Portrait of author

Shashank Gupta:
The human microbiome: one step forward

Date: 28-11-2020    Supervisor: Søren J. Sørensen

Human microbiome is an essential part of the human body. Increasing evidence shows that the composition of the airway and gut microbiome has an important role in human health. Microbiome research is still in its infancy, but with modern technology, it's possible to sequence the DNA of entire microbial communities and study the thousands of genes and proteins that microbiome contains. Studies suggest that environmental factors dominate the genetic factor in shaping the human microbiome, however lack of knowledge about which environmental factors influence the indoor microbiome with which humans have extended daily exposure.

In the first manuscript of this thesis, I compared the microbiome obtained using both the traditional culturing method and next-generation sequencing (16S rRNA gene sequencing). I have discussed both pros and cons of each method for the identification and classification of microbes and further discussed their application in the clinical settings. The manuscript concludes that sequencing provides a wider picture in identifying microbial communities and is almost ready for clinical use. However, further development of a standardized and automated pipeline is required before sequencing can be implemented.

In the second manuscript of this thesis, I explored the influence of environmental exposures on dust samples from children’s beds (age 6 months) together with airway samples (age 3 months). I further explore the relationship between bed dust microbiome and the developing infant airway microbiome. This study observed that the diversity of bacteria and fungi correlated in the bed dust, suggesting an interplay between the two types of organisms in the bed dust. Bacterial and fungal microbial communities in the bed dust were influenced by multiple environmental factors, however, we did not find any strong evidence of transfer of microbiome from bed dust to infant airways. But given an infant’s constant exposure to the indoor environment, infants may still interact in ways that affect their health.

In the last manuscript of the thesis, we have done shotgun sequencing of 662 infant’s gut samples to get a deeper understanding of the gut microbiome in early life. We have reconstructed over 13000 MAGs and calculated their growth dynamics.

This thesis focuses on the human microbiome and how environmental variables influence the indoor microbiome. The analyzed data is culturing, amplicon sequencing, and whole metagenome sequencing data originated from the COPSAC2010 cohort.

The results presented in this PhD thesis not only strengthened the current knowledge of our microbiome but also an understanding of influencers of microbiome composition.