Understanding the benefits and the limitations of functional GI microbiome testing

Testing functional GI markers, as many of our patients have found out, can be really enlightening when patients are dealing with unresolved chronic health and digestive issues. However this interesting recent article in the scientific journal Nature decided to take an in-depth look at what's “underneath the hood” of much of the microbiome portion of the testing. There is an enormous amount of scientific data about the importance of a balanced GI ecology, for its role in health and disease, but that has not always translated into very clear guidelines about on the ground consumer testing , about what's valid and what's still undetermined.

Direct Consumer Testing (the ability of a patient to directly order health tests from a company rather than through their physician) , has further added complication to an already shifting picture. Many of these companies are freelancing by experimenting with new methods that have not been fully validated, and developing interpretation tools that are still very much in their infancy.

This is not to say that there is no merit in doing stool functional testing. We do it pretty routinely and have found it in many instances to be the key to turning around somebody's health by getting the right data set to make new clinical decisions. But this is a word of caution about two different aspects of this sort of testing: the first one is that DCT options will put more power in the hands of patients, however it also may make them more vulnerable to being sold substandard testing products from a strictly clinical perspective. As the article pointed out, several labs fared quite poorly in the reproducibility of their own testing using the same sample. The second aspect is more nuanced. We have a lot of scientific data about the benefits of a balanced microbiome, however we're still rapidly evolving in our understanding of what's healthy and optimal, and we need to understand that when we are looking at raw data to not excessively extrapolate conclusions that are not supported by our current scientific understanding.

https://www.nature.com/articles/s42003-025-09301-3

OSTEOARTHRITIS AND MYOFASCIAL PAIN SYNDROME

An increasing percentage of our population is living above 65, and often for another 2 or 3 decades. This bit of good news if you're approaching that milestone (I am!), Is that you have 2 or 3 more decades to experience and hopefully enjoy life. The bit of bad news is that you will get to live out those 3 decades in a body facing increasing wear and tear.

Osteoarthritis refers to the process by which articular cartilage starts to deteriorate, leading to loss of joint space, and a constellation of associated structural findings and symptoms: instability, spurring, loss of normal motion, chronic pain and inflammation. It should be noted that osteoarthritis is not a linear finding correlating with simply aging. Some patients are more predisposed to osteoarthritis than others because of additional mechanical factors causing accelerated wear and tear on joints of the spine and extremities (which is why chiropractic research has shown some modulation of progressive osteoarthritis in many patient receiving care, reducing unnecessary mechanical stress). Other patients experience worse osteoarthritis because of metabolic factors that have to do with our poor nutrition, lack of blood flow from inadequate physical activity, and other complications from health issues such as medications, medical treatments etc.

One aspect of the constellation of osteoarthritis related findings and symptoms that is often missed or poorly understood is the secondary chronic myofascial pain syndrome and widespread trigger points. There are complex reasons for that that have to do with the local neurology of the deteriorating joint on muscular tone and control. Patients often are frustrated about what they believe to be a completely new problem, until we sit down and explain to them the correlation between myofascial pain syndrome and osteoarthritis, as being the manifestations of one common phenomenon. But there is something unnerving about patients suddenly feeling that every muscle tendon and ligament in their body is starting to hurt.

Myofascial pain syndrome and trigger pointsin the context of osteoarthritis should be treated both concurrently for the best results. Addressing the myofascial pain alone will have little to no lasting results since there's an upstream trigger. Joint adjustments, active range of motion exercise and strengthening, information control will hugely impact the severity of the myofascial pain. Conversely, only addressing the osteoarthritis will often fail to adequately resolve the myofascial pain since it often has become a self-perpetuating condition of its own.

