Your brain is a very privileged immunological site with resident immune cells that protect it from infection and the products of injury. These cells depend on the immune system and the biome of the bowel to support its activities and feelings. (I suspect a bad meal can produce doom and gloom feelings because of this.)

Intestinal microbes change the growth and function of those res[1]ident immune cells, while also supporting nerve cells that make your brain’s connections extremely resilient and remodel certain areas after an injury like a trauma or a stroke. They are not first responders, but more like dedicated electricians and technicians on call to make sure your brain is and remains intact.

Consider two of the most amazing of these cells: microglial cells and astrocytes. Microglial cells perform the functions of white cells within the brain: they are like a robotic vacuum roaming around and eating up bacteria or viruses, presenting foreign substances to antigen-presenting cells as the first line of defense within the immune system, and producing cytokines or communication molecules to invoke inflammation when it is necessary.

While this is going on in the brain’s “gated community,” these cells are influenced directly by the bugs in your bowel and probably in other areas like your skin and reproductive zones. For example, germ-free mice have defective microglial development in their brains from birth.

So we can speculate that too much use of antibiotics early in life might adversely affect the development of these immune cells in the human brain with terrible consequences like psychiatric or behavioral issues and even a propensity to illnesses like meningitis in later life.

Astrocytes are the most abundant glial cells in the brain —  nonneuronal (i.e., not nerve) cells that interact with microglial and other cells in the brain. Astrocytes supervise the border where spinal fluid enters and leaves your brain and maintain the integrity of the accompanying spinal fluid filtration mechanism. They monitor the brain’s blood flow, facilitate nutrient transport, and regulate the excitability of neurons as a result of immune events.

In doing so, astrocytes actually perform immune functions, getting information from the body’s immune system so it is able to recognize bacterial and viral intruders.