Small Intestine Bacterial Overgrowth

Abdominal bloating.  Cramping.  Diarrhea, constipation or both.

If you have these symptoms, you may have been told you have irritable bowel syndrome.  This is probably correct.  But you may also have small intestine bacterial overgrowth (SIBO) as well.

Small intestine bacterial overgrowth is a condition where bacteria present in the colon spread into the small intestine.  The small intestine isn’t normally sterile but large amounts of bacteria are not present.

There are several reasons why bacteria might get into the small intestine where they don’t belong.  As we discussed last week, hypochlorhydria is a condition where the stomach doesn’t make enough acid.  Acid helps to kill bacteria in the food we eat, so that they don’t get into the small intestine.  If there’s not enough acid, bacteria can survive and sneak through.  Long-term use of acid-blocking medications can increase the risk of SIBO.

Another problem that can predispose to SIBO is pancreatic insufficiency.  Digestive enzymes produced by the pancreas also kill bacteria.  Chronic pancreatitis, cystic fibrosis and pancreatic cancer are often complicated by small intestine bacterial overgrowth.

Immune deficiency is another risk for SIBO.  The immune system makes antibodies that help to keep the small intestine’s bacterial population under control.  If the immune system isn’t working right, the bacteria can get out of hand.

If your intestine doesn’t work normally or has had its anatomy changed, these also can increase the risk of SIBO.  Bariatric surgery and other types of small-bowel surgery are examples.  Also, there is a valve that keeps bacteria from moving from the cecum (the first part of the large intestine) into the ileum (the last part of the small intestine) and if part of the cecum has been removed for any reason, that barrier may have been removed too.  Appendicitis and Crohn’s disease are examples of reasons why surgery may have been done on that part of the intestine.

I already mentioned irritable bowel syndrome.  Other problems associated with an increased risk of SIBO are celiac disease, liver disease like nonalcoholic fatty liver disease and liver cirrhosis, diabetes, scleroderma, radiation treatment to the abdomen and pelvis, and fibromyalgia.

OK, so suppose you have one or more of the above problems.  How do you know if you have SIBO?  This is the tough part.  Since it isn’t well understood there are very few tests that can be ordered to diagnose it.  One test is the hydrogen breath test which you can read more about here.  Stool testing can also be done, although it’s difficult to tell when using stool tests whether the bacteria are present in the small bowel or the large bowel.

What can be done about small intestine bacterial overgrowth?  First and foremost the underlying predisposing factors must be corrected if possible.  If you have hypochlorhydria or achlorhydria, taking betaine HCL with meals will correct it.  If you have chronic pancreatitis, taking pancreatic enzymes is key.  If you have celiac disease or other food allergies or intolerances, you must identify and avoid your trigger or allergenic foods.

Probiotics are an important therapy for SIBO.  They help suppress the growth of more dangerous bacteria in the large intestine and support the immune system.  As I have mentioned before, my family and I take Shaklee’s OptiFlora daily to promote digestive and immune health.

Many people with SIBO benefit from treatment with antibiotics to eradicate the bacteria in the small intestine.  This may need to be done periodically since, if the underlying cause(s) can’t be fixed, small intestine bacterial overgrowth tends to recur.

Small intestine bacterial overgrowth is a complication found with many common illnesses like irritable bowel syndrome, fibromyalgia, nonalcoholic fatty liver disease and diabetes.  Its symptoms are nonspecific and the problem isn’t easy to diagnose.  Treating it requires patience and persistence, as it tends to recur.  However, success results in better intestinal health, better immune function and overall better health for the person.

QUESTION:  Do you have any symptoms of small intestine bacterial overgrowth?



My patient Susan has GERD.  Heartburn, upper abdominal pain, the whole package.  She’s been taking acid-blocking medications for years and figures she’s going to be taking them for the rest of her life.  As long as she takes her medicine she’s pretty comfortable so she considers the problem solved.

My other patient Casey has GERD symptoms too.  However, in her case acid-blocking medicines don’t help.  She’s tried high doses of every acid reducer, tried combining different classes of medications, and she has her GI doctor stumped.

A third patient, Marie, has pernicious anemia.  Her immune system has attacked the cells that make both stomach acid and a protein that helps her absorb vitamin B12 from her diet.  She doesn’t have any stomach symptoms.  She was diagnosed because she felt tired and her labs showed anemia and vitamin B12 deficiency.

All these patients have one thing in common:  low stomach acid, called hypochlorhydria.  Actually in Marie’s case she probably has achlorhydria, or NO stomach acid, since the cells that make acid have been destroyed.