Myofascial interventions in patients with moderate to severe osteoarthritis does need some modifications. Levels of pressure, frequency of treatment need to be adjusted down. Qualified soft tissue therapist know how to modify the treatment plan accordingly. Other supporting treatments that have found to be very effective are dry needling, traditional acupuncture needling with caution, as well as a variety of topical intervention such as infrared therapy and counter irritant topicals

https://pubmed.ncbi.nlm.nih.gov/36943163/

WHAT CAN GO WRONG WHEN YOU FALL ON YOUR ARM

https://www.youtube.com/shorts/kKP5KtWSxVw

We've seen so many of these injuries this week that I decided to record a short video with the help of my staff to review all the things that can go wrong when you fall on your arm. I thought it was an important educational material to have available since so many people fall and develop problems that they do not connect to the original incident. Especially since the area of symptoms may be far away from the point of impact on their hand and wrist.

Where the injury exactly will occur along the kinetic chain from the hand to the neck depends on a variety of factors, some of it having to do with the angle, and the speed of reaction and trying to break the fall. I've seen some patients develop along acute cervical disc herniations from the side to side during when they're caught off guard during the fall and the neck experiences a form of lateral whiplash. Probably more common are the areas along the shoulder girdle. I especially find that the sternal clavicular joint, at the end of the anterior kinetic chain, can be a source of continued misery and destabilization along the anterior neck and chest, often overlooked and even more often undertreated.

New low back and hip pain after a knee or hip replacement: the "long leg"

Several of our patients are opting in for planned joint replacements of hips and knees at this season, with the assumption that their work on their rehab and be ready to hit the ground for the season of outdoor gardening vacationing and general fun summer activities with some new and well-functioning hardware. This reminded me of a long-awaited blog as I've seen several cases last year.

I've been in practice 32 years and 1 of the most stunning improvement I've seen that affect my patients in my practice has clearly been the advancement in joint replacement. Minimally invasive, robotics, short recovery, they sometimes come with some challenges that need to be addressed so that the patient has the optimal recovery they're looking for by going under the knife. One such challenge is sudden changes in leg differential that can happen even when surgical intervention has been optimal.

The process of osteoarthritis and articular cartilage joint loss is a slow process that happens over years. The thickness of an intact joint versus that of a fully deteriorated joint can be over 1/2 an inch in difference. (Maybe closer to three quarters of an inch at the knee because of the presence of the meniscus). As a result, the leg affected could be easily an inch shorter from its original status, a process that the body will be able to mostly absorb over time due to its ability to slowly compensate at several levels including the sacroiliac, the lumbar spine, and the ankle.

A joint replacement will overnight reestablish the distance of a joint to its original state, and that can paradoxically be a real big problem. While the body can adjust to half an inch of difference in leg differential that gradually manifests over 2 decades, it doesn't have the ability to adapt to three quarters of an inch overnight. As a side note I should mention that our fine orthopedic surgeons have done an increasingly better job at trying to assess the leg differential and compensate for that during the surgery. But it's not always a perfect process and some surgeries come with inherently more difficulty in maintaining equal leg length, especially for people who have profound damage to the bone in which the prosthesis is going to be inserted (previous fracture of the limb, AVN, osteonecrosis, hip dysplasia, aggressive subchondral cysts to name a few).

The typical presentation looks like this: patient has successful surgery, discharge into rehab. Within a few days of starting to ambulate, they start developing intense pain on one side of their lower back and gluteal area, often the opposite side of the hip or knee replacement. Initially they write it off to limping prior to the surgery or after to the surgery, but the pain only deteriorates as they increase their walking time.

Sometimes the process goes on for a few years before I happen to see the patient. The history will reveal a pretty clear correlation between the surgery and are rather rapid onset of the new pain pattern post surgically and related to increase weight bearing time. During the patient's physical examination, when I observed them standing from the front to the back and walking, is a clear pattern of a very tilted pelvis, most often high on the prosthetic side. By the time the patient has been ambulating with an acutely acquired noncompensated long leg, did create some mechanical stress that will require some manual intervention with chiropractic adjustments, soft tissue mobilization and sometimes some balancing exercises. But as soon as is feasible in the body can tolerate it, I'll start inserting a heel or full-length foot lift gradually, to bring the pelvis and the lumbar spine to its original level. There is some real finesse and how you conduct the leg balancing, often having to start with a few millimeters at the time and increase by a couple millimeters every 2 weeks, and due to complications of mature hips and knees on the affected side, most often will require a full-length lift which sometimes will have to be external in the shoes. I should also note that we don't always have to compensate for the full deficit, but the body will often be able to adapt to approximately half of the leg differential and will just need to shim for the other half. However, the recovery by addressing the acquired long leg from a joint replacement can also be very dramatic and rapid, making everyone happy.

