Microbiome Studies and Kids’ Health


The microbiome, the collection of bacteria and microbes in our bodies, plays a crucial role in our health. And nowhere is this more important than in children and babies. In fact, it begins with the health of our mother’s microbiome when she’s pregnant with us. How and where we are born, and the toxins in our environment, play a role too. I gathered some recent studies on this important subject and wanted to share the highlights with you.

Mom’s microbiome during pregnancy linked to child’s autism risk

Cutting-edge research suggests that the mother’s gut health during pregnancy plays a critical role in determining the child’s risk of developing ASD.

The researchers hypothesized that, in mice, an immune reaction to interleukin-17a (IL-17a), a molecule produced by the immune system, could trigger ASD-like behaviors. 

To test their hypothesis, the team used Jax and Tac mice from two different laboratories. Unlike the Jax mice, the Tac mice had gut microbes that made them susceptible to an IL-17a inflammatory reaction. 

Both groups were exposed to a virus designed to create an immune response. Only the Tac mice (the ones susceptible to inflammation) had pups that developed ASD-like behaviors.

To prevent an inflammatory response, the researchers then artificially blocked the IL-17a molecule in the Tac mice. The pups born did not show ASD-like behavior. 

Finally, the researchers exposed the Jax mice to the gut flora of Tac mice (making them more susceptible to inflammation). Interestingly, they found that pups born after this intervention showed ASD-like behavior. 

Practical tip: Although these findings may not be applicable to humans, pregnant women and those planning to conceive could opt for a gut-friendly (and microbe-friendly) diet and lifestyle. Probiotics (or fecal transplants, when medically necessary) may also positively influence the mother’s microbiome.

Study reference: Lammert, Catherine R., Elizabeth L. Frost, Ashley C. Bolte, Matt J. Paysour, Mariah E. Shaw, Calli E. Bellinger, Thaddeus K. Weigel, Eli R. Zunder, and John R. Lukens. “Cutting edge: critical roles for microbiota-mediated regulation of the immune system in a prenatal immune activation model of autism.” The Journal of Immunology 201, no. 3 (2018): 845-850.

Babies born at home may have a healthier gut microbiome

New research indicates that babies born at home have a more diverse gut and fecal microflora compared to those born in hospitals.

The researchers followed 35 infants and their mothers until the babies were 1 month old. 14 of the babies were born at home (four of them in water) and 21 in the hospital. 

Stool samples indicated that the hospital-born babies had greater inflammatory gene expression in epithelial cells which cover organ linings, skin, and mouth. Moreover, hospital-born infants had lower levels of Bacteroides, Bifidobacterium, Streptococcus, and Lactobacillus, and higher Clostridium and Enterobacteriaceae compared to babies born at home.

Why these differences in gut microbiota between infants born at home versus hospitals? 

Well, the scientists speculate that common hospital interventions, such as infant bathing and antibiotic eye prophylaxis, and the aseptic hospital’s environment could be involved. 

Although more research is needed, this study’s findings favors the idea of home births and/or revamping the hospital environment to mimic home conditions for non-high-risk births. Since the gut flora affects the immunity and metabolism, a healthy microbiome could reduce the babies’ risks of obesity, diabetes, asthma, and gut disorders later in life.

Study reference: Combellick, Joan L., Hakdong Shin, Dongjae Shin, Yi Cai, Holly Hagan, Corey Lacher, Din L. Lin, Kathryn McCauley, Susan V. Lynch, and Maria Gloria Dominguez-Bello. “Differences in the fecal microbiota of neonates born at home or in the hospital.” Scientific reports 8, no. 1 (2018): 15660.

Early disturbance of the microbiome and the rise in autism

A paper reviewing the implications of the disruption of the bacterial microbiome in autism was published in August this year.

Take-home “gems”:

  • Since gut microbes are involved in the production of many vitamins, they influence the overall antioxidant status. Glutathione, the body’s chief antioxidant agent is severely depleted in autism.
  • Gastrointestinal complications are common in ASD and could be caused by increased intestinal permeability, inflammation, and an unhealthy gut microbiome.
  • Individuals with ASD have more firmicutes than bacteroidetes – the ratio of these bacteria can influence the severity of autistic symptoms.
  • Antibiotics can decrease the body’s ability to absorb iron, produce proteins, and digest certain foods. This can further increase the risks of inflammation, autoimmune issues, and gastrointestinal distress.
  • An unbalanced gut flora can lead to many cognitive issues associated with ASD since about 90% of serotonin is produced in the gut.
  • Some antibiotics can prevent mitochondria, the cell’s energy-producing generator, from working properly and thus, impairs brain development.

To keep their microbiome healthy, individuals with ASD may want to (i) support their digestion and gut health, (ii) try an anti-inflammatory diet, and (iii) avoid using antibiotics except when imperative.

