Cheese, the Microbiome and You.


One of the hot health-related topics in the past couple of years or so, is the microbiome and how it affects human health.

We thought it was time, that we broke down the microbiome, what it does, how we affect it, and how the microbiome has been shown to positively – or negtivaley – affect our health. And, of course how eating cheese, and other dairy products will help your microbiome maintain its healthy diversity, which in turn can contribute in a positive way to asthma, allergies, and even response to some types of cancer therapy.

Intriguing, right? Well, read on!


Microbiome? Eh?

A microbiome is a complex community of micro-organisms (microbes), including bacteria, fungi, archaea and viruses, which exist on and in, higher multicellular organisms – like us! This means that on our body, on different surfaces inside and outside, exists a layer of a community of microbes, each community composed differently depending on its location.

The microbiome is responsive and dynamic: as conditions inside and outside our body change, so does the microbial content of the microbiome, reflecting that the changed conditions may be more favorable for growth of one type of microbe, than another.

For example, if we eat a well-balanced diet, then our gut microbes exist in a healthy, co-operative state. If we change our diet, for example, to fatty fast foods, the changes are rapid (within 2 weeks!) and dramatic. Not only is there an overall loss in microbial diversity, but helpful microbes are reduced in number, and microbes linked to cancer and gastric ulcers increase in number. For more information, this is a good place to start.

Incredibly, under normal conditions, our microbiomes do not cause an immune reaction from us. Unlike dangerous microbes, which are immediately targeted by our immune system, they are deemed safe.

Our microbiomes co-exist and are tolerated by our bodies – more on that later.

We have microbiomes on our skin, in our nose, mouth, throat, lungs and gut. Each of the different areas will have a different microbiome content, caused by the different conditions of those different areas: for example, the skin microbiome in between our toes (warm and salty), will be different from the microbiome on our head (dry and agitated), and in our guts (moist, warm and slightly acidic). We have our microbiomes from birth – microbiomes are easily picked up from the environment, but our gut microbiome relies heavily on a natural birth - as our open screaming mouths grasp more than air on the way out of the birth canal.

The role of the microbiome.

A significant amount of research is underway to understand what our microbiomes do, but we already somewhat understand these complex communities.


1) A Microbial Wall. The microbiome provides protection against invasion by harmful microbes, by outcompeting invaders, through their established presence on our body surfaces. When we undergo a course of antibiotics, in addition to pathogenic microbes, our microbiomes are also eliminated, which can cause issues post-treatment (since this 'home-turf' competitive-advantage no longer exists)!

2) Chemical recyclers & messengers.

Microbes are able to metabolise chemicals in their environments, such as salts (skin), toxins (gut) and complex carbohydrates (gut), which may have unwanted side-effects for our bodies, protecting us from their effects. They also produce molecules which have effects in our bodies either at a local site, or at a distant one.

3) Trainers of the Immune System. The microbes act as continuous trainers and tuners of our immune system, it is this which allows tolerance to their presence, and helps reduce excess immune activation.

Let’s have a look at the first two roles of the microbiome, as it involves an active participation by the microbiome.

Communicating with Me, Myself and I

For at least 10 years, it has been known that there is a line of communication between the gut microbiome and the central nervous system (including the brain). However, it hasn’t been clear how this actually exists.


A recent paper in Nature from the Quintana lab in Boston (Nature, 557, 724-728), demonstrated one method where the gut and the brain communicate. Using a mouse model of multiple sclerosis, they showed that particular molecules produced by the gut microbiome travelled to the brain, and inhibited the inflammatory behavior of specific brain immune cells. This directly limited the inflammation and neurodegeneration created by these cells in multiple sclerosis. By examining the brains of MS patients, they saw fingerprints of this activity, suggesting that this method is also at work in humans.

Evidence showing that a healthy gut, means a healthy mind.

Hello, It's Me

How about the other active role of the microbiome - tuning our immune system?

