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Alyssa Simpson RD, CDE, CLT
Alyssa Simpson

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Sibo Doctor Approved
certified gastrointestinal nutritionist
Sibo Doctor Approved
certified gastrointestinal nutritionist

How the Small Intestine Works. And What Happens When It Doesn’t.

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Digestion doesn’t have to be a dirty word. But if you’re here, chances are you’ve got some digestive issues. Whether you’re struggling with IBS, SIBO, or some as yet undiagnosed condition, you may be dealing with symptoms like:

? Diarrhea

? Constipation

? Bloating

? Gas

? Stomach Pain

Whether you’re working with a practitioner, on a therapeutic diet, or even if you’re taking medication, there’s something else you can do to improve your symptoms. And it’s totally free.

Optimize your digestion. It’s only logical that your digestive symptoms are related to the health of your digestive system.

That’s why we’re spending this month talking about what actually happens during digestion, and what you can do to help it happen more efficiently. Most of the time, better digestion = improved symptoms. I’m not saying improving your digestion is going to fix everything. But it can be an important and impactful step on your healing journey.

Here’s what we’ve covered so far:

? How the brain and mouth get the process started. Hint: these steps are really important.

? What happens to your food in your esophagus and stomach. Spoiler alert: stomach acid isn’t the enemy.

This week we’re working our way down the winding path of your small intestine. Let’s start with a bit of an anatomy lesson. I promise it’ll be short and easy.

You probably know about your small and large intestines. But there is more to it than that.

Your small intestine is divided into different sections.


This is the first stop on your food’s trip through the small intestine. The duodenum receives extra digestive juices from your organs — liver, gallbladder, and pancreas — to help neutralize stomach acid and further break down your food.

The duodenum is where you break down the largest food molecules like proteins and starches. The bile from your liver (stored in your gallbladder) helps break down fats. When food (now called chyme) is in your duodenum, your body absorbs minerals like iron and folate.


When chyme leaves the duodenum and enters the jejunum, it’s ready for a workout. The jejunum churns the food back and forth (segmentation), mixing it with the digestive juices that joined the party in the duodenum. And just like the moving sidewalks at the airport, the muscles of the jejunum move food along using contractions called peristalsis.

The jejunum is where your body absorbs proteins, carbohydrates, fats, vitamins, and minerals.


The final stop on the small intestine journey is the ilium. Here the churning (segmentation) slows down and peristalsis moves what’s left of the food toward the large intestine. But there are still nutrients to be found. So in the ilium, your body absorbs bile acids, vitamin B-12, and fluid.

But wait… there’s more!

Have you ever wondered what your digestive system does when it isn’t processing food? Just like your kitchen after dinner, your digestive system needs some cleaning up after a meal. While most of the food has moved successfully through the process, there are food particles that get left behind. This is where the Migrating Motor Complex (MMC) comes in.

The MMC is a recurring pattern of muscle movements that clean up the stomach and small intestine. Next time your stomach growls between meals, you can thank the MMC.

But just like ignoring the dirty dishes in your kitchen, if the MMC falls down on the job, things get messy. When you’re not eating, the MMC goes through four phases that clean out the stomach and small intestine. It’s the housekeeper of the gut. It sweeps away all the bits of food that were left behind during digestion.

The movement of the MMC also keeps gut bacteria in the large intestine where it belongs. But when it isn’t working right, it’s easier for that bacteria to creep up into the small intestine. The presence of this bacteria + the leftover food particles are a perfect recipe for small intestinal bacterial overgrowth, or SIBO.

Better Digestion Tip #1: Space out your meals

In order to give the MMC a chance to do its thing, it’s important to have some time between meals. The MMC moves every 90-120 minutes. But there are times it can go 4 hours in a cycle. So it’s a good idea to space meals 3-4 hours apart. Remember — the MMC only works when you aren’t eating.

Bonus tip:

Pay attention to your between-meal beverages. Caloric beverages can also interfere with this cleaning cycle.

The Pancreas, My Friend and Yours

The pancreas is kind of like a coach at a football game. He never touches the ball, but if he doesn’t do his job, the team’s not going to win.

The pancreas never actually comes into contact with your food, but it’s working behind the scenes. The pancreas secretes enzymes that are related to carb, protein, and fat digestion, as well as insulin & glucagon. But that’s not all… The pancreas produces the chemicals that triggers the neutralization of the stomach acid so that the afore-mentioned enzymes can do their job.

If your pancreas is struggling to fulfill it’s digestive roll, you may experience symptoms like:

? Mucus in stools

? Undigested stool

? Foul smelling stool or gas

? Greasy/poorly formed or floating stool

? Fullness 2-4 hours after eating

Better Digestion Tip #2: Make it easier on your pancreas

If you have the above symptoms, avoiding fatty, greasy meals can help your pancreas out. You can also take some digestive bitters before your meal to help stimulate enzyme production.

The Liver and Gallbladder — Teaming Up for Success

The liver and gallbladder work together to bring bile into the digestive process. Bile emulsifies fats, removes cholesterol, and helps with detoxification. It’s made by the liver and stored in the gallbladder.

Cholecystokinin (CCK) is a hormone from the small intestine that triggers your gallbladder to release bile and your pancreas to release enzymes so you can break down the different nutrients in your food.

Without bile, your body isn’t able to break down fats. Then these unprocessed fats can cause you issues further down the digestive tract in the large intestine — more on that next week.

Remember 3 weeks ago when I talked about how digestion begins in the brain? Here’s where that comes into play. If your brain isn’t involved in the digestive process — like when you eat stressed or on the run — you won’t enter rest and digest mode (parasympathetic). And if your nervous system isn’t in a parasympathetic state, your stomach isn’t going to produce enough stomach acid (HCL). And if you don’t produce enough HCL then these enzymes, hormones, and digestive chemicals aren’t released as they should be.

So you have all this not-quite-digested food barreling toward your large intestine ready to cause a whole bunch of problems.

Better Digestion Tip #3: Start at the top

This tip is basically a repeat of all the other tips. If you want to reduce troublesome digestive symptoms, you’ve got to get things working from the brain down. Remember, digestion is a north-to-south process. Anything that happens at the top affects what happens all the way down.

So if you want things running smoothly, remember to:

✔ Sit down, relax, and breathe before you eat.

✔ Remove distractions and stressors and focus on your meal.

✔ Chew your food thoroughly.

✔ Consider taking some digestive bitters or apple cider vinegar to boost your HCL.

Will doing these things solve all your digestive problems? Probably not. But until you get your digestion running smoothly, your symptoms likely won’t go away even with other measures. And you may even develop new problems.

If you’re struggling with digestion — IBS, SIBO, or troublesome symptoms — working with a practitioner who will take a personalized approach to your specific symptoms and physiology is what’s going to make the biggest difference. You don’t have to go it alone. Even if your doctor has told you nothing is wrong, it’s just part of getting older, or you should just get used to it, don’t give up hope. It is possible to improve your digestive symptoms and get your quality of life back. That’s what I’m here for.

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