disease, human conditions, microbes

Our Microbiomes: In Sickness and in Health

Last week, we took a look at the amazing diversity of microbes (bacteria, fungi, and others) that live on, and inside of, our bodies. This week we’ll dig deeper into our microbiomes and explore what’s known about how they help keep us healthy, and why they sometimes make us sick.

electron micrograph staphylococcus epidermidis skin microbiome

Shown here are Lactobacillus bacteria (the dark-colored rods) in a vaginal smear (the large pink shapes are human cells). An abundance of Lactobacillus bacteria in a vagina has been long thought to be necessary for having a healthy vagina, but it turns out this isn’t always the case. (Image credit: Janice Carr / Centers for Disease Control and Prevention)

How are our microscopic neighbors connected to our health? And why is it so important that researchers try to answer this question? The idea is that by understanding which microbes are beneficial and help keep us healthy, we could develop ways to promote the growth of such microbes (and figure out how to deter populations of pathogenic, or disease-causing, microbes). This sounds simple enough in theory, but in reality things get a bit complicated — it can be difficult to know which are the “good” microbes and which are the “bad” ones (especially since this sometimes varies from person to person). Read on to find out what’s known about our microscopic neighbors, both the good and the bad.

The mouth microbiome: For many decades, scientists have studied how different microbes in the mouth are associated with dental diseases, including periodontitis (gum inflammation) and eventual destruction of tissues in the mouth (e.g., tooth decay). But, fascinatingly, it turns out that these microbes — some 700 species in total, many of which are just passing by, primarily on their way to the gut or lungs — may be associated with many diseases that primarily cause damage far beyond the mouth. For example, researchers have found associations between the mouth microbiome and diabetes, heart disease, certain cancers (including pancreatic and colorectal), arthritis, and other conditions. We still have much to learn about these complex relationships.

The gut microbiome: This microbiome is likely the most widely studied one, and consequently researchers have been able to make many connections between the microscopic critters living there and how they may be affecting our health. But how to use this knowledge in treatments is still very much a developing area. Here are summaries of previous Biology Bytes posts, and other articles, that have explored this topic:

  • What is a ‘Healthy’ Gut Microbiome?” The more we learn about the gut microbiome, the more we find it’s not as simple as we once thought it was. For example, some microbe species we thought to be important for making a person healthy may not actually be needed, and some detrimental ones might be harmless. Interestingly, it was also recently found that hunter-gathers’ gut microbiomes are more diverse than urban dwellers’ (possibly because hunter-gathers eat more unprocessed, raw foods).
  • Aging and the Gut Microbiome:” The gut microbiome has been found to significantly change as an organism ages.
  • The Importance of ‘The Little Guys:’ Our Gut Microbiome:” This post explores how the gut microbiome has been linked to obesity, autoimmune diseases, infections, and other medical conditions.
  • Bacteria and Stress May Trigger Heart Attacks and Strokes:” Bacteria that live in artery plaques might be related to blood clots. Specifically, it’s been found that plaques may be biofilms (little ecosystems) created by certain bacteria, and when these bacteria get stressed, the biofilm could dissolve and cause blood clots, resulting in heart attacks and/or strokes.
  • Chocolate: It Does a Microbe Good:” On the bright side, there’s good news for chocolate-lovers — eating chocolate may help decrease the long-term risk of having a stroke due to gut microbes.
  • Fecal Transplants and C. difficile:” Infection of the gut by a type of antibiotic-resistant bacteria (Clostridium difficile) can be potentially fatal. Researchers have developed some of the first gut microbiome-based treatments to fight this infection — specifically, C. difficile has been found to be effectively treated using fecal transplants (from a healthy person’s guts).
  • Connections between the gut microbiome and malnutrition have also been found. Specifically, malnourished children (ones who have been underfed, or lacked essential nutrients) end up with “immature” gut microbiomes — their microbiomes basically look like those found in younger children, and less like ones in adults. After treatment with a therapeutic food or calorie-rich diet, the microbiomes improved in a month, but then regressed, still being less mature four months later. Like other children who have been malnourished, these children ended up being shorter and underweight when they were older.
  • The gut microbiome is also suspected to play a role in bowel cancer.

The vagina microbiome: It’s been long thought that a healthy vagina is dominated by Lactobacillus bacteria species (which make the vagina have an acidic, low pH that kills pathogenic microbes). However, it’s becoming clearer that the reality is more complex — there’s a much greater variety of microbes than previously thought, with many complex, and poorly understood interactions taking place. There are also great microbiome differences within a given woman, and between different women. For example, a study found that over a quarter of nearly 400 women surveyed had relatively few Lactobacillus and more of other bacterial types. Typically, such a microbial profile would be indicative of a certain vaginal infection (bacterial vaginosis [BV]), but these women were still healthy. The researchers also found that the vagina microbiome appears to be linked to race and possibly risk of preterm labor. (As an interesting side note, the vagina microbiome changes during pregnancy, but it does not appear to resemble the microbiomes that newborn babies have, which may be closer to the placental microbiome and mother’s mouth microbiome.)

The skin microbiome: The microbes that live on our skin are thought to help protect us from pathogens and/or make sure the immune system stays effective (and does not cause an auto-immune response, such as inflammation). For example, Staphylococcus epidermis and Propionibacterium acnes are skin-based bacteria known to help fight off invaders. Researchers have been able to characterize members of the skin microbiome based on the different “environments” they inhabit. However, while there are many suggestive links, we still do not have clear causal connections between specific skin microbes and disease conditions.

The wound microbiome: Fascinating research is just beginning on the wound microbiome, which is the collection of microbes that live in a wound while it heals (or fails to heal). So far it’s been found that, basically, wounds that heal well have a significantly different microbiome than wounds that don’t. Specifically, the well-healing wounds typically have microbes found in the gut microbiome. It’s unclear why this is… but definitely an area of much interest as researchers try to develop more efficient wound-healing treatments.

As researchers continue to learn more about our microbiomes, and gain a better understanding of how they make us healthy or cause us to be sick, more effective treatments should become available for all sorts of medical conditions, since these microscopic critters clearly play many important roles in our bodies.


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