What Is Microbiomics? • Earthpedia • Earth.com
Artists rendering of microbes in the body

What Is Microbiomics?

It may come as a surprise to learn that most of the cells in your body are not your own. Scientists estimate bacteria may outnumber human cells by as much as 10 to 1! Admittedly, this estimate is on the higher side. However, it is generally agreed that there are at least as many non-human cells as human cells in the average person.

This may sound like a terrifying invasion, but don’t fear. These “foreign” cells are your microbiome. They are an essential part of the human “superorganism.”

Since the advent of “germ theory,” we’ve seen bacteria as evil. They’re invaders, hiding out on doorknobs and cellphones. Bacteria is just waiting for you to forget to wash your hands. Then it can infect you and everyone you come in contact with. This view of bacteria isn’t entirely accurate. Though some bacteria can be harmful (and you should definitely keep washing your hands), most are benign and some are helpful!

The microbiome is the community of organisms living inside you (or their collective genes.) These include bacteria, fungi, archaea, and even viruses! The term microbiome can also refer to the communities of microbes in environmental samples. In this article, we will be focusing on the human microbiome.

Scientists are just beginning to research the role of the microbiome in health. The importance of the microbiome to human health has become apparent.

The human microbiome is often associated with gut bacteria. But, the microbiome is not restricted to the digestive tract. Microbes live throughout the human body, and helpful microbes are found in many organs.



What Makes a Microbe Good?

Everyone’s microbiome has many different types of microbes. This microbial community plays an essential role in digestion and our immune systems. The amount of help provided by bacteria can vary. Some species are mutualistic, providing and receiving benefits to their host. Others are commensal, simply living inside our guts without harming or benefiting us.

Microbes play an essential role in digestion. They assist in digesting foods that humans have trouble processing. Probiotics supplements and foods offer a way to boost your gut microbiota. These good bacteria include many species of Lactobacillus and Bifidobacterium.

The microbes in the urinary tract and eyelids keep foreign bacteria at bay. By establishing a community, they make it harder for bad microbes to invade.

Bacteria are by far the most common and most discussed microbe in our bodies. However, the microbiome is far more complex. It also includes fungi, viruses, and archaea. These organisms provide a diverse environment that can respond to changing conditions.



Where Do These Microbes Come From?


Yogurt with oats and strawberries sitting on a table with a plate of strawberries in the corner.


We know the microbiome is an essential part of a healthy human. But where do all these microbes from? It turns out that our first exposure to these microbes happens as early as birth. We are exposed to microbes in the birth canal. The microbial community continues to develop through infancy. Breast milk can also deliver microbes. Though our microbiome is not inherited in the traditional sense it is still passed from mother to child.

The microbiome continues to develop and change throughout life. Diet has a huge influence on how the microbiome grows. It can also introduce new bacteria to the microbiome. Many probiotic or cultured foods contain good bacteria and yeast. Yogurt, kombucha, and kimchi are just a few examples of sources of good digestive bacteria.

Environment, location, diet, and health can all influence exposure to good and bad microbes.



Where Is Our Microbiome?

The microbiome occupies a large number of different organs. The microbes present are different in each. Though they share many functions, each community is unique. Research is ongoing to better understand the microbiome’s role. Imbalances in the microbiome can have far-reaching effects. The microbes can influence many parts of the body.

  • The Skin

The skin is a diverse habitat for a wide range of organisms. These include bacteria, fungi, viruses, and even small mites. These organisms are primarily harmless, while others provide essential services. They protect against invasion by pathogens, train the immune system, and even assist in killing pathogens.

  • The Eye (conjunctiva)

The ocular microbiome is less well-known but can provide essential services. The microbiome of the eye occurs on the conjunctiva, the clear tissue covering the whites of your eye. The eye has fewer microbes than the skin, around 1/100th the number. Healthy eyes usually have only 4 genera of bacteria. The ocular microbiome may be important in many conditions. These include chronic dry eyes and blepharitis.