Susan’s hypochlorhydria is caused by her medications.  Casey, ironically enough, has hypochlorhydria which is MIMICKING reflux disease.  It’s a bit of a cosmic joke that hypochlorhydria can cause heartburn, upper abdominal pain and trouble digesting food.  How’s a poor doc to know?  Even on endoscopy it’s tough to tell the difference.

What can be done to help Casey?  I’m lucky my patients, including Casey, trust me so much!  I was able to get her to try apple cider vinegar which produced a remarkable improvement in her symptoms.  Within a few days she found that her symptoms were essentially gone.

Can you guess Casey’s main issue with this treatment plan?  Yep!  Apple cider vinegar tastes TERRIBLE!  Luckily there’s a supplement that can be used to provide acid to the stomach:  Betaine HCL,  1-3 capsules with meals based on the meal’s protein content. (More on this later.)

Why should Marie and Susan care that they have low stomach acid?  They don’t have any stomach symptoms, after all.  Stomach acid is important for proper digestion and also helps protect against infection.  People with hypochlorhydria have been found to have changes in the intestinal bacteria that can lead to small intestine bacterial overgrowth and irritable bowel syndrome symptoms, among others.

OK, so I’ll just take a probiotic and be done, right?  Not so fast!  Proper digestion of protein requires stomach acid, since pepsin (one of the three enzymes that digest protein) is activated by stomach acid.  If the pH is high (remember high school chemistry?  Acid has a low pH) pepsin doesn’t work and protein digestion isn’t effective.  This may lead to lack of proper protein nutrition, and worse, can expose food proteins to the immune system later in the digestive tract and possibly trigger food allergies.

Also, low stomach acid interferes with absorption of calcium and magnesium.  Calcium salts don’t dissolve if the pH is high.  Taking calcium supplements while taking strong acid-blocking medications is pretty ineffective.  Low stomach acid increases the risk of osteoporosis and hip fractures in women.

OK, so hypochlorhydria interferes with calcium, magnesium and protein digestion.  What do you do?  If you’ve got a history of stomach ulcers and life-threatening GI bleeding, you need the acid suppression so that your stomach doesn’t digest itself.

Turns out betaine HCL is effective at creating stomach acid even in patients taking powerful acid blocking medications.  If you think you might have low stomach acid or if you take acid reducing medications, consider a trial of betaine HCL with meals.  The first capsule is taken with the first few bites of food (NOT on an empty stomach!), and 1-2 capsules can be taken later in the meal if you’re eating a lot of protein.  Betaine HCL works quickly (it takes 5-6 minutes) and lasts about an hour.

Low stomach acid is very common.  For instance, it’s estimated at least 50% of diabetics have hypochlorhydria.  How do you know?  You can test yourself at home by mixing a small amount (a half teaspoon or so) of baking soda in water and drinking it first thing in the morning.  If you don’t belch a few times soon afterwards it indicates you may not have much acid in your stomach, since acid combines with baking soda to form carbon dioxide.

Proton pump inhibitors and other strong acid-blocking medications are great for short-term treatment but have consequences for long-term use.  Poor protein digestion, calcium and magnesium absorption issues, osteoporosis and hip fractures are known risks.  Using a well-tolerated supplement that temporarily restores acid to the stomach for meals can be a great measure to improve digestive function.

If you are under the care of a GI specialist for ulcers, reflux, Barrett’s esophagus or other acid-related problems, please be sure to discuss this with your doctor BEFORE starting a new medication or supplement.  You can print this post or email it to him/her with the research links for consideration.

Betaine HCL is available from health food stores and online.  Unfortunately I haven’t been able to find any guidance about which brand(s) to choose.

Hypochlorhydria is common, it often has no symptoms or has symptoms which mimic GERD, and causes some pretty serious long-term health problems.  Luckily the treatment is readily available and well tolerated, we just have to recognize it!

QUESTION:  Are you going to do the baking soda test?  If so, please post a comment letting me know what your results are!


What is Chronic Fatigue Syndrome?

The Institute of Medicine recently published a report about chronic fatigue syndrome that is very helpful for those of us who take care of patients with this illness.

So what is chronic fatigue syndrome anyway?  Chronic fatigue syndrome (CFS) is also called myalgic encephalomyelitis (ME) and is a very poorly understood illness.  Common symptoms of this syndrome are fatigue, body aches, “brain fog” (also called cognitive dysfunction), inability to tolerate exertion, and orthostatic hypotension.

Unfortunately, CFS is difficult to diagnose and mimics other illnesses.  There are no specific tests to make the diagnosis, and unfortunately patients sometimes get labeled as fakers or malingerers.  This is terrible because even though we don’t understand it, CFS definitely exists.

The new Institute of Medicine report helps to define the illness, which is one of the first steps towards understanding it better.