The moral of the story: if you are having some persistent new unilateral hip lower back or thigh pain after a lower extremity joint replacement, don't give up on yourself and be evaluated. It could be a relatively simple problem to resolve.

NEW YEAR RESOLUTION AND THE LIES ABOUT WEIGHT LOSS

https://www.nature.com/articles/s41591-025-03842-0?utm_source=klaviyo&utm_medium=email&utm_campaign=%28Friday%20Email%20-%20Chris%20Kresser%20General%20News%29%20Chris%27s%20Friday%20Favorites&utm_term=Nature%20Medicine&utm_content=Nature%20Medicine&_kx=ZpXBDTeEF9QJhwDqQXXrImrT_HpFsBz1ZlYMbsx_Vq0.my75y6

Getting healthy is obviously on a lot of people's minds this week. Hopefully not to fade away unnecessarily soon. And among these priorities is often trying to bring body weight and body composition in line with optimal metrics.

A couple of years ago I got into an argument with a colleague personal trainer. The topic was about pre-and post workout high-protein meals. He kept pushing highly processed protein breakfast bars on his clients, to maximize muscle gains from his prescribed exercise routines, and I had advised some of our common patients against that based on metabolic health research, steering them instead to try to meet those goals with a few high protein naturally occurring foods. His mantra was that regardless of the source the metabolic effect was going to be the same and that some of these designer foods were actually a better value. There was a fair amount of research already back then about the fallacy of that statement, and this most recent piece of research puts the last nail in the coffin of the flawed processed food theory.

What struck me about this piece of research is not necessarily the end result, which is in line with previous research, but the scale of the differential of weight loss/weight gain based on the food source. We're talking about DOUBLE the weight loss and weight gain by simply sticking with unprocessed foods. And you have to remember that everything else in micronutrient and calories were exactly the same between both groups.

Let me flesh this out in practical terms: for the same amount of calories, and the same amount of proteins versus carbohydrates, and unprocessed food has a vastly different metabolic effect on your weight. And you may wonder why? Whole foods interacts very differently with the receptors in our gut, especially natural GLP-1 receptors, leptin and ghrelin receptors, which are hormones associated with energy regulation and food seeking behaviors. Whole foods also have a completely different interaction with our normal micro biome, which is highly involved in weight and body fat regulation at the level of the brain through retrograde vagal pathways primarily. It's also noteworthy that designer foods, even those supposedly good quality high protein bars that are often the staple of many people in the gym rat world, are basically so chemically different from the food your brain is meant to encounter that it doesn't know what to do with it and gets very confused about its nutritional and energy value.

It's not that in the real world you'll never be grabbing for a quick food every so often, but it's to emphasize the fact that you never get to where you need to be metabolically if that's the rule rather than the exception. I continuously feel the question from patients, especially parents of teenagers, what's the best breakfast bar or protein bar they can give the kids as they fly out in the morning. I tell them the best bar is no bar at this point. Which often gets a lot of raised eyebrows. Hardly any of them are made with real ingredients, and none of them will have the metabolic effect of grabbing a piece of fruit with a piece of cheese, a boiled egg, some nut butter etc. With a little bit of planning, you can stock your home with whole foods that do not require any prep, but can be tossed into a go bag for those days where more food prep is not an option.

Topical treatment for pain and inflammation

It's a question that comes up frequently and I realized recently that I don't have a good written resource material to direct patients to and I find myself repeating the same thing over and over in the middle of a busy day. Unlike some of my colleagues, who tend to downplay their value in an overall treatment plan, I feel that topical's can have huge benefits to direct therapeutic activity to a local local area, and can overall minimize the patient's need for more toxic oral medications.