  • The Gut

The gut is host to the most diverse and active microbiome. Microbes in the gut are essential for digestion. There is evidence that the gut microbiome may play a role in a wide array of different diseases. This article will focus on the gut microbiome.

  • The Urinary Tract (UT)

In the past, scientists believed the urinary tract was sterile. Any microbes in the UT were assumed to be a UTI. New evidence has shown that a healthy urinary tract has certain microbial communities. Changes in this community have been linked to diseases. These include incontinence, cysts, STIs, pain, and even cancers! Research is being done on how to protect and repair this community. Diet, probiotics, and prebiotics may help regulate the urinary microbiome.

  • The Vagina

The microbiome of the vagina is essential to vaginal health. These communities are complex and change over time. Hormonal and environmental changes have a large influence on this community. In general, the beneficial bacteria that exist in the vagina produce lactic acid. This acid lowers the pH, protecting against pathogens and infections. This protection is essential to prevent STIs, yeast infections, UTIs and bacterial vaginosis.

The vaginal microbiome is also involved in birth. Miscarriages and infertility are associated with an imbalanced microbiome. The vaginal microbiome also exposes newborns to microbes. This process provides many of the microbes that will become the child’s microbiome.

  • The Mouth

The mouth leads directly to our largest microbiome, the gut. With this in mind, it makes sense that the mouth would also host a complex microbiome. The oral microbiome has around 700 species of organisms. Many diseases are associated with imbalances in the oral microbiome. These include cavities, gingivitis, and other conditions. Brushing and flossing are key to maintaining a balanced oral microbiome. Avoiding antibacterial mouthwash may also help.

  • The Lungs

Like the UT, the lungs were historically believed to be sterile. Genetic sequencing has revealed that this is not the case. Though the lungs have fewer total microbes than the gut, they are extremely diverse. However, lung microbes are still poorly understood. The lung microbiome may play a role in lung diseases. Research into the microbial community associated with pneumonia, cystic fibrosis, HIV, tobacco use, and other diseases may reveal important treatment options.



Why Does the Microbiome Matter?



The microbiome is most prevalent in the gut. Here, bacteria play essential roles in digestion. They are crucial to digesting foods that humans naturally cannot. Bacteria digest a group of sugars called FODMAPs. This stands for Fermentable Oligo-, Di, Mono-saccharides, And Polyols. FODMAPs include well-known culprits of digestive issues such as lactose. FODMAPs may also play a role in the rise of reported non-celiac gluten intolerance. Many of these sugars are difficult or impossible for people to digest on their own.

An abnormal gut microbiome is associated with various gastrointestinal disease. Irritable bowel syndrome is one example. In this condition, disrupted gut bacteria interfere with normal bile acid metabolism. Other medical issues including obesity and diabetes are linked to an irregular microbiome. An improved understanding of the role of the microbiome in disease will improve treatment options.


Immune function

The microbiome also plays an essential role in immune health. The microbiome is a training ground for your immune system. Exposure to these bacteria helps your immune cells build a response to pathogens. It also teaches the body that some microbes are not dangerous. This is important to prevent unnecessary inflammatory responses. Without the microbiome, every new food or environment would cause an unnecessary waste of energy.

Experiments on mice have shown that a lack of microbes creates an immature immune system. Adding bacterial flora quickly causes the immune system to improve.

A diverse microbiome provides the best benefits to health and immune function. It is essential that your microbiome remains balanced. Measuring and understanding the variation in gut microbes may help treat immune diseases like Crohn’s. Techniques to characterize the gut microbiome will continue to improve. This will enable individually targeted treatments to rebalance the gut microbiome.


Relationship to the Brain

A drawing on a human brain.


The phrase “trust your gut” may have more truth to it than you ever knew. The gut-brain axis is the connection between the central nervous system (CNS) and the enteric nervous system (ENS). The role of the gut microbiome in influencing these systems is being investigated.