1.  Profound fatigue which leads to a substantial decrease in function, lasting for at least 6 months, which is a significant change from pre-illness levels of function.

2.  Inability to tolerate exertion.  Exertion of any type brings on significant worsening of symptoms and function.

3.  Sleep is not refreshing, which is not due to an identifiable sleep disorder.  To clarify, someone can have both sleep apnea AND CFS, but correcting the sleep apnea doesn’t make the sleep more refreshing.

4.  Problems with thinking (memory, attention, cognition) commonly termed “brain fog” which may be severe enough to make the patient unable to work or care for oneself safely.

5.  Orthostatic hypotension which is a drop of blood pressure on going from sitting/lying down to standing up, or with prolonged standing.

Additional symptoms described with this syndrome include pain and immune dysfunction.  Pain may take many forms, including headaches, joint pain and muscle pain.  Fibromyalgia may also be present.  Immune dysfunction (specifically NK-cell function) is well described as part of the syndrome too.

Now that we have a good definition for the illness, scientists are working hard to find the cause of it.  I suspect we won’t find a single cause.  It’s suspected that a viral infection may trigger the illness (Epstein-Barr virus is commonly suggested).

There is no specific treatment for chronic fatigue syndrome.  Identifying and treating problems that make symptoms worse (like sleep disorders and orthostatic hypotension) is helpful.  Removing chemicals and toxins from the home and especially from the diet is critically important.  Healthy nutrition and smart supplementation to provide needed support and boost the immune system are fundamental to treating poorly-understood but severe problems like this.

If you read this post and thought “Hey!  She’s talking about me!” I would encourage you to talk to your doctor about your symptoms.  You might want to download the Institute of Medicine’s Clinician’s Guide and take it with you to your appointment.  Not that you’re trying to tell the doctor how to do their job, but this is a poorly understood illness that is not taught in medical schools in general.  Be aware you might ruffle the doctor’s feathers, like when my patients come in and say they found something interesting by Googling their symptoms.  Sigh.

Until we know more about this illness, identifying it and managing symptoms are the best treatment plan.  Now that the Institute of Medicine has defined the diagnostic criteria, researchers have a better chance of studying suffers and finding out what the underlying cause(s) could be and how to treat it.

QUESTION:  Do you have any of the symptoms mentioned above?


Colic In Infants

This week I saw a precious 1-month-old baby whose mom brought him in because he won’t stop crying.  She was on the third formula and had tried EVERYTHING!

I’ve been taking care of newborn babies for 15 years and there are very few things more difficult for new parents than colic in infants.  Colic is benign, meaning in the vast majority of cases (at least 95%) no specific medical cause is found, and goes away on its own in time.  There are a lot of theories about what causes colic but no one knows for sure.

Colic is defined as a small baby (starting about 2 weeks of age) that cries for at least 3 hours per day, at least 3 days a week, for 3 weeks.  It lasts until the baby is 3-4 months old and then subsides.  Gender, breast-vs-bottle feeding, birth order, and parenting style make NO difference to whether a baby has colic, and older children who had colic as babies are no different than children who didn’t have colic.

Talk to your baby’s doctor about her symptoms.  The doctor will check your baby to make sure there are no signs of infection or other serious medical cause and that the baby is growing and developing as she should.

So if you have a fussy, colicky baby what can you do?!  First of all, rally the troops.  Caring for a colicky baby is absolutely exhausting.  Make sure you have plenty of help.

Here are 3 strategies that may soothe your baby’s fussiness.

1.  Probiotics.  There is evidence that Lactobacillus reuteri, a specific strain of probiotic bacteria, reduces crying in colicky infants.  Unfortunately on checking (my third-party supplement testing company) there are no reviewed children’s products that contain L. reuteri which passed quality testing.  There are a number of products on the market but I’m not able to recommend a specific one.

2.  Ditch the dairy.  In some cases, sensitivity to cow’s milk protein may play a role in colic.  Changing cow’s milk formula to a soy-based one may help.  Breastfeeding moms may want to try avoiding dairy for a week or so to see if that makes a difference in their baby’s symptoms.

3.  Try some home strategies.  It’s been a while since my kids were newborns so I looked up some current recommendations.  I mentioned to my tiny patient’s mom the ideas of babywearing (using a sling or baby carrier to hold the baby), swaddling and using a swing.  Here are some other ideas from WebMD.

Even though it feels like colic will never end, it eventually does resolve on its own.  In the meantime, make sure to be kind to yourself and take time to rest, let friends and family help you out, and enjoy every sweet little smile.  In a few weeks your baby’s smiles will start to outnumber the fussy times.

QUESTION:  Did you have a colicky baby?  What worked for you?