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ABSTRACT: The lung microbiome- microbial dysbiosis in the infant lung 

       Microbial dysbiosis has been noted extensively in the lungs during allergic asthma. I hypothesized that the microbiota from the lungs of allergy-predisposed mouse pups predisposes pups to development of allergy. Mouse pups were predisposed to allergy by inducing allergy in the mothers. Microbiome was separated from the bronchoalveolar lavage (BAL) of pups of allergic and non-allergic mothers and transferred intranasally at 4 days of age. 16S rRNA sequencing was performed to quantify and classify the lung microbiota. Pups born to allergic mothers had elevated abundance of several genera of the Gamma-Proteobacteria, Firmicutes, and Verrucomicrobia (p<0.05). Pups born to allergic mothers had decreased abundance of genera from Bacteroides, Firmicutes, and alpha-Proteobacteria (p<0.05). Subsequent to lung microbiota transfers, it was found that pups with microbiota from pups born to allergic mothers had an increased susceptibility to allergic inflammation. Therefore, the lung microbiota from pups born to allergic mothers enhances neonate responsiveness to allergen.



       Humans have evolved over the years to have an intimate relationship with microorganisms. Bacteria are sometimes pathogenic, causing a multitude of diseases like strep throat, diphtheria, or black plague to name a few. Other bacteria are innocuous and benefit from us by having a warm place to live and plenty of food around. Many other bacteria are beneficial to us, containing metabolic enzymes that we do not possess that can produce essential metabolites that we could not produce otherwise. The microbiota consists of all the bacterial, fungal, and protozoal organisms that live in and on an individual. The microbiota that lives in and on a human is highly diverse, consisting about 10,000 species of bacteria. The microbiota also varies from individual to individual based on factors like lifestyle, genetics, diet, medicines, and environment. Microbes have been found living under normal, healthy conditions all over the skin and on every mucosal surface from the digestive tract to the respiratory tract to the urinary tract.

        I first became interested in the microbiome when I was an undergraduate. I was interested in microbiology, and my last year of college, I took a course called Microbial Ecology as an elective. Having taken General Microbiology, I was fascinated by all the different niches that the microbes can occupy and was eager to learn more. In Microbial Ecology, I grew fascinated more so by all the interactions the microbes make between individuals of the same species and of different species. I began to think of microbiology in an ecological sense. In a microbiome, there exist predator-prey interactions, organism-environment interactions, and organism-disease interactions (bacteria have viruses too). The techniques used to study the microbiome are different from the techniques used in classical microbiology. For over 100 years, microbiologists have isolated and cultured individual bacterial species in order to identify their properties like metabolism, biochemistry, and pathogenic mechanisms. The more recent technological advent of high throughput sequencing has allowed us to quantify and assess entire microbial communities without culturing them. When you integrate this technology with what is known about metabolic pathways and human disease, undiscovered avenues unfold, which is why studying the microbiome is so exciting to me.

       The main disease I study is allergic asthma. Allergic asthma is especially burdensome in children, and I am interested in the mechanisms that drive allergy development early in life. Clear links have been drawn between some bacterial and fungal species inhabiting the lungs and asthma in children. Early in life, colonization with bacteria like Hemophilus influenzae 1 and Streptococcus pneumoniae 2 can predict future development of asthma.

       My current research is focused on the role of the lung microbiome in regulating the development of allergy and the role of the immune system in regulating the microbiome. I study these effects in newborn mice because mice model an interesting phenomenon seen in humans: that offspring born to allergic mothers are predisposed to developing allergies themselves. Others in our group have made interesting and important discoveries using this model. For instance, when mothers are supplemented with the dietary Vitamin E isoform, alpha tocopherol, during pregnancy, allergy predisposition in their offspring is blocked. We found that microbial dysbiosis is present even before the mouse pups are subjected to allergen sensitization and challenge. When the microbiota was transferred from allergy-predisposed mouse pups to non-allergy predisposed pups, the recipient pups became susceptible to allergen hypersensitivity, and alpha tocopherol blocked this effect. All these details can be found in our recently published paper linked below.


1. De Schutter I, Dreesman A, Soetens O, De Waele M, Crokaert F, Verhaegen J, Piérard D,
Malfroot A. In young children, persistent wheezing is associated with bronchial bacterial
infection: a retrospective analysis. BMC Pediatr. 2012 Jun 22;12:83. doi: 10.1186/1471-2431-
12-83. PMID: 22726254; PMCID: PMC3420249.


2. Teo SM, Mok D, Pham K, Kusel M, Serralha M, Troy N, Holt BJ, Hales BJ, Walker ML,
Hollams E, Bochkov YA, Grindle K, Johnston SL, Gern JE, Sly PD, Holt PG, Holt KE, Inouye
M. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection
and risk of asthma development. Cell Host Microbe. 2015 May 13;17(5):704-15. doi:
10.1016/j.chom.2015.03.008. Epub 2015 Apr 9. PMID: 25865368; PMCID: PMC4433433.

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