Wednesday, 29 August 2018 13:18

Microbiology Resource of the Month: ZetaHunter

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Published in mBiosphere

The scope of the ASM Journal Genome Announcements has been expanded in a big way to create Microbiology Resource Announcements. The new journal publishes all resources that may be valuable to researchers in the microbial sciences.

Each month, we’ll highlight a new Microbiology Resource and how it will help researchers with their scientific endeavors.

 

 

Why Microbiology Resource Announcements? 

“Scientific research has benefited from the resources developed and shared between scientists — from software published on Github to plasmids made available on Addgene. These resources facilitate our work and allow researchers to build on and extend the work of others. Indeed, some of the most impactful papers have been those describing resources — the E. coli Keio Knockout Collection manuscript, for example, has been cited nearly 5,000 times.”

“Many resources are worth sharing. We hope your next submission will spur someone else’s work or, potentially, inspire collaboration in our community.” – Microbiology Resource Announcements Editor-in-Chief Irene Newton

 

Month: August 2018

 

TEM micrograph of ZetaproteobacteriaZetaproteobacterium Mariprofundus ferrooxydans cell (light grey bean) with Fe-oxyhydroxide mineralized twisted stalk. Molecular studies of Zetaproteobacteria will be aided by the ZetaHunter software. Source.

Announcement: ZetaHunter, a Reproducible Taxonomic Classification Tool for Tracking the Ecology of the Zetaproteobacteria and Other Poorly Resolved Taxa

 

Resource: ZetaHunter software

 

What is ZetaHunter? Software that assigns 16S rRNA gene sequences from bacterial groups with poor taxonomic resolution into previously described operational taxonomic units (OTUs). 

 

Why is ZetaHunter the MRA of the month? The software can be applied to any curated database. The publication used Zetaproteobacteria based on the authors’ research interests, but any group can use the software with a database of their bacterium of interest.

 

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Clara Chan and Sean McAllisterSean McAllister and Clara Chan on their way to the Loihi Seamount to hunt for Zetas. Photo courtesy C. Chan.

MRA first author Sean McAllister and senior author Clara Chan provided insight to the application of ZetaHunter in their own studies and those of others. 

 

How will you use ZetaHunter for your research?

Chan: Zetaproteobacteria are a class of organisms known as autotrophic iron-oxidizers. We use ZetaHunter to identify the Zetaproteobacteria, either new isolates or in environmental samples, to see if they are novel or ones we have seen before. Zetaproteobacteria are common in iron-rich marine systems, from near-shore waters and sediments to deep-sea systems mats, and we want to know who is who in order to understand their ecology and biogeochemical contributions.

 

How will ZetaHunter improve on currently available software for zetaproteobacteria studies?

McAllister: Currently, online databases can only identify these microbes as "Zetaproteobacteria.” There are nearly 60 identified Zetaproteobacteria OTUs, based on a 97% similarity. Therefore, the current low-resolution classification hinders understanding of Zetaproteobacteria ecology and what it might mean to find different OTUs in different habitats.

This question is not limited to the Zetaproteobacteria, which is why we designed ZetaHunter to work with any database where researchers want to curate a more highly resolved taxonomy.

 

Who will benefit from using ZetaHunter?  

Chan: ZetaHunter will aid researchers studying microbial contributions to marine iron oxidation, but also anyone who studies taxa that lack a classification system.

McAllister: This software can also help researchers who study other poorly resolved microbial taxa. For instance, we give an example for candidate phylum OP3 (Omnitrophica) in the online documentation. 

 

How have you or others used the software for research studies? 

McAllister: In our recent study of the stratified water column at the Chesapeake bay, we used ZetaHunter to robustly identify the Zetaproteobacteria species involved in iron cycling at the oxic-anoxic transition zone.

Our collaborators have also used ZetaHunter for large-scale studies at Lō’ihi Seamount. In Scott et al. (2017), scientists identified specific high-resolution ecotypes that were found in different iron mat types and anchor those ecotypes to a known taxonomy using ZetaHunter. In Fullerton et al. (2017), we used ZetaHunter to link genomes to their taxonomy, in the first high-resolution attempt at determining what the Zetaproteobacteria are capable of in the environment. 

 

Last modified on Friday, 07 September 2018 17:28
Julie Wolf

Julie Wolf is the ASM Science Communications Specialist. She contributes to the ASM social media and blog network and hosts the Meet the Microbiologist podcast. She also runs workshops at ASM conferences to help scientists improve their own communication skills. Follow Julie on Twitter for more ASM and microbiology highlights at @JulieMarieWolf.

Julie earned her Ph.D. from the University of Minnesota, focusing on medical mycology and infectious disease. Outside of her work at ASM, she maintains a strong commitment to scientific education and teaches molecular biology at the community biolab, Genspace. She lives in beautiful New York City.

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