Our immune system is a complex system which is able to recognize self- from non-self. Inside our thymus glands and bone marrow, we develop certain types of immune cells called T and B cells. During their development, these cells come into contact with ‘pieces of self’. Each B or T cell is genetically programmed to recognize different ‘pieces’, and if any of these cells recognize ‘self’ too strongly, then they die. If the cells don’t recognize ‘self’ during this period, they mature, develop further recognition machinery and leave, to become active in our immune system.


This is not the end to the cell’s ‘Immune Education’. The gut lining is an area of intimate contact between our cells and the microbiome. A cell called Type 3 Innate Lymphoid (ILC3) cell, actively engages the microbiome and presents ‘pieces’ of the microbiome to the mature T and B cells. The extra recognition machinery of T & B cells developed when they matured is not engaged by ILC3 cells, therefore T and B cells which recognize the microbiome pieces, die without engaging a full immune response, creating a tolerance for the microbiome. (For a good book on Immunolgy, try this one, from Roslindale-resident Geoffrey Sunshine).

Immune education, such as this occurs in other microbiome environments in the throat and airways as well.

So, why is this important?

In both humans and mice there is overwhelming evidence that disrupting this close interaction/education between our microbiomes and immune system is a cause of health issues. This continuous training keeps our immune system focused on dealing with harmful bacteria, rather than over-reacting to harmless stimuli. The best training for our immune system is provided by a diverse selection of microbes (which may differ between the gut, lungs etc.).

Studies in mice and children show that lessened exposure to environmental microbes during development (for example from farm or house dust), shows a correlation with airway hypersensititvity (asthma) and, at least with mice, reintroduction of particular microbes found in these dusts, relieves this hypersensitivity. There has been extensive comparative work on the children from Hutterite (clean mechanized farms) and Mennonite (old style, manual, dusty farms), showing the latter benefit from the exposure to microbes. Try this review for an in-depth survey of current literature.

The process of fecal microbiota transplantation (FMT) was a brief case report and is now the basis of major innovations in the treatment of Clostridium difficile infection (CDI) and, potentially, inflammatory bowel disease (IBD). A pill of frozen poop (from a healthy donor!) is provided to a patient, and this increases the diversity of the microbiome and alters the metabolic pathways active in the intestinal flora, causing C.difficile to be eliminated – without resorting to antibiotics.

Cheese-me Up!

How does this all relate to cheese?

All cheese is a fermented food – certain microbes breakdown the lactose to lactic acid and CO2, which is one of the first steps of cheesemaking. Microbes (from the milk) then start to work on the other components of the cheese to provide flavors and aromas, and to affect the texture. If the milk is pasteurized, which eliminates all the microbes present, then the cheesemaker has to introduce their own selection of microbes to produce the desired flavor profile. If the milk is unpasteurized, then the cheesemaker just rolls with what the environment has provided!

There is therefore a vast number of microbes in both pasteurized and unpasteurized cheese – although there is likely to be a much higher diversity of microbes found in unpasteurized cheeses.


As we have seen above, a broad microbial diversity is beneficial to our health, which all points to this:

Eat cheese, and if you can, eat unpasteurized, raw milk cheese. This will maintain a natural gut microbiome, and provide the broadest selection of microbes possible.

Other dairy products work too, such as yoghurt, as do other fermented foods to some extent (eg Kombucha, rather than beer!), as long as they have microbes within them, but these tend have a producer, who makes a selection of desired microbes, therefore will not have the microbial diversity of unpasteurized, raw milk cheese.


Currently it is unclear is there are specific microbes which have specific benefits. For example, a recent study on response to a cancer therapy (anti-PDL1) identified one specific microbe as being important, although two other similar studies did not find the same connection (see a summary here). Our microbiomes are so complex, that it will likely take a long time to figure out — if at all — any direct, causative link between one microbe and one solution.

A cheese designed purely to boost cancer therapy is therefore some way off!

#microbiome #rawmilk #dairy #realcheese