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Australia's Microba Taps Google Cloud for Human Gut Microbiome Data Processing


NEW YORK (GenomeWeb) – Australian microbiome company Microba has selected Google's cloud infrastructure to handle data and computing needs for its products and research focused on the human gut microbiome.

Microba said the collaboration will combine its scientific knowledge with Google Cloud's analytics and machine learning capabilities with support from artificial intelligence consultancy Max Kelsen. With access to the Google Cloud and BigQuery technology, Microba has the requisite infrastructure to store, process, and share terabytes of genomic datasets using its proprietary bioinformatics solution, called the Metagenomics Analysis Platform.

The company will also use Google's tools to continue building out a reference database of microbial genomes that supports its informatics infrastructure and to support planned products focused on clinical and research use of human microbiome data.

Microba claims to be Australia's first company to offer gut microbiome profiles using metagenomic sequencing. The company spun out of the University of Queensland at the end of 2017 to commercialize intellectual property that its founders had initially developed for analyzing data from environmental microbial communities. They believed that the technology could be applied to human microbiomes and could improve on existing technologies for gut microbial analysis.

"Those existing technologies primarily are cultivation-based approaches for looking at microbial communities or use the 16s ribosomal gene as a fingerprint or marker of the organisms in your gut," Microba Founder Gene Tyson said in an interview. Prior to moving into human microbiome analysis, Tyson and other colleagues used high-throughput sequencing-based approaches to explore the functionality of microbial communities in things like corals and permafrost, but started  optimizing its methodologies and bioinformatic pipelines to more fully explore the human microbiome and its link to disease, health, diet, and exercise, he said.

In February 2018, Microba raised A$7 million (about $5.6 million at the time) as part of a series A fundraising round. The funds allowed the company beef up its informatics research and development and  sales and marketing teams, and push towards the launch of its first product, Microba Insight, which offers microbiome testing directly to consumers and provides information on the abundance and functional potential of microorganisms living in the human gut. Customers receive a sampling kit that they use to collect a sample from a used piece of tissue paper and send to Microba, which extracts the DNA, sequences the microbial community, and analyzes the data with its informatics pipelines.

"What we see these kits doing is giving people the right level of information about their gut microbiomes the first time," Tyson said. "We explore the microbiome with a level of detail that you don't get from other approaches." Customers receive an online report that includes an overview of what lives in their gut, how it compares to a healthy cohort, and the microbiome's ability to produce important metabolites such as short-chain fatty acids. They can also access a more detailed report that provides in-depth information such as  associated diseases. This report groups organisms by species and abundance, highlights important species, and provides information about how the customer's diet compares to standard dietary recommendations and the digestion potential of their microbiome.

The company also gathers metadata from customers around their health including data on sleep quality; medications they may be taking including antibiotics, antifungals, and immune suppressants; sleep patterns; diet; and lifestyle. They also collect demographic and health information including recent health conditions. Some of this information is used to design personalized dietary plans and food recommendations that the company says may boost the growth of beneficial organisms in their guts.

Microba began offering Insight last July. The company is using Google cloud to analyze customer data for the reports that it provides as part of the product. It currently takes about two days to complete Microba's analysis process. "Part of our speedy turnaround is the ability to fire up as many systems as needed to process our data as quickly as possible [and in a] really cost-effective and scalable way," Tyson said. "We could certainly run our own [hardware] system but the additional overhead of having to do that …  is alleviated by using an established provider like Google."

Microba reviously worked with an unnamed cloud provider but opted to change providers because Google was less expensive. Furthermore, Tyson said, Google was "the most receptive to working with us in and around enhancing our pipelines to be more efficient," he added.

Since Insight launched in 2018, Microba claims to have delivered over 3,000 reports to customers. The average turnaround time is around 17 days, but customers could potentially wait up to four weeks. The bottleneck is waiting for a sufficient number of samples to come in before running the sequencing step. "One of the decisions we made early on was to go with [the] Illumina NovaSeq 6000 and that gives us a lot of flexibility in the number of samples we run at any given time," Tyson said. "[The] smallest number of samples that we would run is 96 and, … we are able to run that at least once a week."

Customers' results are backed by peer-reviewed research on the microbiome and must pass a "rigorous" internal validation process before being included in reports, Tyson said. Furthermore, customers can take advantage of a 15-minute microbiome coach session as part of their service during which they speak with a trained dietician about the dietary recommendations the company makes.

Most of these have been purchased by customers directly, but some have been the result of clinician recommendations as part of patient care. Later this year the company plans to launch a version of Insight specifically for clinical use, Tyson said.

"That will be basically a more tailored Insight product specifically for clinicians with additional validation in and around the robustness of the test," Tyson said. "We are in the process of doing all that validation and comparison to existing technologies so that we can directly compare the results that we are getting through our metagenomics analysis pipeline relative to existing qPCR and PCR-based approaches."

The company also plans to develop an iteration of its product specifically for research use, and has gotten interest from research groups in using its MAP infrastructure for their metagenomic research projects. These projects could be "a data sharing-type agreement … or it can be a process where they own the data outright and we are a service provider," he explained.

Meanwhile, Microba has established what it has dubbed the Future Insights Program, which aims to identify new correlations between the gut microbiome, health, diet, and lifestyle. Under the terms of the program, customers agree to share their anonymized data with the company for research focused on links between the gut microbiomes, disease, health, and so on. Through the initiative, the company hopes to contribute to the development of diagnostics and therapeutics for people suffering gut health issues, intestinal diseases, and other health conditions.

"We are doing this because we believe very strongly that gut microbiome is an important microbial community for human health [and] the only way that we are going to understand all these links is by researching them," Tyson said. As these insights come to light, he anticipates that the current skepticism about giving customers health-related advice based on the microbiome will dissipate. So far, about 75 percent of Microba's customers have agreed to participate in the program, Tyson said.

Microba also plans to develop products focused on other human microbial communities including those from skin, oral, and vaginal sites, Tyson said.