Here are some ideas that I, perhaps with some overconfidence, think would be useful to share.
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Mitigating methane emission from livestock with ozone-degrading halomethanes. Are we moving too fast or too slow?
Disclaimer: This blog post is a primer intended for scientists and policymakers with an interest in limiting methane emissions from cattle. My qualifications are that I am a microbiologist with expertise in microbial metabolism. I have studied microbial metabolisms, authored a review on the biogeochemistry of chlorine, and obtained my Ph.D. in a laboratory studying……
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Thoughts on Untargeted, Scaleable Isolation of Small Epibiotic Bacteria and Archaea
In late 2016, I was excited. I had observed (Barnum et. al 2018) that a set of simple communities enriched from bay mud contained abundant bacteria from the Candidate Phyla Radiation (CPR) and an abundant archaeum from the DPANN superphylum. CPR and DPANN organisms may form large portions of the tree of life and share……
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Online Datasets for Microbial Comparative Genomics
You are a student researcher and have identified an interesting protein with a fabulous function. You’d like to know what other organisms have this protein, and whether or not they are fabulous as well. However, the only tool you know of (yet) is the NCBI’s BLAST web server. The BLAST web server is very helpful……
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Other Resources for Microbial Comparative Genomics
The following tutorials and documentation will be helpful for researchers considering similar approaches. Using the command line A command line enables you to perform diverse operations programmatically. That is, you can do a lot of things with it, and you can automate the process for easy repetition, alteration, and sharing. You should learn how to……
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How to Search Large Sets of Genomes for Important Genes
Note: This is a tutorial for researchers new to studying large datasets of bacterial and archaeal genomes. It was originally written to specifically access the Uncultivated Bacteria and Archaea (UBA) dataset. Outline Introduction Using HMMs to search a large dataset (Uncultivated Bacteria and Archaea (UBA)) Addenda: Limitations and Alternatives Supporting files on github: https://github.com/tylerbarnum/metagenomics-tutorials Introduction New……
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How to Use Assembly Graphs with Metagenomic Datasets
Note: This is a tutorial to help other microbiologists learn a research method from a recent publication (EDIT: open-access PDF). This method can be applied to de novo genome and metagenome assemblies from short read sequencing data (e.g. Illumina) but is not relevant for assemblies using long read sequencing data (e.g. PacBio). Code In Brief As the below article……
Tyler Barnum 