The recent COVID-19 pandemic was a pivotal event that increased the general societal awareness of the billions of microbes all around us. The newly formed perspective on the tiny “bugs” that surround us, however, panned out to be decidedly negative – these bugs are not our friends. Sales of personal sanitizing products increased dramatically in 2020 when the worldwide outbreak of SARS-CoV-2 began. Campaigns promoting basic hygiene were everywhere, and the CDC notes that the pandemic increased awareness and practice of handwashing in certain situations. The general consensus? Microbes = bad. Pathogens, or disease causing microbes, certainly warrant keen awareness and as a society, we have several lines of defense— including vaccines, antibiotic and antifungal medicines, and handwashing. However, not all microbes are bad, and it’s important that we are aware, and protective, of the good bacteria, viruses, and fungi that are essential to our health.

What is our microbiome?

Our bodies are covered in millions of tiny life-forms – fungi, bacteria and viruses – that work in tandem with our natural biological systems to maintain our health. The collection of these microorganisms is called the microbiome. The microbiome plays an important role in several facets of our body’s function, including digestion, immune response, maintenance of skin and other barrier health, and mood regulation. The makeup of the microbiome varies among populations and from person to person. Despite your precise microbiome composition being unique to you, scientists are finding trends within the microbiome among groups of people who are affected by the same diseases.

The microbiome and digestion

The human body alone is not capable of getting all the nutrition we need from the foods we eat. Luckily, our friendly gut bacteria supplement our digestion capabilities by helping to break down our food to a form that we can more efficiently utilize. For example, consider a complex carbohydrate like plant fiber. Certain bacteria of the genus Bacteroides possess enzymes called glycoside hydrolases that break down the bonds within this starchy plant material. In this way, some of the fiber we eat can be processed into short chain fatty acids that we can use to create energy. Our gut microbiome also synthesizes amino acids – essential and non-essential, as well as some vitamins, including B and K.

Illustration of stomach with bacteria inside and around it.

Beneficial Gut Bacteria by NIH Image Gallery. License Info: CC BY-NC 2.0 Deed

The microbiome and immunity

The impact of your microbiota on the health and development of your immune system starts at birth. Babies are colonized with the bacteria present in a mother’s birth canal. These microbes work together with a natal immune system to regulate inflammatory responses with growth of commensal (beneficial) bacteria, and create a working balance. Interestingly, some researchers believe babies born by C-section, who get colonized by skin bacteria rather than vaginal bacteria, will tend to have differential immune related outcomes, but the evidence is not yet conclusive. 

Later in life, the microbiome contributes to our immune response in a myriad of ways. For one, it can defend against infection from pathogens by producing antimicrobials. It also plays a key role in regulating inflammatory responses to antigens, especially food and self-antigens.

Microbiome changes are reflected in disease state

Gut microbiomes are quickly becoming a key player in our understanding of mechanisms of disease. Differential compositions of gut microbiomes have been associated with diseases such as obesity, irritable bowel disease (IBD), and more surprisingly, depression and cancer. Fecal transplants have garnered interest as a way to colonize our guts with bacteria associated with better health outcomes.

Antibiotics and probiotics

Since the microbiome is such an important part of our physiology, you might find yourself wondering about antibiotics and whether they can be a detriment to your microbiome. Indeed, antibiotics have been shown to disrupt the gut microbiota, both temporarily and indefinitely. These changes can have adverse effects on a patient, especially if they are otherwise immune compromised. Despite this negative effect, antibiotics remain an integral and necessary part of our healthcare, the benefits of which outweigh the costs of microbiome disruption. While antibiotics may change our microbiome landscape, a healthy individual with a one-off infection doesn’t need to worry about taking antibiotics. On the other hand, some people champion probiotics as a way to proactively maintain and nurture your microbiome. Some have even gone so far as creating topical products containing active cultures to benefit the skin microbiome. These approaches don’t seem to be harmful, but the jury is still out on whether probiotics are really useful for the general public. 

Though we may have managed to shift our microbiomes through the rigorous isolation and sanitizing protocols brought on by COVID-19, our bacteria are here to stay. We’ve been living with our friendly neighborhood bacteria, fungi and viruses for millennia, and we won’t be getting rid of them anytime soon – nor should we want to. We rely on them for our basic functions. Certainly don’t stop hand washing or buying hand sanitizer, as these methods are accepted ways to slow the spread of various illnesses and promote general hygiene. But remember to be nice to your hard-working, friendly microbiota.


Peer Editors:  Devan Shell and Emily Hand

One Reply to “America Runs on the Microbiome”

  1. Microbiome and immunity are you share this topic with us through this article are very useful. microbiome are important in human body are you mentioned detail information thanks for sharing keep sharing

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