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Spanish Startup Microomics to Tackle Human Microbiomes, Multiple Markets With Metagenomic Assays

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NEW YORK (GenomeWeb) – Recently receiving seed funding from Spain's Centre for Genomic Regulation (CRG), startup Microomics plans to engage multiple markets by searching different microbiomes for potential pathogens.

The Barcelona-based firm, which spun out from the CRG and Catalan Institute for Research and Advanced Studies (CIRAS) in November, is initially looking at human health, focusing on oral and pulmonary microbiomes. It is also exploring other markets including the food industry, substitution of chemical fertilizers in the environment, livestock farming, and obesity research.

Around four years ago, Microomics Cofounder and CSO Toni Gabaldón was working on a large-scale Spanish study to understand how the adolescent oral microbiome fluctuates depending on dietary and hygiene habits. Collecting over 2,000 oral-rinse samples from high school students across Spain, Gabaldón's team coordinated with the CRG to analyze and review the relative abundance of species in the oral samples.

During the study, Gabaldón's group was approached by multiple clinicians and hospitals that needed help implementing diagnostic techniques in procedures, including the detection of oral implant infections. Overwhelmed by the amount of requests, Gabaldón's team found that they could not devote themselves to both academic research and provide the requested diagnostic services.

Aware of a potential opportunity for a niche company having necessary metagenomic expertise, Gabaldón's team realized it could partner with these firms and clinics to exploit genomics-based methodologies to understand processes involving microorganisms.The group used a proof-of-concept model to win a CRG competition and receive a small amount of funding to work on a business plan, eventually culminating in Microomics.

Partnering with the CRG, Microomics will use the center's core facilities for first year of its operations, and will share any IP on assays that the group develops.

Microomics offers full molecular diagnostic services including study design, sample handling, nucleic acid extraction, sequencing, and computational and statistical analysis. Microomics' researchers then advise customers on how to best use the microbial data to achieve long-term results.

Microomics' clinical services include shotgun metagenomics, transcriptomics (RNAseq), and whole-genome analysis for bacteria and fungi. While the sample type used may depend on the specific test, Microomics' assays can currently use fecal, oral-rinse, bronchoalveolar lavage, and vaginal tissue samples.

According to Gabaldón, Microomics is "developing the assays ourselves, but currently depend on the [CRC's] technology, which runs on the Illumina MiSeq and HiSeq platforms." He noted that the company plans to eventually test some of its assays on other sequencing platforms like Oxford Nanopore's MinIon to address questions that are better suited to different technologies.

While researchers have found links between a person's microbiome and their health issues, doctors have not diagnosed specific diseases based on the microbiome. Gabaldón, however, believes that the human microbiome might have potential for specific diagnostic purposes.

Microomics is initially examining the oral microbiome in its assays, as a person's mouth acts as the entry point for both the digestive and respiratory systems. The firm has also collaborated with dental clinics to study the impact of interventions such as implants, in addition to the appearance of microbiota related to dental and gum disease.

"The oral microbiome is the second most diverse microbiome, yet less explored [than the gut microbiome], and is less understood," Gabaldón explained. "We can act on it very easily, and it is involved in many common diseases that affect a great number of the population."

In addition to the oral microbiome, Microomics' assays examine relationships between the pulmonary microbiome and airway pathologies. Gabaldón's team at CRG has worked on several such projects involving bronchoalveolar lavages samples, and Gabaldón pointed to a review article published recently in Cancer Letters exploring the interplay between the lung microbiome and cancer.

"We want to [learn] about a microbiome that is poorly understood, and [the potential risk] in cancer or immunocompromised patients ... for infection through airways by opportunistic pathogens, such as Aspergillus and Streptococcus," Gabaldón explained.

The costs and turnaround time for Microomics' services vary and depend on sample type, test design, and the type of downstream analysis provided to address the client's goals.

For example, Agostino Carvalho, an assistant researcher at the Life and Health Sciences Research Institute in Braga, Portugal, used Microomics' services to detect the presence and relative abundance of bacterial species in patients with lung diseases. Having previously collaborated on lung cancer studies with Gabaldón, Carvalho and his team sent lung bronchoalveolar lavage samples to Microomics for nucleic acid extraction and 16S sequencing.

"What we learned was how the bacterial species were distributed in patients, in terms of relative abundance," Carvalho explained. "Comparing cases versus controls, we saw there was much less diversity in the cases of infection we were studying."

Carvalho noted that the entire diagnostic process required about five to six weeks and cost about €5,000 ($6,169) to sequence and analyze a total of 70 samples. His group is now working with Microomics to develop bioinformatics methods for the startup's assays.

While Microomics is a young company, Gabaldón believes that it can target multiple markets because the firm's core expertise involves the technology and interpretation of microbial communities. Microomics plans to partner with larger companies that need microbiome analysis expertise in specific industries such the food market, livestock farming, and clinical research.

"We decided not to limit ourselves to a single market, and instead explore as far as we can reach, and are open to different technologies over time," Gabaldón said.

Gabaldón admits that several other companies provide similar metagenomic services. However, he argues that competitors only specialize in either sequencing or bioinformatics analysis. He also emphasizes that most current companies do not specialize in microbiome analyses.

"Often these companies lack the microbiology or statistical expertise to add value to a standard processing analysis, so they are not well suited to customers that do not have that expertise," he argued.

The firm also believes its assays move beyond standard analyses and fit the needs of complex or specific projects, and touts high customization capacity as one of its distinctive features.

Microomics' current investors mostly include its founding members, CRG and ICREA. After receiving an undisclosed amount of seed capital, Microomics began working with customers in Spain, Portugal, and Mexico in order to produce metagenomic results. Gabaldón said the company is also currently negotiating agreements with various international companies. The firm also plans to eventually expand into other parts of Europe and the US market.

The firm does have plans for follow-on financing, and is open to hearing investor proposals. In addition, the company is applying for grants to develop additional technologies and fund research.

Within the next couple of years, Microomics plans to detach from the CRG and establish its own labs, eventually increasing its services and customer base. Gabaldón aims to funnel research into examining the skin microbiome, as many skin diseases and conditions like allergies are caused by changes in skin microbiome composition.

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