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The Ever-Evolving Microbiome: Part Two

The dynamic and evolving microbiome (Part 1) is characterized by distinct changes across the lifespan, and each stage of life is marked by unique considerations that require age-appropriate interventions. Common challenges at every age, with personalized probiotic protocols to manage shifts, offset disruptions and optimize the microbiome throughout the lifespan:


Infancy: Birth to Age 2.

Common challenges: Cesarean section delivery, formula feeding, antibiotic use. 

Mode of delivery has a profound influence on the development of an infant’s microbiome and immune system. “Infants born through Cesarean section (C-section) acquire a gut microbiota that significantly differs from those delivered vaginally, impacting immune and metabolic disorder risks,” says Jason Hastings, PhD, Senior Manager of Science and Education at SFI Health. Abnormal intestinal colonization in infants delivered via C-section may prolong postnatal immunological immaturity and hinder proper immune initiation, and in one study, babies delivered by C-section showed lower microbial diversity with higher levels of hospital-associated pathogens compared to vaginally delivered infants.1, 2, 3

Breastfeeding allows the mother to pass on beneficial microbes to her baby, as well as human milk oligosaccharides (HMOs), shown to affect the infant’s immune system through various mechanisms. Breastfed infants exhibit a distinct gut microbial composition with significantly increased levels of Bifidobacterium and Bacteroides and a closer resemblance to a mature, healthy microbiome. Formula feeding—especially without specific probiotic or prebiotic supplementation—leads to a different microbial colonization pattern that could have implications for infant health. And antibiotic use is also linked with marked disruptions in the composition and metabolic activity of gut microbiota.4, 5, 6

Personalized probiotic protocols:

  • “If an infant is delivered via C-section, was not breastfed or has had a lot of antibiotic exposure, the microbiome will be diminished,” says Tara Skye Goldin, ND, FABNG. “The favored probiotic at this age is Bifidobacter or bifidus.” Supplementation can help replenish the infant’s microbiome, and in studies, interventions that included Bifidobacteria were associated with reduced autoimmune and childhood diseases.7, 8
  • Probiotic formulas with a blend of targeted Lactobacillus and Bifidobacterium strains designed specifically for infants can restore normal microbiota disrupted by C-section delivery, formula diets, medications or other factors, to meet an infant’s unique intestinal and immune support needs.
  • For mothers: supplementing during the third trimester with Lactobacillus fermentum formulas can enhance lactation comfort and promote infant immune health through breastfeeding.


Childhood: Ages 3 to 12.

Common challenges: introduction of solid foods, infections and antibiotic use, environmental factors.

As children transition to solid foods, a balanced, high-quality diet is critical for microbiome development and, by extension, immune function. Healthy eating patterns in childhood have been shown to improve gut microbiota composition and promote immune system maturation. On the other hand, excessive sugar, unhealthy fats and low intake of prebiotic food sources disrupt the microbiome. Protein deficiencies alter intestinal microbiota, impact immunity and impair gastrointestinal barrier function and nutrient absorption, which can lead to micronutrient deficiencies linked with greater vulnerability to ear infections and diminished healing status. Poor diet, microbiome imbalances and compromised immunity result in more infections and increased antibiotic use, further disrupting the microbiome.9, 10, 11

Environments of high microbial diversity, like those found outdoors, are also crucial for establishing a healthy microbiome and immune function. “Research shows restricting microbial exposure in early life after initial colonization can impair normal gut microbiota development and promote innate immune activation,” says Hastings. “These studies suggest continuous outdoor microbial exposure is necessary for optimal immune and microbiota development.”12

Personalized probiotic protocols:

  • Research shows probiotic supplementation may prevent acute middle ear infections in some children and reduce the number of children taking antibiotics for any infections.13
  • Other studies suggest probiotic supplements can treat inflammatory bowel disease in children and manage diarrhea, and in one review, probiotics effectively lowered the incidence and duration of upper respiratory tract infections in children, while decreasing antibiotic use.14, 15
  • A broad-spectrum, hypoallergenic probiotic supplement designed specifically for children two years of age and older, with Lactobacillus and Bifidobacterium species, helps support gastrointestinal health and immune function in children.