Journal reference: Eshraghi, Rebecca S., et al. “Early disruption of the microbiome leading to decreased antioxidant capacity and epigenetic changes: Implications for the rise in autism.” Frontiers in cellular neuroscience 12 (2018): 256.

Home cleaning products may increase the risk of children becoming overweight by altering their microbiome

Canadian scientists analyzed fecal samples from 757 3- to 4-month-old infants to assess their gut flora. They also recorded the children’s weight at ages 1 and 3 years. The infants’ mothers self-reported their use of disinfectants, detergents, and eco-friendly products at home.

What the research found:

  • Household cleaning products adversely affected the children’s gut microbiome irrespective of birth mode, intake of antibiotics, or breastfeeding.
  • Regular use of disinfectants increased Lachnospiraceae species by 1.3 times which, in turn, increased the risks of overweight at ages 1 and 3. 
  • Haemophilus bacteria levels dropped with daily use of disinfectants and regular use of household wipe products.
  • The children whose mothers used eco-friendly products daily had lower levels of Enterobacteriaceae. However, the scientists speculated that the mothers who used these products probably led a healthier lifestyle during pregnancy and transmitted fewer Enterobacteriaceae to their babies during vaginal delivery.

Practical Tip: Since, common household cleaners can cause children to become overweight by disrupting the bacteria in the body, avoid these cleaners. Instead switch to eco-friendly products; even simply baking soda and vinegar can often do the trick. It’s easy to do and it will make a big difference for you and your family.

Journal reference: Tun, Mon H., et al. “Postnatal exposure to household disinfectants, infant gut microbiota and subsequent risk of overweight in children.” CMAJ 190.37 (2018): E1097-E1107.

Gut health and inborn errors of metabolism

Inborn errors of metabolism (IEMs) are rare disorders involving a faulty gene that makes it difficult for the body to convert food into energy.

The treatment for IEMs typically involves dietary manipulations, which along with genetics, can influence the health of the microbiome. For instance, excessive food intake or food restriction, can lead to gut dysbiosis, an imbalance in the type and/or quantity of bacteria present in the gut.

This gut dysbiosis can further alter the metabolic state of a person with an IEM by worsening the functions of the liver and the brain, the two major organs already affected by IEMs.

As such, an unhealthy microbiome can cause:

  • Neurocognitive issues (mood and behavior disorders, coordination problems, and cognitive disorders)
  • Liver problems (cirrhosis and non-alcoholic fatty liver disease)
  • Issues with the gut-brain interactions, increasing risks of cardiovascular risk, multiple sclerosis, Alzheimer’s disease, depression, autism, and anxiety.

Journal reference: Colonetti, Karina, Roesch, Luiz Fernando, & Schwartz, Ida Vanessa Doederlein. (2018). The microbiome and inborn errors of metabolism: Why we should look carefully at their interplay?. Genetics and Molecular Biology, 41(3), 515-532.

PANDAS and the gut microbiome

“PANDAS” is the acronym for pediatric autoimmune neuropsychiatric disorders associated with streptococcal infections. 

It refers to a form of obsessive-compulsive disorder with symptoms such as tics, frequent urination, and rigid or repetitive behaviors caused by a streptococcal infection. These behaviors may increase sleep disturbances and mood disorders in children. 

A new study shows that streptococcal infections modify the composition of the gut microbiome by favoring the growth of certain bacterial species. This, in turn, promotes inflammation in PANDAS patients. 

In the study, scientists analyzed the gut of 30 PANDAS patients and compared them with 70 healthy individuals. They found that, regardless of age, the PANDAS patients had a less diverse gut flora compared to healthy individuals.

Moreover, younger PANDAS patients showed a decrease in short-chain fatty acids, D-alanine, tyrosine and dopamine pathways involved in some neuronal functions. These patients also had a lack of anti-inflammatory elements like unsaturated fatty acids and dioxin degradation. 

Conversely, the healthy individuals had increased D-alanine metabolism and higher concentrations of Roseburia bacteria which help preserve the gut function. These bacteria promote the production of butyrate, a type of fatty acid that helps the gut function effectively. 

More research is needed to better understand the role of the gut’s microbes to assess the disease and how to adapt treatment to the patient’s needs. 

Journal Reference: Quagliariello, Andrea, et al. “Gut Microbiota Profiling and Gut–Brain Crosstalk in Children Affected by Pediatric Acute-Onset Neuropsychiatric Syndrome and Pediatric Autoimmune Neuropsychiatric Disorders Associated With Streptococcal Infections.” Frontiers in microbiology 9 (2018): 675.

Julie Matthews is a Certified Nutrition Consultant and Educator, globally respected nutrition expert, published researcher, and accomplished author. Her guidance is backed by over twenty years of clinical experience and scientific research with complex neurological and physiological needs; particularly autism, ADHD, and related disorders. Julie is the award winning author of Nourishing Hope for Autism and also the founder of BioIndividualNutrition.com. Download her free guide, 12 Nutrition Steps to Better Health, Learning, and Behavior.


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