Love Your Microbiome: Creating Homeostasis in Our Micro-World

 In Gastrointestinal

Maria Del Mar Rodriguez-Berrios, ND

Vis Medicatrix Naturae

Early childhood is a critical phase in terms of being exposed to a variety of microbes and developing strong immunity.1 When I was a little girl, I remember running through green fields and rain showers and playing in the mud. I constantly exposed myself to a diversity of “germs” while growing up, including many kids who were sick. Despite all that, I caught very few colds and flu bugs. Today’s young generation is less inclined to go outside to play, and many parents tend to be germophobic. Moreover, we are seeing children for whom the vast majority of their interactions are with electronics, not microbes. Could this be one of the reasons we are seeing increasing numbers of chronically sick people in our society?

Over its history, microbes have been classified in the United States as enemies. By introducing and maintaining antiseptic practices (eg, antibacterial soap), and antibiotic use as a standard of care, our micro-world, as I describe it to patients, has been altered, by killing not only pathogenic bacteria but also the commensals that contribute to our body’s homeostasis. Historically, antibiotics have been used to eradicate epidemics. Antibiotics obviously kill bacteria, but this also has metabolic consequences, including the promotion of inflammatory processes and overgrowth of other pathogenic microbes.

The most dangerous consequence, however, is the risk of developing antibiotic resistance. As a person repeatedly takes the same antibiotic, some of the pathogenic bacteria can overcome the drug’s therapeutic properties and become resistant, replicate easily, and contribute to persisting infection. This is one of the reasons that many primary-care physicians have stepped back their prescribing of antibiotics for common health concerns. Many of us clinicians believe that there is a place and time for specific treatment options that include antibiotics. For instance, many cases of upper respiratory infections, and patients with risk of sepsis, immune-compromise, and many life-threatening circumstances can greatly benefit from these drugs. However, the healing power of our own bodies and nature have been proven to transcend the overuse of antibiotics and its guidelines for decades.

Microbiome Diversity & Development

I became fascinated by this topic when I had the opportunity to collaborate with Dr Maria Dominguez-Bello at her microbiology laboratory during my undergraduate studies. We studied and compared the gut microbiome of domesticated wild cattle vs farmed cattle, and found antibiotic-resistant bacteria in the farmed animals.2 Dr Dominguez-Bello is currently investigating the associations between human microbiome diversity and predisposition to develop certain health conditions.

It is interesting to observe the role of microbes throughout history in humans and civilizations living on planet Earth, including the effect of expansion into developing countries. These effects transcend geographic location, cultural influences, dietary intake and lifestyles, birth, and the introduction of medicines. It is fundamental to understand as a society that every individual has their own genetic predispositions and expression, including their very own microbiome world. According to scientists studying the human microbiome, our bodies are composed of trillions of microbes (viruses, bacteria, fungi, etc) that are coexisting and interacting with our own cells.3

These ecosystems are habitat-specific, and species vary according to their anatomic location. Microbes live mostly on our skin and inside the epithelia lining the gastrointestinal cavity from mouth to anus. These microorganisms work synergistically within us to keep us healthy, and any disturbance in their balance may predispose us to illness. We all acquired our initial microbiome from our mothers if born vaginally – our first inoculation. Later on, our own microbiome took shape during our first 3 years of life, through environmental exposure. Exposure to beneficial bacteria at an early age is essential for the development of a healthy immune system as we grow.1 In our modern society, delivery via Cesarean section has been associated with an increased risk of metabolic and immunological diseases such as asthma, allergies, obesity, and diabetes.4 However, swabbing babies born by Cesarean section with microbes from their mothers’ birth canals has been shown to restore the microbial diversity that is found in vaginally delivered infants; thus, this represents a promising therapy.4 Babies’ gut microbiomes increase in diversity as they are introduced to human contact, different environments, and food. Breast-fed babies tend to have greater diversity of flora in their guts, compared with formula-fed babies.4 Acquired bacteria in the early stages of life may be linked to increased immunity. It has been shown that decreased intestinal microbial diversity during infancy may predispose to health conditions such as type 1 diabetes and allergies, as well as obesity in adults.1,4

