Assessing the Link Between the Microbiome and COVID-19 Requires Multiple Partners


The news regarding potential therapeutic options for COVID-19 patients is dominated by vaccines, monoclonal antibodies and other similar treatments. As the understanding about the novel coronavirus continues to unfold, some researchers are honing in on the microbiome and its role in the disease.

Since the global pandemic began earlier this year, researchers at the U.C. San Diego Center for Microbiome Innovation (CMI) have been striving to better understand how the human microbiome is involved in the development and severity of COVID-19. Researchers have since been evaluating samples from patients worldwide to find biological and epidemiological discoveries about the SARS-CoV-2 virus.

Although COVID-19 primarily presents itself as a respiratory disease, a number of associations have been discovered between the microbiomes and a number of diseases. Yoshiki Vázquez-Baeza, CMI’s Associate Director of Bioinformatics Integration, told BioSpace in an interview that a number of deaths associated with COVID-19, particularly in hospital settings, are related to bacterial infections that occur simultaneously. There is an interconnection between those viral pathogens and the microbiome, he said.

Vázquez-Baeza said the CMI researchers began working on a project that characterizes the longitudinal progression of COVID-19 in patients staying at a local hospital. It’s from that research that they have been able to capture the microbiome and viral information of these patients. The research undertaken by CMI is still preliminary, Vázquez-Baeza said, but noted they are seeing a relationship in the microbiome of COVID-19 patients, regardless of whether or not they are symptomatic or asymptomatic. While it’s early to predict where the research could take the team, Vázquez-Baeza said based on other studies, certain microbiomes could increase the availability and efficacy of some drugs to treat the disease.

Because they are working with the microbiome, which is a multitude of organisms, the research requires significant computational power. For CMI, that research could not be conducted without a key partner – Sunnyvale, Calif.-based Panasas, a data storage company. Vázquez-Baeza said CMI’s research project is amassing massive amounts of data, which requires significant storage and computational power. The storage capabilities provided by Panasas are vital to the ongoing research and analysis required for this kind of research, he noted. CMI and Panasas have been working together since 2015, but with the COVID-19-related research being conducted by the team, CMI was required to secure more data storage.

Research is rarely linear, so rarely do you have the information in the exact order. This leads to a lot more space being required,” Vázquez-Baeza said.

“If we have to limit the benchmark methods because of storage concerns, we wouldn’t be able to explore the full breadth of scientific options. Panasas technology supports the mission of the center because it never limits our exploration.”

Vázquez-Baeza described the amount of data storage and computing power as a massive spreadsheet with thousands of columns and thousands of rows. Each of those columns and rows have different biological properties and samples that all have unique meta-data descriptions. The text files used are immense, he added, usually amounting to about a couple of hundred gigabytes each, which means it requires a massive amount of storage.

Adam Marko, Director of Research Solutions for Life Sciences at Panasas, concurred with Vázquez-Baeza’s descriptions. He explained that the data needed by life sciences organizations like CMI are vast. Marko said globally the genomics data generated is 2.5 times that of the data that YouTube uses across its platform.

CMI director Rob Knight, who is also a UC San Diego professor of pediatrics, computer science and bioengineering, said the storage capacities offered by Panasas are incredibly valuable as we evaluate critical RNA data to better understand the SARS-CoV-2 virus and how the human microbiome may be involved in COVID-19 susceptibility and severity.

While CMI’s research has been in the early stages, Vázquez-Baeza predicted that some actionable data could be available for use by the end of the year. The team is conducting analysis of data taken from a sample collection from the COVID-related hospital healthcare workers and patients. Once they run assays that quantify the viral loads of about 1,000 different samples, the CMI team will analyze the data and prepare for some publication.

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