Connecting the Microbial Ecosystem

The Microbiome – A Growing Field Within Research and Development

An emerging field of research across multiple industries is the study of the microbiome. Understanding the components of the microbiome, such as bacteria, viruses, and fungi, impacts food production, animal health, environmental restoration and, perhaps most importantly, human health. We now understand that the human microbiome plays a role in gene expression. The upregulation or deregulation of those genes is vital in determining health outcomes, which is why the National Institute of Health has created the Human Microbiome Project to enable “comprehensive characterization of the human microbiota and their metabolic capabilities and analysis of their role in human health and disease.”[1] Biopharmaceutical companies are also developing targeted treatments for microbiome-associated diseases.

While the entire human genome contains ~22,000 genes[2], the Meta-HIT Consortium has reported a gene catalog of 3.3 million non-redundant genes in the human gut microbiome[3]! The diversity in the microbiome between two individuals is immense compared to genomic variation, creating a promising future for the use of personalized medicine in this area. Researchers in this field commonly use techniques such as cell culture, flow cytometry, mass spectrometry, qPCR, and next-generation sequencing.

Utilizing New Technologies and Software to Support Microbiome Research

Unique to microbiome research, is the vast amount of data that is produced when identifying a potential target of interest. To identify and isolate a target, researchers must perform many different assays, including running multiple next-generation sequencing runs. The use of high-throughput sequencing machines, such as the Ion GeneStudio S5™, has revolutionized the rate at which microbiome research can be performed. The use of these sequencers combined with the variety of assays performed has resulted in a new obstacle for microbiome researchers – enormous amounts of data.

The microbiome community is now challenged with tracking, managing, and storing data of such a large magnitude. In 2015, the United States government created a cross-industry committee comprised of sixteen federal agencies including the NIH who were focused on the study of the microbiome[4]. In April 2018, they published their Interagency Strategic Plan for Microbiome Research. The committee identified three different ways that microbiome research could be transformed. One of these recommendations highlighted the need for “Developing platform technologies to generate critical insights and to improve access to and sharing of microbiome data across ecosystems.[5]

Thermo Fisher™ Platform for Science™ software provides a solution specific to the microbiome that assists scientists in managing and maintaining their data sets. Platform for Science software works alongside lab processes, capturing and tracking all data generated, such as study protocols, media components, gel electrophoresis results, or sequence information. The ability to quickly generate a report on analyses run or study progress streamlines the preparation process for scientific review meetings, or filing for submissions such as an IND.

Managing Animal and Patient Demographics

Microbiome research relies on the donation of biological specimens by humans and by conducting animal studies. To comply with industry best practices and regulatory guidance documents, scientists in this field must know what analyses have been performed on a specimen and its exact location at any point in time. Platform for Science software securely tracks subjects, blinds patient information, and associates clinical samples with its derivatives. It is also able to support the animal value chain from IACUC protocol to routine measurements including observations made such as animal health.

A Platform Solution that Can Scale with Your Business

Platform for Science software is built on a cloud-native infrastructure that can easily scale as your business grows. The Platform for Science Marketplace provides its users the opportunity to quickly add new pieces of functionality to their workflow as the need is identified, such as the animal PK study or preclinical study management applications.

If you are interested in learning more about how Platform for Science software can support your research organization, visit the Microbiome Solution page.


[1] “Human Microbiome Project – Home.” National Institutes of Health, U.S. Department of Health and Human Services, 23 Apr. 2018,

[2] Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65

[3] Consortium IHGS. Finishing the euchromatic sequence of the human genome. Nature. 2004;431:931–945.

[4]“Human Microbiome Project – Microbiome Project Program Highlights.” National Institutes of Health, U.S. Department of Health and Human Services, 23 Apr. 2018,

[5] Microbiome Interagency Working Group, Interagency Strategic Plan for Microbiome Research FY 2018-2022; 2018; 4-5