Understand that this is a generic list, and that you will probably need to figure out with your own individual healthcare provider which 1 of these may be the best, and understand that you may need different topical treatments at different times. Also understand that while mostly safe, a few of them do have some potential contraindication related to other medications and comorbidities that you should be aware of.

Topical treatments full in different broad categories matching their mode of action: counter irritant, vasodilators, anti-inflammatory, analgesics, and some of them crossover into more than one category.

COUNTER IRRITANTS: those agents tend to create a local receptor response that competes with pain receptors, thus tricking the body in perceiving sensation rather than pain. Menthol is probably the most common one. It's found as a base in the majority of topical treatments. It's usually quite safe, short acting and reversible. There's a huge variety of products available, and ultimately it boils down to preferring water-based versus oil-based, and how much of an overlying sent or not you want to have.

VASODILATORS: those agents tend to increase local blood flow by increasing vasodilation of smaller blood vessels. The main benefit is to improve circulation to a particular area, especially in the periphery of the body. The main ingredient is capsaicin, derived from hot peppers. On the tail end of the activity, they tend to have a mild analgesic effects. The benefits are to improve blood flow to deliver soft tissue repair nutrients, especially oxygen, in areas that are having a hard time healing or are somewhat avascular because of previous trauma or general health issue with blood circulation. You have to be quite careful with them, since they can create great irritation to the skin, and they are more medical contraindications to using them, especially with peripheral vascular disease and diabetes. It comes in different potencies, and you also have to be extremely careful not to rub your eyes after applying them.

ANTI-INFLAMMATORIES: it's a relatively broad category, with many agents having a secondary anti-inflammatory effect in addition to another primary effect. The effect pathways of information in peripheral tissue. This includes both pharmacological over-the-counter substances as well as naturally occurring substances.

- salicylate and dicofenac are topical versions of pharmacological oral equivalents, which are available over-the-counter. (Aspercream or generic equivalent is the most common version). They are quite effective, have a moderate acting range, but have to be used very carefully especially if it's used consistently in the long term because it does eventually reach your bloodstream. I think there is definitely a time and a place for short-term use during acute trauma recovery, to minimize the need for oral pain medication. There are some definite contraindications, so best to check with your provider before using.

-Essential oils like frankincense: should be used in small amounts in a carrier oil because of their potency, but can be a very nice long-term alternative because in smaller doses they really quite safe.

- Arnica: increasing in popularity in the US, I grew up with Arnica as a mainstay in our pharmacy box. It's a little bit of an atypical anti-inflammatory, which is used mostly for acute trauma and contusions. It has virtually no side effects so that one is safe for just about everyone to try.

- CBD: an oil-based extract from the hemp plant, CBD alone has no psychotropic effect and is relatively easy to use in the long term quite safely. I find that CBD takes a little bit to kick in, and I think it's best used for long-term management of chronic joint or soft tissue inflammation rather than as an acute aid.

- MSM: a sulfur based compound, it has a great safety profile when used topically. It has a mild anti-inflammatory effect, but is primarily used to support chronically injured collagen, such as osteoarthritis of joints, and chronic ligamentous or tendon injuries.

ANALGESICS: it's a little bit of a difficult category to pain, since analgesics means pain reducer. The mechanism of pain can vary in different patients, so all of the above can act as analgesics in a particular patient. However technically only very few compounds are considered true analgesics and they are relatively uncommon. The most commonly available over-the-counter is a pharmacological compound called lidocaine usually applied in transdermal patches. Lidocaine is powerful, short to moderate acting, but it has a fair amount of side effects and many medications adverse interactions for a lot of people so I would use that one was a lot of caution and with the green light of your provider. There are very few nonpharmacological true analgesics, such as California Poppy.

This is not an exhaustive list, with several other less commonly used compounds such as homeopathic's, and many bundled products. But this should at least be enough of a background for patients to start asking the right questions to select the right topical for their personal use.