Adolescents and Teens: Ages 13 to 19.

Common challenges: poor diet, shifts in sleep patterns, stress, anxiety and mental health.

Adolescents experience a wide range of external challenges and stressors, including unhealthy eating habits, sleep disruptions, stress and mood—all known to alter intestinal microbiota and impact immunity. “During adolescence, diet and nutrition are critically associated with the composition of the gut microbiota,” says Hastings, and a healthy microbiome is especially important during this stage of life.

The complex, bidirectional relationship between intestinal microbiota, diet, stress and mental health in adolescence is well established. Adolescence is a pivotal period for brain development, and gut microbiota disturbances during this time are implicated in stress, anxiety and adolescent-onset depression. Dramatic changes in the teen brain also make it especially vulnerable to stress, drugs, infections, dietary deficiencies, inflammation and environmental factors, and external sources of stress likewise influence intestinal microbiota.16, 17

A balanced, varied diet that promotes optimal gut microbiota composition is associated with improved mood, well-being and behavior in adolescents. In addition, interventions aimed at modulating gut microbiota show promise for preventing and treating psychiatric disorders, especially those that manifest during adolescence.18, 19

Personalized probiotic protocols:

  • Specific probiotic strains have been shown to improve depressive symptoms, anxiety sleep quality and mental health in adolescents, as well as mitigate inflammation, reverse dysbiosis, and decrease vulnerabilities to brain disorders later in life. “Adolescents may benefit from probiotics like Lactobacillus rhamnosus GG and Lactobacillus reuteri to support the gut-brain axis, along with omega-3 fatty acids, magnesium, and B vitamins to manage mood and stress,” says Rosia Parrish, ND.20, 21
  • Probiotic formulations that feature a blend of indigenous, essential colonizing, and beneficial transient probiotic microorganisms, including Lactobacillus and Bifidobacterium species, maintain a healthy, balanced microbiome and support normal intestinal and systemic immune functions.
  • Prebiotic formulations that include soluble dietary fiber with prebiotic activities can stimulate the growth of beneficial bacteria and enhance gastrointestinal and systemic immune function. Ingredients to look for: chicory inulin is shown to increase populations of Bifidobacterium, Lactobacillus and Eubacterium—a butyrate-producing species indigenous to the bowel—to promote a healthy immune response. Larch arabinogalactan supports immune function and selectively stimulates Lactobacillus species, and purified yeast beta-glucan has broad, beneficial effects, enhancing immune responses to a wide spectrum of fungal and undesirable microorganisms.


Adulthood: Ages 20 to 64.

Common challenges: work-life stressors, sleep disturbances, weight management, sedentary lifestyles.

“In early adulthood, the stress of establishing independence and career pressures can be overwhelming,” says Parrish. “Midlife introduces metabolic shifts and an increased risk of  metabolic syndrome, weight gain and chronic diseases. The gut-brain axis also plays a prominent role in mental wellness, stress and sleep, so supporting the microbiome is critical.”

The gut microbiota, pivotal in normal healthy brain function, are significantly influenced by stress, and disruptions exacerbate stress-related behaviors. Stress, in  turn, impacts sleep, while sleep deprivation and changes to normal sleep patterns further alter the structure and diversity of intestinal microbiota.22, 23

A sedentary lifestyle, common during midlife, also harms microbiota composition. Increased activity is linked with alpha diversity of the gut microbiota, and an active lifestyle has been shown to benefit gut microbiota, potentially through increasing the fecal concentration of short-chain fatty acids. Other studies suggest physical activity influences the presence of the phylum Firmicutes and bacteria known for their association with obesity and metabolic diseases. Aerobic activity has the most significant effect, but even moderate-intensity physical activities, like walking or cycling to work, can positively affect gut microbiota diversity.24, 25, 26, 27