The CNS and ENS are independent but connected by the vagus nerve. This connects the gut directly to the hypothalamus and limbic system. These parts of the brain regulate emotion. The limbic system and the gut send signals back and forth. This relationship may be important in psychiatric disorders. Depression, anxiety, and even schizophrenia are linked to the microbiome.

Microbes can create neurotransmitters. These compounds are what our neurons use to communicate. These end up circulating in the blood. As a result, they affect day to day experience. In addition, bacteria play a role in modifying metabolism. As a result, levels of important precursors to neurotransmitters such as serotonin are changed.

The relationship between the gut and the brain is not well understood. However, it is clear that your microbiome has the potential to influence your emotions.



How Do We Study the Microbiome?




Petri dish with microbes growing on it. Microbes are yellow on a black background. The dish is labeled "Falcon"


The simplest way to look at a microbiome is to try and grow it in the lab. They place samples from the gut or another organ on nutrient-rich media. After that, the samples sit at body temperature until the microbes begin to grow. Finally, they grow each species on its own. Therefore, culturing microbes allows them to isolate individual species. Finally, they characterize species by appearance and chemistry.

However, culturing faces major hurdles. It is not possible to culture all the organisms present in the gut. Some need specific conditions only found in the gut. Reproducing these in the lab can be extremely difficult. Others need oxygen and will die immediately when removed from the body. Some species may be completely impossible to grow in the lab.

In addition, identifying microbes is difficult. For example, many species have similar appearances.

Even when culturing techniques succeed, they can be misleading. The species that grow may not represent the actual expression of genes and proteins. This is because they may behave differently outside of the body. Therefore, understanding the functional microbiome requires genetic techniques.




An artistic rendering of the double helix of DNA. 3 Blue strands of DNA on a black background.


To get an accurate impression of the microbiome, you need genetic techniques. Sequencing helps determine the species present as well as the microbiomes gene expression. Both of these are important in understanding how the microbiome relates to health. Sequencing all the RNA and DNA in a sample gives a better picture of the function of the microbiome.

There are many techniques to sequence the genome. As technology improves detailed sequencing is more available. In the future, it may even be practical to use sequencing to diagnose patients.


rRNA Sequencing

rRNA is a special type of RNA that helps create protein. This RNA sequence changes very little because it is so important. It also occurs in all cells. This makes it a great way to identify species.

rRNA sequencing lets researchers determine the diversity of species in the microbiome. It can also help determine which species are most common. This information is essential to help characterize the gut microbe community.

It is not always easy to identify the sequenced species. The meaning of “species” becomes a lot less clear with bacteria. These organisms readily share genes. They also reproduce so quickly that they evolve in real-time.

This makes it difficult to classify species. Instead, researchers group genomes by their similarity. Preset cutoffs define the groups. They call these cutoffs operational taxonomic units (or OTUs).


Shotgun Sequencing

The alternative to rRNA sequencing is metagenomic, or “shotgun” sequencing. This technique involves sequencing tons of small pieces of DNA. Computers can reconstruct the genome. First, they find overlapping sequences. With enough overlapping sequences, you can reconstruct the whole genome.

This strategy has the potential to reveal the full genomes of microbes. Knowing this could provide better detail of the diversity of the microbiome.


Genetic techniques and technologies continue to improve. These improvements will help researchers understand the microbiome. This research could pave the way towards microbiome diagnosis, which might provide early warning signs of diseases like IBS, diabetes, and obesity.



The Microbiome Provides New Insight

The role of the microbiome in health is complex. These communities are ecosystems with complex relationships. Each microbe interacts with their hosts (you and me) and each other. This complex network of interactions can have important impacts on health and disease. An improved understanding of these systems will help us to diagnose, prevent, and treat human disease. As advances in genetic sequencing continue to open the door to a better understanding of the microbiome, ongoing research into the human microbiome holds great potential.


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