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Building a Healthy Microbiome From Birth

Medically reviewed by 
 
Building a Healthy Microbiome From Birth

Humans are inhabited by various microorganisms (bacteria, viruses, and archaea) referred to as microflora, microbiota, or normal flora. It is estimated that we are comprised of a hundred trillion bacteria cells alone—our bacteria out numbers our human cells by 1.3:1.

These tiny organisms (with their collective genetic material, the microbiome) exert a powerful influence on our mental health, physical state, and disease vulnerability. Our microbes co-exist with us as their human hosts and perform many vital functions. This results in our coevolution with them, forming a mutually beneficial relationship. (1-9)

This article will explore how the gut microbiome changes across human development and how to optimize its health to prevent disease.

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The Human Gut Microbiome

The gut itself accounts for over 70% of the human microbiota. Besides processing about 60 tons of food throughout our lifespan, the gastrointestinal tract (GIT) and its microbial inhabitants interact with a plethora of other organisms from the environment passing through it.

Our microbiome composition develops and shifts concomitantly with us throughout our lifespan and is influenced by these dietary and microbe exposures and various other factors. These include our genetics, lifestyle practices, environment, and geographic location. (1-23)

The intestinal microbiota is divided into six major classifications (microbial phyla). These include:

  • Firmicutes
  • Bacteroidetes
  • Actinobacteria
  • Proteobacteria
  • Tenericutes
  • Fusobacteria.

In adults, Firmicutes and Bacteroidetes are predominant and make up 90% of the gut microbiota. However, our microbiota evolves into this ratio over time, and the evolution begins in utero.

The Microbiome In Utero to Birth

Most scientific literature has reported that the fetus is sterile until it becomes colonized with bacteria through the vaginal birth canal. Yet microbes have been found within the stools of preterm infants and in the amniotic fluid of mothers with preterm labor. This helps theorize that mothers pass bacteria to their fetuses before childbirth. This could be possible through amniotic fluid- as a baby in utero typically swallows 400 to 500 milliliters of amniotic fluid daily. (10-19)

Another study has shown that oral microbes and stool of newborn babies contain a microbiome similar to the mother's uterus and the placenta.

In another study with six preterm infants, healthy babies versus those who developed a dangerous infection (sepsis) were compared. Overall, infants who developed sepsis began life with low microbial diversity and were exposed to antibiotics which they then acquired a predominance of Staphylococcus throughout the study.

In contrast, healthy infants who had not been exposed to antibiotics had more diversity of beneficial bacteria and a predominance of Clostridium, Klebsiella, and Veillonella.

All these studies support how gut microbiota development can be affected by various early life events, such as the mode of delivery (cesarean section versus vaginal delivery), a mother's microbiome health, and maternal antibiotic usage. Later, the initiation of breastfeeding, formula, or mixed feeding and the cession of breastfeeding also shapes a child's gut microbiota. (10-19)

The Infant's Microbiome

Many studies on the infant microbiome report that Bifidobacterium consists of most of the baby's microbiota species. Although bacteria changes based on the term infant's delivery, mode of delivery, and infant diet. (10-19)

Vaginally Delivered Babies

Vaginally delivered babies have been found to have colonization similar to their mother's vaginal tract, including Lactobacillus, Prevotella, or Sneathia spp. Interestingly vaginally delivered children, as compared to those delivered through Caesarean section, display lower rates of sickness, including asthma, atopic symptoms, and diabetes which could be accredited to the beneficial microbiome bacteria they are exposed to.

C-Section Delivered Babies

Microbe populations more consistent with maternal skin and oral microbes, such as Enterobacter spp, Haemophilus spp, Staphylococcus spp, Streptococcus australis, and Veillonella spp, are more dominant in infants delivered via C-section. Infants born by C-section were also found to have a lower abundance of Bacteroides over time, regardless of feeding mode. Specific colonization of the microbiota in children delivered through Caesarean section was delayed by up to one month, and the diversity and number of colonies in their microbiota were lower.

Breastfed Infants vs. Formula Fed Infants

Breastfed vs. formula-fed infants also have a microbiome that differs. Breastfed babies predominantly have Lactobacillus, Staphylococcus, and Bifidobacterium in their guts, whereas formula-fed infants contain more Roseburia, Clostridium, and Anaerostipes.

The cessation of breastfeeding and the timing of food induce changes toward a microbiome more similar to adults. Formula-fed infants appear to have a microbiome that shifts earlier towards that of an adult and to have more organisms associated with inflammation.

Other Factors That Affect The Microbiome in Infants

Antibiotics, pets, siblings, hygiene, and preterm vs. full-term delivery were also factors of the microbiome characteristics at birth. Genetics, gastrointestinal mucosal processes, and stress may also be at play.

Due to the impact of the microbiome on growth and development, neurological development (via the gut-brain axis), immune health, and respiratory health, among others, these changes could impact health or disease risk as the child ages.