Personalized probiotic protocols:

  • Research demonstrates the beneficial effects of Lactobacillus and other probiotics on metabolic changes and weight maintenance. A growing number of studies also suggest restoring intestinal microbiota balance can regulate sleep and mental state via the gut-brain axis.28
  • Certain probiotic strains, including Lactobacillus helveticus R0052, Bifidobacterium longum R0175, Lactobacillus rhamnosus (JB-1), Lactobacillus plantarum P8, Lactobacillus casei Shirota and Bifidobacterium longum NCC3001, have been linked to improvements in psychological outcomes and show promise for mood and stress management, says Parrish.
  • A comprehensive, broad-spectrum blend of probiotics designed for overall support should supply a complete spectrum of synergistic and complementary species shown to promote both innate and acquired immunity, strengthen intestinal epithelial barrier integrity, protect against undesirable microorganisms and modulate inflammation.


Seniors Years: 65 and Older.

Common challenges: age-related shifts in the microbiome, medications, inadequate nutrition, sleep and mood disturbances, cognitive decline.

In seniors, lifestyle factors and the normal process of aging lead to dramatic alterations in the microbiome. Disruptions to the microbiota have been shown to promote susceptibility to infections and chronic inflammation, and research links age-related changes to the microbiome with increased inflammatory status—known as inflammageing.29

Medication use also exacerbates dysbiosis and reduces microbial diversity, and studies show a significant negative correlation between the number of drugs taken and microbiome biodiversity among elderly patients. “Research highlights the complex relationship between polypharmacy and the gut microbiota in the elderly,” Hastings says. “Studies suggest interventions aimed at minimizing unnecessary medications could benefit microbiota composition and, consequently, the health and well-being of seniors.”

Meanwhile, a variety of physiological and lifestyle factors associated with aging typically alter eating patterns and nutrient intake, including inadequate consumption of protein and micronutrients. These shifts in diet impair the microbiome and lead to dysbiosis, characterized by a decrease in diversity and butyrate-producing microbes, with an increase in anaerobes that tend to favor a more inflammatory state.30, 31, 32

Disruptions to the intestinal microbiota and a pro-inflammatory status of the immune system heighten the susceptibility to disease  and risk of infection. Dysbiosis is further linked with diminished duration and quality of sleep, and plays a key role in behavioral disorders, including depression. Impaired gut microbiota impact brain integrity and are strongly implicated in the pathogenesis of Alzheimer’s disease and related dementias, and research points to correcting microbial imbalances as a promising therapeutic target for reducing the risk of neurodegenerative diseases.33, 34, 35


Personalized probiotic protocols:

  • Probiotics have been shown to positively influence gut microbiota, mental flexibility and mood in older adults. In one trial, seniors consumed either placebo or probiotics containing Bifidobacterium bifidumBGN4 and Bifidobacterium longum BORI. After 12 weeks, the probiotics group demonstrated greater improvements in mental flexibility test and reductions in stress.36
  • Other research suggests probiotic supplementation enhances cognitive function and benefits sleep quality in older adults with mild cognitive impairment. In other studies, probiotics significantly improves cognition, mental performance and learning in people with mild cognitive impairment or Alzheimer’s disease.37, 38
  • In a 12-week controlled clinical trial of patients with Alzheimer’s, supplementing with Lacticaseibacillus acidophilus, Lacticaseibacillus casei, Bifidobacterium bifidum andLimosilactobacillus fermentum improved test scores compared to a control group. In another study, Alzheimer’s patients who took combination of various species of bacteria and fungi demonstrated improvements in in attentive, executive and language functions, visual-spatial function, abstraction and constructive abilities and memory.39, 40
  • Probiotic formulas specially formulated for seniors that include a blend of specific Lactobacillus and Bifidobacterium species help maintain balanced and diverse microbiota and support normal gastrointestinal health and immune function in adults over 60.



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