Gut Bacteria & Human Health

As a naturopathic physician, I am particularly interested in assisting and restoring my patients’ ability to heal using the most natural and beneficial routes possible. As a researcher and enthusiast of many ongoing investigations, I have acknowledged particular emerging studies about the microbiome that confirm what we already know: the healing power of nature. Many factors, such as environmental toxins, stress, and the overuse of drugs like antibiotics and antacids, can disrupt microbiome homeostasis, and consequently long-term health. I have therefore been assessing – but mostly educating – many patients about the importance of their overall health, which includes restoring harmony and homeostasis in their individual microbiomes. As part of the clinical support I use to address gut dysbiosis (microbe imbalance), I usually provide my patients of all ages personalized lifestyle and dietary recommendations that serve to minimize inflammation, maintain optimal digestion, and promote a well-balanced gut microbiome. This includes, of course, self-care practices such as managing high stress levels, which is so common in our society. Gut dysbiosis is commonly identified as the root cause of many chronic health conditions in my practice. By focusing clinically on this component, I reaffirm what Hippocrates had maintained: “All diseases begin in the gut.” Now science is investigating and confirming this basic principle.

The gut microbiome has significant influence on many essential functions of the human body, including immunity, nutrient absorption, and direct mediation of neurotransmitters and hormones. Modifications to existing intestinal microflora via fecal transplants, prebiotics, and probiotics have been shown clinically – and recently through scientific research – to be beneficial to a variety of patients with health conditions, such as those with irritable bowel syndrome who present with anxiety or depression along with gastrointestinal symptoms.5 This therapeutic efficacy is a result of a more effective gut-brain connection and HPA axis, whereby gut microorganisms directly influence neurotransmitter release6 – another reason to call the gut our “second brain.”

The future of medicine is being influenced by ongoing studies examining the use of “psychobiotics”  for mental disorders such as ADD7 and Alzheimer’s disease. Innovative clinical trends in the medical field may include the administration of specific species of probiotics to also manage chronic disorders such as diabetes, a growing epidemic worldwide. Recent evidence suggests that certain bacterial species may interact with human metabolism to stimulate enteric hormones and other systems outside of the gastrointestinal tract. An example is low-grade, chronic inflammation that promotes adiposity and insulin resistance, brought about by the introduction of pathogenic bacterial fragments into the circulation through a malfunctioning gut barrier, aka leaky gut syndrome.8

Treatment Considerations

In my own clinical practice I have found that my patients’ gut health is directly related to inflammatory disorders, metabolic syndrome, obesity, and type 2 diabetes. Leaky gut and dysbiosis, particularly bacteria and fungal overgrowth, eg, Candida albicans, have been commonly observed in patients with clinical presentations and predisposition to metabolic disorders. Following an individualized and comprehensive naturopathic protocol for these presentations is key. This consists of completing appropriate assessments including comprehensive laboratory testing, and especially becoming familiar with the patient’s medical history, including how they were born (ie, vaginally or by C-section), history of antibiotic use, and their presenting symptoms.

The lab assessments are recommended in order to understand the root cause and to manage and prevent further health complications of each individual patient. They may include a comprehensive stool analysis; breath tests for small intestinal bacterial overgrowth (SIBO) or Helicobacter pylori; and blood work to evaluate cardiometabolic predispositions such as insulin resistance (ie, insulin, fasting and post-prandial glucose, HbA1c), and inflammation (ie, hsCRP). Abdominal bloating, constipation, sugar cravings, insomnia, anxiety, and fatigue are the most commonly reported symptoms by patients in my practice. However, many patients with autoimmune disorders, (eg, Hashimoto’s thyroiditis, rheumatoid arthritis), or other chronic disorders (eg, fibromyalgia) may present with more systemic symptoms, or be asymptomatic. Therefore, further clinical assessments are needed to evaluate their root causes and to manage them accordingly.