Childhood and Adolescence Microbiome

Around ages one to five, there appears to be agreement that a child's microbiome starts to shift towards resembling an adult's microbiome and is more stable. School attendance, pets, peer interactions, diet, and hormones all impact the microbiota makeup through childhood and into the teenage years, eventually leading to a predominance in Bacteroides and Clostridium.

Adult Microbiome

Since many outside influences modulate the gut microbiome, the changes become more visible over time and are related to specific health conditions as age increases. These variations start to become evident in mid-to-late adulthood.

As time passes, the gut microbiomes become increasingly personalized to individuals and can be a factor in determining health span. Yet, it is noted that those in advanced years often have reduced biodiversity (population of microbial species) and compromised stability of these bacteria. Furthermore, opportunistic, pro-inflammatory bacteria increase with advancing age.

The ratio of microbiota in the elderly has also been shown to correlate with measures of frailty, co-morbidity, nutritional status, and inflammation. These alterations have been linked to less short-chain fatty acid production and changes in digestive functioning in the colon.

Interestingly, less production of short-chain fatty acids in the gut has been observed in older women vs. young women. This could relate to the changes that occur with sex hormones in menopause with age and its impact on the gut microbiome. One study found that postmenopausal women had changes in their microbiota that were more similar to men. Their guts had less diversity in their composition than younger women. This demonstrates that a more robust gut and reproductive microbiome may have been needed to address hormonal shifts in younger years.

How We Share Bacteria With Each Other

As noted earlier, our environment and diet can shape our microbiome as we age. Most of the bacteria we are exposed to are usually harmless and may even be necessary.

Even kissing can impact our microbiome. (26-28) In a study that investigated the effect of intimate kissing on the oral microbiota, clear correlations were found between the similarity indices of the salivary microbiota of couples, microbial communities on the tongue, and self-reported kiss frequencies.

Diving into the details of bacteria and swatting spit, the controlled experiment required participants to ingest a probiotic drink. It was found that the imbibing romantic had an average transfer of 80 million bacteria per intimate kiss of 10 seconds, mainly of Lactobacillus and Bifidobacterium, to the kiss receiver. However, even with this vast inoculation, the intimate kiss changes were transient and did not lead to an additional increase in the average similarity of the oral microbiota between partners.

Another study indicated that household members, mainly couples and pet owners, shared more of their microbiota, through the skin, than oral or fecal microbiota. There is also evidence that exchanging bacteria through sexual contact may contribute to reproductive and mating processes. (26-30)

These facts suggest that direct and frequent contact with our cohabitants likely shapes our microbial communities.

What is Dysbiosis?

Between the germ spreading, cohabitating, environment, diet, lifestyle factors, and kissing, the microbiota can become imbalanced by the very things that influence them. This is known as dysbiosis.

Gut dysbiosis can arise from the following situations:

  • A lack of diversity in the types of microbes present in the gut
  • A lack of beneficial gut microbes, or
  • An overpopulation of harmful bacteria.

Dysbiosis Signs & Symptoms

Since the microbiome influences every system in the body, directly or indirectly, signs and symptoms that can indicate a state of dysbiosis in the gut are vast. They also vary from person to person. Below are a few of the common signs and symptoms: (31-33)

  • Gut-related symptoms include gas and bloating, constipation, acid reflux, diarrhea, bad breath, abdominal pain, and mucus in the stool.
  • Mental health and brain disorders include anxiety, trouble with focus or concentration, depression, chronic fatigue, or brain fog.
  • Skin health problems such as acne, eczema, dark circles under the eyes, psoriasis, dandruff, and atopic dermatitis.
  • Immune dysregulation via proinflammatory triggers aggravating immune disorders, autoimmunity, and inflammation.

Functional Medicine Labs to Test The Gut Microbiome

The following tests can be performed for moms, pre- and during pregnancy, all adults, and children over two years old.

Dysbiosis Testing

Assessing for dysbiosis and digestive health is imperative to establish a healthy microbiome that can foster a balanced digestive tract. Comprehensive stool tests offer a complete look at gut health by measuring pathogens and analyzing digestion, nutrient absorption, inflammation, intestinal permeability, and immune function (including celiac markers), all of which impact digestion and the microbiome.

A SIBO (small intestinal bacterial overgrowth) test, H.pylori, and additional pathogens (infectious markers) can also be considered to assess for infectious causes of reflux disease, irritable bowel syndrome (IBS), ulcers, and other digestive disorders.

Organic Acid Testing (OAT)

OAT testing reports on bacterial byproducts from the intestine that can occur with dysbiosis. It also assesses vitamin deficiencies that are important for overall digestive and general health.

