Science Word of the Week: Crypt

In the popular world, a crypt is often seen as a burial place with creepy, mysterious, or even spooky overtones. But in the world of life sciences, the crypt is not where zombie uprisings occur, but rather where new life rises from the pit of the intestinal gland. The crypt is a pit found within the small and large intestines of our bodies. Our intestines are lined with what is called “villi,” which are finger-like structures composed of many different cells that aid in food digestion, mucus production, or nutrient absorption just to name a few. In between certain villi within our intestines lies the crypt.

standing person using fork and knife on preparing food
Photo by Fidel Hajj on

If there is any place in the human body I could shrink down to the size of a cell and visit with awe, the stomach and digestive system would not be one of them! As the sites of food digestion and nutrient absorption, the stomach and intestines would be a very dangerous place to visit. The production of Hydrochloric acid to break down food makes our stomachs a hostile environment and would eat our own skin if we were exposed to it. In order to protect our cells so they can do their jobs within the stomach and intestines, a special mucus is produced to cover our exposed cells within these harsh environments. But even with that added protection, many cells within our stomach and intestines die within a 24 hour period. That is where the unicorns of the cellular world come into play: the stem cells.

Tucked away deep inside the crypt lies the stem cells. These stem cells are far enough away from the action of digestion to be safe. Stem cells represent “new life” in the cellular world. Once a stem cell matures, it can differentiate into virtually any type of cell within our bodies. The stem cells within the crypt will mature and rise up out of the crypt and take its place in the front lines of digestion. They may take on the form of cells that produce mucus to protect other cells, or they may take on the form of cells that absorb nutrients from remaining food particles passed into the intestines by way of the stomach. The options for stem cells in nearly infinite, those are just two specific options within the digestive system of our bodies.


The crypts within our intestines do not always contain a happy ending filled with new life and new purpose for our cells. Recent studies show that certain signals within our bodies cue the production of stem cells, as well as the maturing and differentiating of these stem cells. When these signals are disrupted, cancer rears its ugly head and corrupts the crypt. If the signal to mature and differentiate is blocked while the signal to produce stem cells is stuck in the ‘on’ position, we have major problems and cancer soon develops. The more we learn about these signals, the better our chances are of finding another cure for various cancers that take over our bodies.

The crypt is a magical place. It holds new life and secrets into the world of debilitating cancers. Hopefully the “Lara Croft” of the science world can raid this crypt and discover the secrets of stopping the cancer before it rises from its tomb and infests our entire bodies.


For more secrets from the crypt, check out this online resource:



5 thoughts on “Science Word of the Week: Crypt

  1. Wonderful post! Reminds me of a paper on gut biogeography which implied the probable limitations of stool testing. The colon has two distinct mucus structures, but stool testing only sheds light on those bacteria on the outer layer, leaving the all-important inner crypts for dead. Minority populations are not detected by metagenomics on fecal samples but should not be neglected. Commonly used methods such as 16S rRNA sequencing tend to underestimate low-abundance taxa which may include keystone species such as segmented filamentous bacteria that exemplify the mucosal “minority report” paradigm. Specific minority gut microbes induce T-dependent IgA responses that involve B2 cells of the Peyer’s patches. So metagenomics studies that mostly detect majority bacterial populations may be missing out on commensals critical for adaptive immunity regulation.


    1. Nita, thank you for the comment and the follow! Admittedly, I am a novice when it comes to in depth human physiology, but I found this topic fascinating since I hadn’t heard much about “the crypt” before and it’s obvious implications to cancer though intestinal stem cell generation. But your comment intrigues me and makes me realize I still have much to study and learn on the topic!

      Liked by 1 person

      1. Yes, crypts perform so many restorative functions both as sites of intestinal stem cell regeneration as well as refugia for microbial commensals. Interestingly, the human appendix, long considered a vestigial organ, likely also serves as a safehouse from which to recolonize the gut following infectious gastrointestinal illnesses.

        Liked by 1 person

  2. Recent estimates suggest that the appendix has evolved at least 32 times among mammals, refuting Darwin’s hypothesis that the small structure had no function. Gut-associated lymphatic tissue (GALT has been found in both the rabbit and human appendix, and probiotic biofilm and colonization are also heavily concentrated in the appendix.


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