As a part of our microbiome interview series, we spoke with Dr. Tasha Santiago-Rodriguez, Scientist and Team Leader Microbiome at the Institute for Life Science Entrepreneurship (ILSE), in New Jersey. Dr. Santiago-Rodriguez received her Ph.D. from the University of Puerto, Rio Piedras. Later, she did her postdoctoral research at University of California, San Diego and California Polytechnic State University. Her research interests include modern and ancient human microbiomes, viromes and resistomes in association with health and disease. We interviewed Dr. Santiago-Rodriguez to discuss her current research and future plans.

 

What is your background and how did you become interested in science?

 

I was the first one of my family to have access to higher education and the only one so far to become a scientist. The importance of education was ingrained in me by my mom, and my grandmother from an early age, although my mom was pursuing a career in nursing while I was completing my Ph.D., and my grandmother did not have access to high school education. I have always been interested in science and mathematics since elementary school. When I was in high school I was fascinated with microorganisms after watching a documentary about how microorganisms pretty much affect health. This fascination brought me to pursue a Ph.D. in Biology with emphasis in Public Health Water Microbiology.

 

Can you provide a summary of your project?

 

I am currently working on the development of synthetic and uniquely-tagged bacterial cells as spike-in standards that can be used in microbiome research. Microbiome research is in the need of spike-in controls that could help have reproducible results across laboratories. The reason is that biases can be introduced at different stages of microbiome research: from sample collection and storage, to the DNA extraction kit used, library preparation, sequencing platform and data analysis.

 

Are you working on any other new projects in the field of microbiome research? If so can you tell us a little about these?

 

I am also working in the characterization of the microbiome and resistome of ancient human samples including mineralized dental plaque from extinct indigenous cultures from Puerto Rico, and mummified gut remains from the Incas (South America), and Nobility (Europe).

 

Results from the mineralized dental plaque is providing further insights of oral health and disease, as well as potential dietary habits, of extinct cultures in the Caribbean.

 

Characterization of mummified gut remains from South America and Europe is providing information about the microbial ecology during the process of mummification of the human gut. Results are also providing support of archeological information of ancient dietary habits and how these may have affected the human gut microbiome throughout part of human history.

 

Can you describe a typical day for you in the lab?

 

A typical day in the lab consists mainly of supervising the work of the microbiome team at the institute. But I also have some hands-on work in some of the technical aspects of constructing uniquely-tagged bacterial cells, DNA extraction, library preparation, sequencing and microbiome data analysis.

 

What do you find most interesting about your project? What is the most interesting or surprising result you have found?

 

There have been several of them. Before starting the project of developing microbiome spike-in standards, I did not realize the need to develop tools that could enable scientists to have reproducible results across different laboratories.

 

I also had very surprising results with the study of the ancient oral and gut microbiomes and resistomes. Although it is very challenging to authenticate and convince the scientific community that what we are working with is authentic ancient microbial DNA, getting information of a potential microbiome associated with the process of mummification of the human gut is extremely interesting. It is also very interesting to challenge the current dogma when you show that sequences similar to modern antibiotic-resistance sequences have been present in the human gut prior the antibiotic therapy era.

 

What are the important benefits of your research to science/human or animal health?

 

Standardizing microbiome research is essential for reproducibility and to move microbiome research towards a translational stage. This translational stage will enable scientists develop drugs that could target specific members of the microbiome that could be directly correlated with specific diseases.

 

In terms of the ancient oral and gut microbiome and resistomes, the information is essential to understand how modern microbiomes, as well as diseases have evolved. Information can be used to potentially predict the evolution of the human microbiome and antibiotic resistance.

 

What are your hobbies?

 

I am usually working, but I enjoy traveling to different cities and countries. I also enjoy art, music and trying new food.

 

What are the major challenges you face in your research with regards to sample collection, nucleic acid isolation and data analysis?

 

These are probably the most challenging aspects of microbiome research. In terms of sample collection, we collect them in appropriate sterile containers and freeze them immediately at –20ºC or –80ºC, if they are not to be processed immediately. The challenge becomes in knowing if how the samples are being handle[d] affects the resulting microbiome.

 

Nucleic acid isolation is extremely challenging. In my experience, when testing different extraction kits, I noticed how they provide different extraction recovery and efficiency. When performing further diversity and taxonomy analyses, the differences are noticeable between kits. For stool samples, for example, we have noticed that the QIAGEN products provide a better yield of a sample being spiked with our uniquely-tagged bacterial cells.

 

Which MO BIO or QIAGEN products do you use/have you used in the past and what did you like about the products?

 

I have used QIAGEN products since I was a postdoc and I always recommend them for any project. One of my favorites are the QIAamp Stool Kits, which provide good DNA yields. Also, the process is not really as time consuming as when using other kits. I am also a fan of CLC Genomics Workbench and CLC Main Workbench, which I used with other bioinformatic tools.

 

This interview was facilitated and conducted by Dr. Vishwadeepak Tripathi.