Food Sensitivity Testing

Food sensitivity testing is popular with many integrative physicians. Some may choose to run these tests to see if any food is currently triggering an immune response in the gut that can lead to dysbiosis over time. Food sensitivities are not allergic responses and are not life-threatening. However, they create an inflammatory reaction where the body attacks antigens in foods. Below are two examples:

  • The ALCAT test measures immune reactions through the stimulation of leukocytes. It is used to analyze sensitivities to 150 commonly consumed foods. This test cannot be ordered for patients younger than six months old.
  • The Array 4 - Gluten-Associated Cross-Reactive Foods and Foods Sensitivity Profile from Cyrex Laboratories examine sensitivity to additional dietary proteins and foods that cross-react with gluten, a common sensitivity for many individuals and linked to intestinal permeability and inflammation.

How to Balance The Microbiome

The following are functional medicine approaches to balancing the microbiome throughout the lifespan.

Lifestyle

Exercise has been shown to alter the gut microbiota and has evidence for changing brain neurochemistry to support mood. (34-37) One study found that aerobic exercise improved the diversity and abundance of genera from the Firmicutes phylum, which may relate to the benefit on the brain via the gut-brain axis.

Stress and Sleep Management. Emotion and physiological stress can alter the composition of the gut microorganisms, increasing inflammatory mediators and leading to dysbiosis, resulting in mood and sleep problems through the gut-brain axis. This creates a feed-forward negative cycle, as the microbiome has also been found to influence and regulate sleep and mental states. This is due to various metabolic functions of the gut microbiome activities interacting with the circadian rhythms and emotions of the host. Managing stress and proper sleep hygiene techniques can help to balance the gut microbiome. At least 7-8 hours of sleep are optimal for most adults, more for children and infants.

Nutrition

Following a low inflammatory whole foods diet like the Mediterranean diet has been shown to increase beneficial bacteria in the gut microbiome of humans. On the other hand, the Standard American Diet has been shown to increase gut permeability and decrease beneficial bacteria, which is responsible for metabolic endotoxemia. Therefore it is recommended to avoid processed fatty foods and refined sugars and increase whole foods to build a better microbiome.

Fiber has been found to support bowel health and can enhance microbiome health by feeding our good bacteria and increasing short-chain fatty acids. (40-43) Sources of fiber in the diet include beans, peas, and whole grains. Some fruits and vegetables are also relatively high in fiber.

Fermented foods, such as yogurt, kefir, kimchi, tempeh, and sauerkraut, contain microbes that can support a healthy microbiome by feeding good bacteria.

Supplements and Herbs

Recently it was found that there is an interaction between the gut microbiota and herbal medicines through two pathways. First, the gut microbiota "digests" the herbal medicines into absorbable, active small molecules which produce biological changes. Secondly, herbal medicines alter gut microbiota composition and its secretions, leading to physiological changes.

For example, many herbs contain polysaccharides that cannot be digested by regular digestive processes. Therefore, specific microbes, such as Bifidobacterium and Bacteroides, can secrete various enzymes to break them down into smaller metabolites that can have multiple health impacts on the body.

The following supplements and herbs may be helpful for digestive imbalances and symptoms based on assessment and lab results:

  • Digestive enzymes, bitters, bile salts, and intestinal integrity support (glutamine) can assist with digestive function, nutrient balance and improve gut health.
  • Prebiotics and probiotics support microbial diversity and balance the immune response.
  • Saccharomyces boulardii can help to enhance intestinal integrity through SIgA (a marker of intestinal health and immunity) and supporting microbial balance. It also has evidence for treating diarrhea.
  • Grapefruit seed extract has antibacterial and antifungal properties. These properties may support digestive health and help to tackle particular pathogen invasions and dysbiotic overgrowth.
  • Omega-3 fatty acids with resolvins may assist with soothing inflammation and help with digestive issues. They have also been found to support vessel integrity which can be compromised by long-term, systemic inflammation. Inflammation can lead to dysbiosis and an imbalanced microbiome.
  • Essential oils such as peppermint and ginger have antimicrobial and gastrointestinal-supportive properties and can help combat dysbiosis. Many essential oils also relax the mind-body and decrease stress, which can affect the microbiome in beneficial ways.

Summary

The influence of digestive function on human health is profound and has been a source of fascination for thousands of years. The root of disease beginning in the gut was touted by Hippocrates in 400 BC. Modern-day scientists have vindicated his ancient claim with the discovery of the microbiota.

When in balance the organisms that lie within our body and on our skin form great allies in promoting our overall wellness. However, when there is an imbalance in our microbiome, disease can ensue.

Understanding how the microbes shift throughout our lifespan and knowing that even in utero, mamma's guts influence her babies' belly bugs is empowering information to utilize. Lifestyle factors, diet, environmental exposures, and social contacts all can be considered for their impact on how our microbiome takes shape from birth onward.

By addressing these factors and supporting our gut microbiome and digestive function with personalized functional medicine support, we can rest assured that we can stay "young at gut" and age healthfully.

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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