Patients presenting with SIBO often benefit greatly from reducing their dietary intake of short-chain carbohydrates via a low-FODMAP diet, due to their difficulty digesting these foods. These short-chain carbohydrates include fructose (in fruits and some vegetables), lactose (in dairy), galactans (in legumes), and polyols (in sugar alcohols).

A food antibody panel can also be a useful clinical tool for identifying and eliminating possible triggers. The elimination of highly-reactive foods will promote improved immune response and gut healing in patients. L-glutamine can be used to promote gut healing in patients with leaky gut and dysbiosis. I have found that patients respond well to antimicrobial agents such as Berberis vulgaris and allicin. These have been generally shown in clinic to have broad antimicrobial properties when used correctly, and to effectively eradicate dysbiosis. In most patients, the antimicrobial treatment phase should be around 6-8 weeks, along with a longer-term low-carbohydrate, anti-inflammatory diet that includes the removal of processed foods and the incorporation of nutritious food groups (eg, vegetables such as kale, broccoli).

Reinoculation of the gut with diverse bacteria is essential after using antimicrobials. In metabolic disorders, a well-designed formula of probiotics may promote weight stabilization and help regulate inflammation and immune health. Probiotic intervention strategies may become an increasingly important element in diet and lifestyle alterations aiming to prevent or attenuate obesity and related metabolic disorders. A few bacterial strains have been identified as having health-promoting potential in animal studies,9 though non-specific increases in bifidobacteria or lactobacilli in the large bowel may also be achieved through the introduction of “functional foods” such as live-culture yogurt. Consuming prebiotic agents, such as non-processed fermented foods, chicory root, dandelion root, psyllium, and artichokes may facilitate the growth and conservation of diverse beneficial bacteria.

After promoting gut health, digestion and absorption, an assessment of nutritional deficiencies and replacement of a wide variety of micronutrients (eg, vitamin D, B12) is also necessary for managing and preventing chronic disorders, as well as to inhibit a pro-inflammatory environment that fosters the growth of pathogenic bacteria.10 With such measures, a diverse and healthy gut microflora may happily thrive.

Closing Comments

Human microbiome data is now been collected and compared to a unique tribe of Amazonian hunters and gatherers whose microbiome is significantly more diverse and has not been as exposed to pro-inflammatory conditions as microbiomes in westernized populations.11 As this population is exposed to more modern and urban environments, its members may start developing chronic diseases. Our challenge is to apply what this civilization can teach us about how to promote and maintain homeostasis of our beneficial bacteria in order to decrease the risk and manifestation of inflammatory and metabolic diseases.

Moreover, it is fundamental to support the whole person naturopathically in order to foster microbiome homeostasis, as supporting an individual’s digestive health ultimately impacts their overall health. Our bodies have the innate capacity to heal themselves, and our microbiome is working synergistically to make this possible by helping to digest our food, stimulate our immunity, and prevent disease. The specific roles and identities of our entire human microbiome are now been studied,12 but it is already evident that these microbes help establish homeostasis. We humans should be aware of and live in harmony with our micro-world. Beyond novel discoveries in science and technological advancements, sometimes all these interesting findings are also telling us: let’s get back to basics in our human existence and live a well-balanced life; let’s play more in the mud and explore nature; let’s care for ourselves and our microbiome.

Disclaimer: The author is not currently affiliated or sponsored by any of the mentioned research projects.


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Image Copyright: <a href=’’>sifotography / 123RF Stock Photo</a>

Maria Del Mar Rodriguez-Berrios, ND, is a licensed naturopathic physician who graduated from Southwest College of Naturopathic Medicine. Prior her medical training, she obtained her bachelor’s degree in Natural Sciences at the University of Puerto Rico. She has offered personalized medical care to diverse communities and underserved families in Mexico, Puerto Rico, and the United States. She has broad experience in clinical research in digestive microbiology, public health, and cultural-appropriate intervention programs. She recognizes the importance of current clinical research and public health education for the management and prevention of health conditions. Her commitment and passion is to serve communities globally through compassionate integrative care.

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