Wiki: Microorganisms & Cheese Making

This Wiki Article provides an introduction to microorganisms common in cheese making. Microorganisms are organisms that are unicellular or live in a colony of cellular organisms such as bacteria, fungi, archaea, and protists; microscopic plants (green algae); and animals such as plankton and the planarian. Microorganisms were the first forms of life to develop on Earth, approximately 3–4 billion years ago, the study of microorganisms is called microbiology.

Microorganisms live in all parts of the earth’s biosphere where there is liquid water, including soil, hot springs, on the ocean floor, high in the atmosphere and deep inside rocks within the Earth’s crust. Microorganisms are critical to nutrient recycling in ecosystems as they act as decomposers. Microorganisms are present in raw milk and are used in controlling the fermentation process in making cheese, either natively or by additionally applying, and are critical in developing different cheese types flavours and aromas, and in inhibiting undesirable organisms. Microorganisms are also used in brewing, winemaking, baking, pickling and other food making processes. Historically and in many cases currently cheese has been made in very rustic facilities with many ambient/wild microorganisms, which does not necessarily mean unsanitary, but does result in cheese quality that is too inconsistent for modern cheese factories but good for home and artisan cheese making.

The main types of microorganisms used in making cheese are shown below.


Bacteria are a biological kingdom of simple single-celled, prokaryote (lacking a cell nucleus) microorganisms. They are typically a few micrometres in length and have a wide range of shapes ranging from spheres to rods and spirals. Bacteria are ubiquitous in every habitat, growing in water, soil, acidic hot springs, as well as in organic matter and the live bodies of plants and animals including humans. There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water; and in total form a bacteria with a biomass which exceeds that of all plants and animals. There are approximately ten times as many bacterial cells in the human flora as there are cells in the human body, large numbers of bacteria are on the skin and in the intestines. Bacteria are vital in recycling nutrients, however most bacteria have not been characterised, the study of bacteria is known as bacteriology, a branch of microbiology.

Bacteria reproduce asexually by simple division of the cell and its contents, called fission. The doubling time can be as short as 20 min, and as each cell grows and divides at the same rate as the parent cell, this could under favourable conditions translate to an increase from one to 10 million cells in 11 hours. However, bacterial growth in reality is limited by lack of nutrients, accumulation of toxins and metabolic wastes, unfavourable temperatures and dessication. Bacterial populations are expressed as colony forming units (CFU) per gram or millilitre.

Bacterial growth generally has several phases:

  • Lag Phase: Time for bacteria to become accustomed to their new environment. There is little or no growth during this phase.
  • Log Phase: Bacteria exponential growth begins; the rate of multiplication is the most rapid and constant.
  • Stationary Phase: Rate of multiplication slows down due to lack of nutrients and build-up of toxins. At the same time, bacteria are constantly dying so the numbers actually remain constant.
  • Death Phase: Cell numbers decrease as growth stops and existing cells die off.

Milk is sterile at secretion into the udder but is contaminated by bacteria before it leaves the udder. Except in the case of mastitis, the natural microflora of bacteria at this point are harmless and few in number. Further infection of the milk by microorganisms can take place during milking, handling, storage, and other pre-processing activities. If significant lactic acid producing bacteria are in raw milk, it will, with time and warmer temperatures, multiply, acidify and curdle the milk (commonly called clabber) after which whey can be drained. However, depending on bacteria amount and types this can result in either inefficient, uncontrollable, and unpredictable and thus variable results and if lactic acid producing bacteria are minimal, an environment for unwanted/unhealthy bacteria to reproduce. Thus to extend shelf life, milk is commonly pasteurized to kill off most of the bacteria, both good and bad types. Commonly in cheese making, wanted lactic acid producing bacteria are added (inoculation) to the milk, to out-compete unwanted native bacteria, these are called starter cultures.

Common bacteria used in making cheese are:

  • Lactic Acid Producing Bacteria: Commonly called starter cultures, naturally in milk but commonly added to milk to ferment lactose in milk to lactic acid causing coagulation and release of whey to condense remaining milk ingredients into cheese for longer shelf life.
  • Brevibacterium linens which is ubiquitously present on the human skin where it causes foot odor and applied to give cheese rinds an orange colour and a very pungent aroma, examples are Limburger and Port-du-Salut.

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In biological terms, Fungi are a Kingdom and thus different from other Kingdoms such as plants, animals, and bacteria. Fungi are made up of yeasts, molds (spelt moulds in Britain) and mushrooms. The discipline of the study of fungi is called mycology, a branch of microbiology. Fungi are abundant worldwide but most are inconspicuous because of the small size of their structures. They may become noticeable when fruiting, either as mushrooms or molds. Fungi perform an essential role in the decomposition of organic matter and have fundamental roles in nutrient cycling and exchange. Fungi have long been used as a direct source of food, such as mushrooms and truffles as a leavening agent for bread, and in fermentation of various food products, such as wine, beer, soy sauce, and cheese.

Little is known of the true biodiversity of the Fungi Kingdom, which has been estimated at around 1.5 million species, with about 5% of these having been formally classified. Most fungi grow in cylindrical, thread-like structures 2–10 µm in diameter and up to several centimeters in length called hyphae. From these they grow by a combination of apical growth and branching/forking resulting in mycelium, an interconnected network of hyphae which is normally more visible to the naked eye, (ie fuzzy mold on damp walls, spoiled food such as bread, or on cheese where used to provide flavour and aroma.

Yeast Fungi

Currently yeasts are thought to be about 1% of all fungal species, about 500 have been described by mycologists. Yeasts ferment carbohydrates to carbon dioxide and alcohols, and are common in baking such as bread making for their carbon dioxide forming attributes and in for their alcohol making attributes in alcoholic beverage making such as beer and wine.

Yeasts are intentionally used in making some cheese types to enable rind development and are also a source of unwanted “infections” resulting in rising bread/beer yeasty smells and swelling. Note that Swiss types cheeses with eyes (Emmenthaler, Leerdammer) are not made with yeast but with Propionibacterium freudenreichii, a bacteria.

Mold Fungi

Molds grow like mushrooms, they have a surface component and send down roots called mycelia into the insides of the cheese where they break down the fats and proteins and create different flavors and textures, some penetrate just cheese rinds, some penetrate the whole paste (for example Brie or Camembert.

Common molds used in making cheese are

  • Geotrichum.
  • Penicillium white strains used in making the fluffy coating on Brie/Camembert.
  • Penicillium blue strains used in giving blue cheeses such as Roquefort and Stilton their distinctive blue to blue-green veins.

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