pigmented strains of certain lactobacilli have been linked with 'rusty spots' in some cheeses, and the non-starter Propionibacterium species may sometimes cause brown or red spots in Swiss cheese. Pseudomonas fluorescens forms water-soluble pigments while other pseudomonads cause darkening and yellowing of curd. Yellow discolouration of cheese surface may be attributed to production of flavin pigment by Flavobacterium species and Bacillus species have been associated with dark pigment formation on the cheese surafce.