• Microbigals

Microbial Party in the Human Gut Microbiome

Good morning, class! Settle down now. Larry, take your seat please! We have a fascinating topic today. The human gut microbiome has really become a “buzz” word with the humans lately and what it means has perhaps become convoluted by their media. Of course, we microbes have been living and creating the human gut microbiome since before the humans were giants! But what is the human gut microbiome? How does it affect their health? What makes a good or poor gut microbiome? And most importantly can they change it to improve health? We will address all these questions and more in this primer on the Human Gut Microbiome!

What Is the Human Gut Microbiome

Put simply, the gut microbiome is the amazing microbial world housed in a giant's gut. This may include bacteria, viruses, fungi, yeast, and even archaea. This means the gut is home to every kingdom of organisms known to man! In the past 2 decades, the microbiome has been linked to health in a number of ways including, helping to metabolize food, protect from diseases, and are even the coaches of the immune system!

So how diverse is the human gut? Well, the giants' guts are in constant flux depending upon who is there, but on average, a healthy adult microbiome can host up to 1000 different microbial species and a trillion different organisms! To put that into a bit of perspective, the average zoo houses less than 200 species of animals, their gut is 5x more diverse than their local zoo! Primarily the gut microbiome consists of two different phyla bacteroidetes and firmicutes. There is a considerable amount of diversity within phyla, for instance, each giant and pretty much every animal seen in the zoo would be grouped as the same phyla.

And just like the zoos across the world, all gut microbiomes may have the “tiger” microbe, the “lion” microbe, and the “elephant” microbe but they also have a unique set of species not seen in any other zoo. The gut microbiome is unique and has been growing and changing with each human for their entire life. Quite literally, from the moment the tiny giant passes through the birth canal, to breastfeeding, to eating sand from the sandbox, their first kiss, to their first break up, to getting their first apartment, the gut microbiome has always been there for, changing with, and giving each giant all the support it can.

But just as some clothes just don’t work on certain giants, some microbes are actually harmful to the gut and health of its host. When there are too many microbes that aren't a good fit, it is called dysbiosis and this can cause a whole slew of issues for the giant and their health from cancer, to mental health, to autoimmune diseases, the gut microbiome profile can influence them all. Each gut microbiome is unique to each giant, and trying to optimize it isn’t a one-size-fits-all like they make them buy probiotics and other products, no it is more complicated than that, far more complicated!

Why The Gut Microbiome is Important

OK, so you know what the microbiome is, but why is it important? Well, a lot of things actually. One big function is dealing with short chain fatty acids, or SCFA. Humans can’t digest dietary fiber, but bacteria can. They ferment the fiber into an intermediate which other bacteria use to make short chain fatty acids with the most common being butyrate, propionate, and acetate, all of which the human body needs.


o Energy source for colonocytes or the cells lining the large intestine

o Beneficial effect on glucose and energy homeostasis

o Essential for the body to make the intestines anaerobic, or without oxygen, which gut microbes love


o Helps regulate glucose generation in the body as well as the feeling of fullness


o Important in cholesterol metabolism and the metabolic formation of fat

o May be involved in appetite regulation

In addition, studies of SCFA have correlated their presence with reduced insulin resistance. So, remember it is important for the giants to eat the recommended amount of daily fiber for good health!

Dysbiosis, or the microbiome being out of whack, along with lower diversity, or the number of different species of microbes, have been linked or correlated to many different health conditions. In particular, studies have shown that lower microbial diversity in the human gut has been seen in irritable bowel disease (IBD), diabetes, psoriatic arthritis and Crohn’s disease. In addition,

lower diversity and dysbiosis have been correlated with immune dysregulation, long term weight gain and obesity. One of the most famous studies was collecting human fecal samples by healthy and obese individuals that were then implanted into mice. Interestingly, the poor mice that got the fecal implants from obese people gained more weight then their healthy counterparts!

The gut microbiome may even help protect against some infections in the gut. A great example is with the bacteria Clostridium difficile (C. diff). Even though people can become sick when infected with this microbe, it is actually commonly found in healthy peoples' microbiota, but a healthy bacteria balance keep it in check. An issue arises when the microbiome can become dysbiotic, such as taking antibiotics. With the lack of microbes, C. diff can grow causing a diarrheal disease that can be hard to treat.

The gut microbiome is also important in vitamin production. Many microbes in the intestines can make water soluble vitamins including vitamin B. In fact, humans only get vitamin B12 exclusively from the gut microbiome, if they don’t take a supplement that is. In addition, half of the needed daily vitamin K also comes from the gut microbiome.

There may also be a connection between the microbiome and the human brain called the gut brain access. Those that have irritable bowel syndrome have higher cases of depression and those that have autism tend to have digestive problems. There was even a study that showed that in a study of 1000 people, those that had depression had deficits of 2 bacteria Faecalibacterium and Coprococcus. The gut microbiome may even influence the release of neurotransmitters in the body. The bacteria act on cells in the gut called enteraoendocrin cells which, in turn, release hormones and serotonin into the body.

So, as you can see, we microbes and the microbiome we form in a giant's gut influences many aspects of their health. It should be noted though that a lot of these studies can find correlations and observations. This does not mean that they can assume cause and effect quite yet and they need more research to be done to unlock the mysteries of the microbe zoo going on in their own gut! We will be talking much more about this and our favorite giants, the Microbigals are doing their own experiment on it, it should be fun to follow along on their microbial journey!

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