First trimester pregnancy and low back pain: caught off guard ?

I have recently completed an online review of pregnancy related neuromuscular skeletal common issues. Quite a bit of it was just that, a review of things that I already knew and practiced for 3 decades, but there are always a couple new nuggets of information that are worth savoring.

The common thought about the 1st trimester of pregnancy from a neuromuscular skeletal standpoint is that is pretty routine because you have not started growing a lot of weight in the front of your lumbar spine and pelvis yet, and that most of the problems will start as your pregnancy advances. Nothing could be further from the truth and reality. Here are some facts that explain why some women are caught off guard and feeling quite silly about the amount of problems they are encountering before showing off a baby bump

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• The key hormone associated with softening of soft tissues and especially ligaments, called relaxin, actually peaks in the 1st trimester, and has a 2nd smaller peak in the 3rd trimester. This hormone creates a softening of the ligaments that are beneficial to prepare a wider pelvis during labor, but also indiscriminately affect all the thoracic lumbar and pelvis ligaments. During the 1st pregnancy, this means that practically you start developing a slightly hyper mobile pelvis and increased lumbar lordosis (anterior curve or sway back) very early on, sometimes even before you may know for sure that you're pregnant. Increased nonspecific lower back pain associated with hyperextension and facet syndrome is extremely common, as well as reactive discomfort in the gluteal and anterior hip area. Even the rib cage can feel like it's easily strained with normal activities. A whopping 25% of women will have a major fall during the 1st trimester of pregnancy because the center of gravity has already started shifting and the brain has not quite caught up with that.

• Women are not expected to significantly curb the activities during the 1st trimester of pregnancy because their body looks un-pregnant yet. Women need to understand that on the outside their body may still look the same but from a functional standpoint the stability of many of the thoracic lumbar and pelvic joints is already altered, and may require more care and stability during activities and exercise. This is especially true with subsequent pregnancies after baby number 1. It's okay for women to give themselves permission to curb back a little bit on the household chores when they find out they are pregnant even if they're not showing yet.

• Seeking chiropractic care during the 1st trimester of pregnancy can be really beneficial for variety of reasons. Not the least of which is to address some of the more immediate discomfort, but also to get a better baseline of any long-term structural issues that will require some time and intervention including a fair amount of home care to optimize women's body for labor and delivery.

• From a functional standpoint every woman can start working on a little better lower abdominal strength, making sure to center the trunk over their pelvis as it's naturally wanting to shift more anterior, be little more aware of fall prevention by limiting tripping hazards in your environment. Incorporating deep decompression flexion stretches as part of your wellness routine is also remarkably comfortable during the 1st trimester.

Tips on winter oral health

A little bit off the chiropractic path but worth a mention because of the number of questions that are starting to come up. Integrative dentistry and oral health somehow has been bubbling up on several of my health podcasts, that I listen to during my daily commute. The oral cavity is unique in that it ties into our respiratory system, and in this matter very much connected to our immunity to airborne pathogens, as well as the beginning of our digestive tract, and in that matter very much connected to our overall digestive health.

While oral health is a year-round issue obviously, underlying problems tend to be accentuated during the winter months because our indoor air quality and dryness.

Before I dive into a few specifics, I obviously want to remind everyone that basic care when it comes to proper nutrition and basic oral cleaning should be your foundation. You do not want to be snacking on starchy or sugary foods and drinks, and you want to make sure you brush your teeth at least twice a day and floss appropriately.

Beyond that, there are a few practical approaches to chronic oral problems, which involve gum irritation, cold sores, poor breath etc.

As a backdrop: the oral cavity is its own very micro biome rich environment under optimal circumstances, very much like the rest of you digestive tract, although the optimal microbial distribution is somewhat different than the lower digestive tract. Some of the same factors that tend to suppress digestive micro biome tend to suppress oral micro biome: unbalanced diet with high process foods especially sugars, food preservatives; carbonated beverages which disrupt the oral pH; artificial sweeteners of any kind that tend to kill of good bacteria (all the sugar alcohols are major problem in that regard and often overlooked, especially in things like gum). Additional factors that are unique to the oral cavity include chronic mouth breathing, which creates abnormal dryness of the oral mucosa and selectively allows non-beneficial gram-negative strains to dominate. Harsh anti-septic such as alcohol-based oral rinses will compound the problems, since they will indiscriminately kill all bacteria including the beneficial ones.

