What is a Microbiome?

15 March 2021by Manoj Dadlani

Recently, microbiomes – that is more specifically, human microbiomes – have been experiencing a bit of a popularity surge in the mass media. Both the gut microbiome and skin microbiome are terms that are regularly appearing in health columns as we all become hypervigilant of our health in the wake of a tumultuous pandemic.

This is great news for the microbiome which often goes unnoticed and underappreciated (although not by us). However in light of such an influx in popularity, it’s only natural that people are beginning to ask “Ok but, what is a microbiome?”

Thankfully, this is kind of our area so we’re on hand to shed some light on one of the most important aspects of all living things.



What is a microbiome?

Now by the word “micro”, you may be thinking that a microbiome is one tiny singular thing. This is actually half correct, and half not. A microbiome refers to the community of living microorganisms, or microbes, that all live together in the same habitats.

Microbes are ubiquitous, which means that there isn’t really anywhere that they can’t be found. But when they are found all together, that is when they form the microbiome.

The following habitats all house one or more microbiomes:

  • Humans

  • Plants

  • Animals

  • Soils

  • Oceans

Watch a YouTube video on What a Microbiome is, here.

What does the microbiome do?

Microbiomes play an important role in the health of all living things. Whilst more research is still being conducted to fully understand what roles they play in relation to specific areas of their habitat, we are beginning to learn more about the human microbiome, as well as the marine microbiome.

One example of an area in which research is prevailing is the aforementioned human gut microbiome.

We know that the human gut microbiome aids digestion and nutrition, and allows the body to extract more energy from foods through microbes breaking down dietary fibres. Further research is beginning to show that the human gut microbiome could be linked to conditions such as obesity, and could also influence our moods.

Other beneficial roles of microbiomes found in humans include:

  1. Protecting against infection

The microbiome can stimulate the adaptive immune system. When small numbers of bacteria found on the skin enter tissues through scrapes and cuts, the human body naturally prepares an immune response to them. Healthy bacteria found in the microbiome therefore give the immune system a first exposure to proteins that the immune system knows to attack because it already knows they are foreign.

2. Promotes oral tolerance

The human microbiome also appears to be able to play a distinct role in helping the immune system to develop oral tolerance. Studies into the actions of regulatory T cells indicate that early and consistent exposure to microbes which are found in the gut from foods stimulate the T cells and prevent the immune system from overreacting to harmless microbes and substances.

3. Produces substances vital for health

It is thought that bacteria in the human gut biome can produce vitamins B12, thiamine, riboflavin and Vitamin K.

Away from the human microbiome, microorganisms that form a microbiome and are found in aquatic life such as in our freshwater rivers and oceans help the larger organisms that live in these ecosystems, such as the animals and plants, to undergo metabolism in such a way that they mutually benefit from it and survive.

Read more about why fiber could be influencing your gut microbiome here.

How do humans get microbes?

The primary theory behind humans developing their own microbiomes is that it begins once we are born. As we emerge through the birth canal, a handover of bacteria takes place containing microbes that attach to the skin and form in the digestive tract.

During pregnancy, a mother’s microbiome changes to create an optimum mix for the offspring. However, babies that are born by caesarean section may miss out on some of these essential microbes. Early studies are suggesting that the differences in birth may be why caesarean section babies have a higher vulnerability to conditions such as asthma and type 1 diabetes.

Throughout the first two years of a baby’s life, the gut microbiome will change considerably. It is thought that these changes are brought about by microbes in breast milk. Studies show that breast milk contains microorganisms as well as carbohydrates that specifically appear to nurture a healthy gut microbiome in the intestinal tract.

However, microbiomes can also be shaped by the environment as well as other additional factors and it will stabilise by the time an infant is around three years old.

As we grow into an adult, our environment, long-term diet, exposure to stress and any drugs we take will continue to play a part as we age, which means that at any point throughout our lives our microbiome can continue to change.

On average though, an adult carries over 100 trillion microorganisms and each individual’s microbiome diversifies entirely. These individualistic attributes could explain individual preferences in food and allergic reactions.

Research into these differences is partly why the microbiome is going under the microscope. As more studies are conducted, we’re starting to see links between the makeup of a microbiome and its ties to conditions such as diabetes, autism, obesity and even anxiety. There’s also evidence to link the microbiome to how well cancer patients respond to chemotherapy, how individuals respond to drugs like antibiotics and even a tentative connection with how well we sleep.

Closing thoughts:

The microbiome plays such an important role in our daily lives that the more research we can do around it, and the more we can learn about ourselves and the makeup of the world around us, the better.

At CosmosID we can’t shout loudly enough about the importance of the microbiome. That’s why we’ve dedicated an entire education section to it, which you can access here.

Manoj Dadlani

Mr. Manoj Dadlani serves as Chief Executive Officer at CosmosID, Inc., the Maryland based provider of industry-leading solutions for unlocking the microbiome. Previously, Mr. Dadlani served as a partner at Applied Value Group, a management consulting and investment firm, and was co-founder and CEO at Rasa Industries, Ltd., a leading beverage manufacturing company. Mr. Dadlani has substantial experience in strategy, M&A, supply chain management, product development, marketing and business development. Mr. Dadlani received his bachelor’s and master’s degrees in Biological Engineering from Cornell University. Services offered by CosmosID’s CLIA certified and GLP laboratory cover the entire workflow from study design to sample collection, extraction, library preparation, sequencing, data analysis and publication support. CosmosID’s cloud-based metagenomics application offers user-friendly access to the largest curated databases for microbial genomics, antimicrobial resistance and virulence data and has been independently validated to return metagenomic analyses at strain level resolution with industry-leading sensitivity and precision.