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The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes’ characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses.
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- Centrifuge-download -o taxonomy taxonomy centrifuge-download -o library -m -d 'archaea,bacteria,viral' refseq seqid2taxid.map. To build the index, first concatenate all downloaded sequences into a single file, and then run centrifuge-build.
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Publications and Research
Title
Authors
Document Type
Article
Publication Date
1-5-2018
Archaea Terata Mac Os Download
Abstract
The Microbe Directory is a collective research effort to profile and annotate more than 7,500 unique microbial species from the MetaPhlAn2 database that includes bacteria, archaea, viruses, fungi, and protozoa. By collecting and summarizing data on various microbes’ characteristics, the project comprises a database that can be used downstream of large-scale metagenomic taxonomic analyses, allowing one to interpret and explore their taxonomic classifications to have a deeper understanding of the microbial ecosystem they are studying. Such characteristics include, but are not limited to: optimal pH, optimal temperature, Gram stain, biofilm-formation, spore-formation, antimicrobial resistance, and COGEM class risk rating. The database has been manually curated by trained student-researchers from Weill Cornell Medicine and CUNY—Hunter College, and its analysis remains an ongoing effort with open-source capabilities so others can contribute. Available in SQL, JSON, and CSV (i.e. Excel) formats, the Microbe Directory can be queried for the aforementioned parameters by a microorganism’s taxonomy. In addition to the raw database, The Microbe Directory has an online counterpart ( https://microbe.directory/) that provides a user-friendly interface for storage, retrieval, and analysis into which other microbial database projects could be incorporated. The Microbe Directory was primarily designed to serve as a resource for researchers conducting metagenomic analyses, but its online web interface should also prove useful to any individual who wishes to learn more about any particular microbe.
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Biochemistry, Biophysics, and Structural Biology Commons, Cell and Developmental Biology Commons
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Biology Posters
Title
Authors
Document Type
Poster
Publication Date
2016
Abstract
Natural gas (methane) is emerging as a viable power source for many industrial, commercial, and domestic applications. Bio-methane provides a promising replacement for mined natural gas. Methanogenic bacteria produce this bio-methane. These anaerobic bacteria pertain to the Domain Archaea, and are found in extreme environments where few other bacteria survive. They are employed by Up-Flow Anaerobic Sludge Blanket (UASB) reactors in the digestion of wastes to a marketable product (methane). The genome of methanogenic bacteria can be amplified using polymerase chain reaction (PCR), a synthetic DNA replication system. This system employs specific sequences of DNA called primers. The primers employed in this study focused on 16S rRNA amplification providing a fingerprint of the organism’s identity. Previous design of these primers was unsuccessful and resulted in non-specific binding.
Recommended Citation
Walters, Andrew; Doloman, Anna; and Miller, Charles, 'Development of Archaeal and Algalytic Bacteria Detection Systems' (2016). Biology Posters. Paper 27.
https://digitalcommons.usu.edu/biology_posters/27
Included in
To view the content in your browser, please download Adobe Reader or, alternately,
you may Download the file to your hard drive.
NOTE: The latest versions of Adobe Reader do not support viewing PDF files within Firefox on Mac OS and if you are using a modern (Intel) Mac, there is no official plugin for viewing PDF files within the browser window.