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A Data Note published and currently undergoing peer review on Gates Open Research from the lab of Christoper Mason describes a collective research effort to profile and annotate more than 7,500 microbe species. Two of the article’s authors, Heba Shaaban and David Westfall, describe their work in this guest blog.   

Microbial communities are a fascinating and genetically diverse set of organisms that live with us, in us, and around us. In order to better understand these communities, we created the Microbe Directory. The Microbe Directory is a collective research effort to profile and annotate more than 7,500 of these unique microbial species that include bacteria, archaea, viruses, fungi, and protozoa. Our project comprises of data collected and summarized on various microbes’ characteristics, such as, but not limited to: optimal pH, optimal temperature, Gram-stain, and antimicrobial resistance. This database can be used downstream of large-scale metagenomic taxonomic analyses. These additional data allow researchers to explore their taxonomic classifications at a deeper level, which may help uncover additional insights into the microbial ecosystems they are studying.

Using Microbe Directory to create a bigger picture

For instance, say a researcher collects a sample of her own saliva, extracts DNA from the sample, and processes her findings to discover which 437 microbial species live in her mouth. The Microbe Directory can then be utilized to profile the set of species in terms of their microbiological characteristics. In this hypothetical situation, she may find that 32% of the species are resistant to known antimicrobials, while 85% grow optimally at a pH below 7. This knowledge can very beneficial in gaining a better understanding of her sample overall, but also it can help shape how she wants to take progress further with her research. Before the Microbe Directory, there was no tool that aggregated these data in a form that can be used for computational analysis.

Making science more equitable and accessible

The Microbe Directory was curated by a team of trained undergraduate, graduate, and medical students from City University of New York (CUNY) Hunter College, Macaulay Honors College, and Weill Cornell Medicine, students involved were listed in the Acknowledgements section of our article. The student-researchers were selected from a pool of applicants and underwent a training session that provided clear instructions on how to curate the literature for the parameters for each species. After every entry, students inserted citation links to the sources they utilized for the information they inputted.

One of the main reasons students were recruited to partake in this project was our drive to make science more equitable and accessible. We have many brilliant, budding minds that can really make significant contributions to science if only given the chance. Such a project requires a large workforce to be completed in a timely fashion and provides a great opportunity for young scientists to showcase their skills independently. While there is always the potential for human error in manually curated databases, the Microbe Directory has a feature where anyone can make an account and submit edits and changes to the information hosted in the database if necessary, and we also performed double-curation for subsets of the data to check our annotations.

Microbe Directory as a community resource

We envision the Microbe Directory as being a widely-used platform for metagenomic analyses. The Microbe Directory can also be used by anyone wishing to learn more about a particular species by accessing its online web interface. We hope that individual contributions to the site will one day help refine our understanding of all the microbial communities that are invisible to the naked eye, but have profound ecological, physiological, and chemical effects!

Gates Open Research provides all Gates Foundation-funded researchers with a place to rapidly publish any results they think are worth sharing. All articles benefit from immediate publication, transparent refereeing and the inclusion of all source data. If you are a grantee of the Gates Foundation you can find more information about how to publish on Gates Open Research here.