Here are some practical tips to improve your oral health this winter:

– recognize and address mouth breathing. It's a broad category and it sometimes complicated. Practice nose breathing multiple times a day, to break the habit of painting through your mouth. Obviously nasal congestion that prevents or limits nasal breathing can be a difficult and challenging problem over time if you dealing with chronic infections or allergies, but you can still start working on improving the amount of time you breathe through your nose rather than your mouth. You may need to work with a healthcare provider for some underlying root causes including myo functional oral therapist.

– Practice good meal timing habits by trying to have 4-5 hours between meals, wash your mouth or clean your teeth after meals, and limit your intake to water between meals or any unsweetened beverage such as tea or coffee. This will allow you oral micro biome to restore itself between eating.

– Limit or eliminate your use of gums. People do not realize how many of them have artificial sweeteners or other chemicals that kill off normal oral bacteria.

– Use gentle non-alcohol-based oral rinses if needed, but simple salt and water rinsing and gargling may be all you need.

– The acidity of your saliva can be a big contributing factor to problems with gums, lips, and especially canker sores. Ideally you saliva should be at a pH between 6.2 and 7.5. Over acidic saliva is mostly related to dietary imbalances with too much fast acting sugars, however some people are much more predisposed to acidic saliva than others, as evidenced with increased gumline cavities. You can test your saliva away from meals, using over-the-counter pH strips. If you find yourself constantly closer to 6, you can also use baking soda oral rinses to raise the pH. Those can easily be made at home using the following recipe:1 tsp (5 g) of salt and 1 tsp (5 g ) of baking soda in 4 c (1 L) of water

– If dealing with chronic gum or oral infections, supplement your dental care with anti-infectious natural agents. You may need to work with a provider on how to select the right agent, but typically you want to start with something a little stronger, such as anti-infectious essential oil rinses for 2 or 3 weeks, then transition to gentle immune maintenance agents. Some examples would be essential oils of clove, tea tree, oregano for an initial antibacterial treatment, then transitioning to more immune support therapies such as propolis, echinacea etc. There are a lot of over-the-counter available products that target natural oral health that you can leverage. If you are dealing with more chronic viral overgrowth such as cold sores, HSV6, you will spend less time trying to kill off and more time trying to restore your normal oral immunity.

– Oil pulling is a great way to help root out chronic pockets of nonbeneficial bacteria are an infection. You can use something as simple as coconut oil by itself to start out, with an oil pulling time of a minute while you work up the patience and endurance to swish your mouth longer. You should not rinse out your mouth after oil pulling, simply spit out what you have in your mouth and let the rest coat you oral cavity to prevent dryness. If you're concerned about a severe infection to start out, rinse your mouth and then take 1/2 teaspoon of coconut oil in your mouth and let it dissolve in your mouth without spitting it out. You can also add 1 or 2 drops of your essential oil to your coconut oil.

– Oral probiotics are becoming readily available over-the-counter. They are the equivalent for the oral cavity of what a traditional digestive probiotic is for your lower intestines. They target strains that are more prevalent in the mouth. Once you have cleaned out infections and pathogenic bacteria, it's a great way to prevent a reinfection and re-colonize your mouth with a stable oral micro biome. You probably only need to do them once a day initially for 6 weeks, then twice a week for maintenance.

– For some people with unique oral challenges (certain immune modulating medications that we can soft tissue such as autoimmune Biologics, certain long-term chemotherapy agents, post radiation etc.), you may need to consider oral red light therapy. There are some over-the-counter device at a very affordable price point nowadays, which you can purchase with your HSA, which offer red and blue light therapy known to control surface infections as well as increase soft tissue repair.