The Bacterial Cutting Board – What’s Actually Going On In My Stomach?

Armed gut bacteria (1)

I am a biologist, and I love to tell my kids about the ways their bodies work, including how fascinating it is that millions of strange little organisms live inside their gut and help with the digestion of their food.

It’s priceless when you later get these questions that show just how much they think about the things we have discussed, and how they try to apply their knowledge-of-the-world-so-far into the new concepts they’ve learned.

Our original conversation about enzyme scissors was a bit longer than a comic easily permits, so let me elaborate:

It’s not exactly like a knife, but there are many different kinds of little molecular machines, that bind to their very own specific bits of food, that add little molecules that persuade parts of the big food molecules to go their separate ways.

I couldn’t find a simple illustrations of bacterial CAZymes (Carbohydrate-Active enzymes) breaking down complex branched vegetable carbohydrates, so I decided to make my own (the finer molecular points of difference we can save for later when they are at school ;). A simple sucrase version of a similar enzymatic reaction looks like this:


Bacteria are pretty rad

The bacterial world is such a rich area of life that we still have plenty to learn about it. Consider the bulk of the visible life around you: plants and animals. Each group has somewhat different cellular characteristics, but within the groups, and even across them, the basic chemical processes used to grow and multiply are much alike – there is an astonishing degree of similarity between human and plant house-keeping genes, coding for the basic staff of proteins maintaining the cell (within phyla, human and fruit fly share about 40 %). Not so with bacteria!

Different families of bacteria may rely on entirely different types of chemical reactions to survive, utilising a dizzying array of enzymes to accomplish their diverse goals. Think of nitrogen fixing bacteria (the only process – apart from lightning – producing nitrogen fertilisation to plants before the Haber-Bosch reaction in early 20th century); bacteria that live on compounds leaking from ocean floor thermal vents, supporting entire small ecosystems thanks to their chemosynthesis; or bacteria that survive and maintain themselves inside 34,000 years old salt crystals, to throw in just a few of the examples of their biochemical prowess.

It comes as no surprise, then, that until recently no one had realized just how rich a variety of services our gut bacteria provide for us, and how wide a variety of enzymes they use for the job.

CAZymes – The ‘Sugar Scissors’

Most of us have learned that the fibrous plant wall material, cellulose, is something we can’t digest, and that it only provides useful fiber material that keeps our stomachs going. Our own cells produce enzymes like amylase, but those only break down relatively simple sugars, not complex branched carbohydrates like cellulose. But it turns out our bacteria can and do! From PLOS Biology, How Bacteria Turn Fiber into Food:

…with the help of symbiotic bacteria in our guts, we can actually get some nutrition from the complex carbohydrates such as cellulose, hemicellulose, and pectin that make up plants’ cell walls. The bacteria produce an arsenal of enzymes that break down these carbs into simple sugars, which are then in turn fermented to create short-chain fatty acids that human cells can absorb—and which can contribute as much as 10 percent of the calories our own cells require.

Our guts and the helpful bacteria (especially of the Bacteroides family) allow us to use more plant materials to our benefit. High-cellulose material, like grasses, still remain unavailable to us – only ruminants have the truly specialised enough bacterial arsenals (and stomachs) required to squeeze out the energy from those.

In my comic I decided to use the simple example of a Glycoside Hydrolase – enzyme that cleaves the sugar bonds by adding a water molecule, that splits into H and OH, each binding with their own end of the cleaved sugar molecule. To nod at the true complexity of the matter, however, I’ll add that there are a whole host of CAZymes that catalyze the breakdown, biosynthesis or modification of carbohydrates and glycoconjugates. From the CAZy database:

  • Glycoside Hydrolases (GHs) : hydrolysis and/or rearrangement of glycosidic bonds
  • GlycosylTransferases (GTs) : formation of glycosidic bonds
  • Polysaccharide Lyases (PLs) : non-hydrolytic cleavage of glycosidic bonds
  • Carbohydrate Esterases (CEs) : hydrolysis of carbohydrate esters
  • Auxiliary Activities (AAs) : redox enzymes that act in conjunction with CAZymes

Many enzymes that are structurally within the Glycoside Hydrolase (see the CAZyme Wiki) family don’t actually use a water molecule, but a simple sugar, or a phosphate, or they may degrade part of the sugar molecule itself.

It’s complex! I’ll make sure to take that up with my kids, er, in a few years.

For more reading, you can see How bacteria break down human food blog piece in Scientific American on CAZymes, take a look at the site Types of Bacteria for the Friendly Bacteria of the Digestive System, or Ask a Biologist on How Germs Eat for You:

if it weren’t for the help of bacteria living in your gut, there are many things that you wouldn’t be able to digest at all.

logo basic

For more science-with-kids comics, see Getting a feel for physics or Extreme Natura Spells – When scientists’ kids fight. If you would like to discuss the topic below, you are very welcome, but please take note of my Commenting policy.

In a nutshell:

  1. Be respectful.
  2. Back up your claims with evidence.

About Thoughtscapism

Cell Biologist, science communicator, an agricultural and biodiversity analyst, and a fiction writer.
This entry was posted in biology, nutrition, parenting and tagged , . Bookmark the permalink.

2 Responses to The Bacterial Cutting Board – What’s Actually Going On In My Stomach?

  1. marianwhit says:

    Love your work…totally…refreshing, and always worth my time:)


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