HIV and The Gut Microbiome: Prebiotics and Probiotics

In the previous article, I introduced the microbiome. To review, recall that our bodies are essentially a reservoir of billions, even trillions of bacteria and other microorganisms (viruses, fungi, parasites). They are essential to helping us stay healthy. Disease occurs when harmful organisms invade our bodies (e.g. influenza, malaria, hepatitis C, Staphylococcus). The microbiome refers to the diversity of microorganisms associated with a specific organ at a specific time.

When we are healthy, the microbiome contains a delicate balance of bacteria and other organisms that actually help us. But disease can also occur when the microbiome is disrupted by harmful bacteria and the balance is thrown off from normal. In the previous article, we discussed how disrupting the normal balance of bacteria in the vaginal microbiome can increase the risk of acquiring HIV. The largest volume and diversity of bacteria is found in the gut (intestinal) microbiome. HIV infection has a profound effect on the gut microbiome and this may provide opportunities to improve control of the disease.

Very soon after the HIV viral infection reaches the blood, the viruses launch an aggressive attack on the largest immune system complex in the body. This complex of specialized tissue surrounds the gut (intestines) and the HIV virus kills off many of the important immune cells that protect our bodies; cells known as CD4+ lymphocytes or T lymphocytes. This damage is irreversible. Even with very effective therapy for decades, these cells from the gut that are killed off during the early infection are never replaced. HIV’s attack of the immune system around the intestines produces two major effects that have long-term importance in the disease. First, the virus causes subtle damage to the intestinal wall which allows small amounts of bacteria to leak out from the intestine into the bloodstream.

The immune system begins to attack these bacteria slowly streaming into the blood from the gut. This results in a mild form of inflammation. When I say inflammation, this means that the body is reacting similarly to what we see in patients with diseases like arthritis and inflammatory bowel disease. Some of the same chemicals produced in these diseases can be found in the blood of HIV patients.

The good news: HIV medications reduce the amount of inflammation as they control the virus. The bad news is the amount of inflammation is still higher than normal, even with effective HIV treatment. This inflammation in HIV is a problem because it can cause damage in the blood vessels and increase the risk of cardiovascular disease.

The other problem in the gut is that HIV disease causes a change in the composition of bacteria living in the gut. HIV infection alters the gut microbiome. The good bacteria that are normally in the gut are slowly replaced by bacteria that are not so good. Keeping these good bacteria in the gut is very important because they help us digest food and absorb nutrients and even are needed to produce certain vitamins that we use.

Is there any way we can target the gut microbiome and improve health outcomes for HIV infection? There are two ways that we may be able to do this. Prebiotics are foods or supplements we consume take that can nourish and increase levels of good bacteria. These foods and products contain dietary fiber that undergoes a special process in the large intestine (fermentation) that nourishes the growth of good bacteria.

Probiotics are the actual good bacteria themselves. They can be acquired from eating fermented foods, such a yogurt with live cultures or sauerkraut. They contain important good bacteria like Lactobacillus (sound familiar?) and Bifobacterium. There are also tablet supplements that contain these bacteria. So the big question is: Do they work? In a number of studies, eating yogurt enriched with probiotic bacteria has led to some mild increases in CD4+ lymphocytes in HIV patients on treatment. In other studies, probiotic supplements have produced a number of benefits which include reduced inflammation, possible reductions in bacteria leaking from the gut and normalization of the gut microbiome.

But before you run out and binge on yogurt, a precaution: There have been some isolated cases of HIV patients eating yogurt and developing infections from the probiotics. In these rare cases, all of the individuals had very advanced HIV disease and were not on treatment, and they all had other disease conditions that could have contributed as well. Modest consumption of yogurt or a supplement in a person controlled on HIV medication is probably safe.

It is important to remember that while some of the damage caused in the gut by HIV may be permanent, taking effective HIV therapy is the most effective way for maintaining long-term health. The use of probiotics and healthy diet (with prebiotics) may provide additional benefits. Discuss this with your healthcare provider and/or a nutritionist. [see the article in “10 types of Bacteria that are good for you” Nov. 2, 2016]


Dr. Crawford received a B.S degree in Biology from Cornell University and a B.S. in Pharmacy from Temple University. He completed a residency in clinical pharmacy at the National Institutes of Health. He earned a doctorate in Pharmacology from the Uniformed Services University of the Health Sciences in Bethesda, Maryland. He completed a post-doctoral fellowship at the National Institutes of Health, studying microbial biochemistry and genetics.

He is currently with the Division of AIDS at the National Institutes of Health. He has over 25 years of experience in HIV treatment and clinical research. This article reflects his personal views and opinions.