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The Microbe Directory

Guidelines
Guidelines

GUIDELINES FOR DATA QUERY

What is The Microbe Directory?

The Microbe Directory (TMD) is a database aimed to annotate microbial species with their most important characteristics. The Microbe Directory was first developed in 2016 (Shaaban et. al, 2018) as a collective effort to fill the gap of reliable microbial information available.

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The Microbe Directory: An annotated, searchable inventory of microbes’ characteristics⁠

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We want to make TMD the ultimate microbial database. Our goal is to have ecological and phenotypical data available for every microbial species. TMD is now composed of about 69,000 microbial species and aims to become the most used microbial database worldwide. This is why volunteers are so important. Without their help it would be even much more difficult to compile such big amounts of data.

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The Microbe Directory v2.0: An Expanded Database of Ecological and Phenotypical Features of Microbes⁠

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What will be my tasks as a volunteer?

The volunteer task is to search microbial data on books, articles and webpages. The list of microbes to annotate will be sent by email every Monday. All annotations will be compute into the KoboToolbox interface, in which each volunteer will have their own username and password. You must submit data through your personal credentials. Once you have submitted your data no further actions are required until your next weekly task.

Where is the KoboToolbox?

You can access to KoboToolbox though the following link:

KoBoToolbox ⁠

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Your username and password will be sent by email once you enroll as a volunteer.

Please see

KoboToolbox Instructions⁠

to learn how to submit your annotations.

Important notes when searching

Not all sources of microbial information have been scientifically corroborated. Avoid using links of unidentified sources. It is common that scientific articles focus on either a specific specie or a group of microorganisms. It is OK to select unknown if you have searched for a while and have not found any information about that specific microorganism. It is always better to select unknown than to annotate wrong data.

The average search time per species can range from 10-30 minutes. Some species might take less time, depending on the data availability. It is common that more information is available for microbes that are relevant for research, human health/disease, biotechnology or economic use. If after a thoughtful search you have not found any information about a specific microbe, select Unknown option. If you find that the specific feature you are trying to answer does not apply for that microbe, select N/A.

Example:

If you found that given microbe does not produce biofilm, you should select No.

If you cannot find whether a given microbe produces biofilm or not, you should select Unknown.

If you found that certain characteristic does not apply to your group of organisms, such as biofilms in virus, you should select N/A.

If your microbe was is unclassified to species level (i.e. unidentified proteobacterium or - unidentified marine eubacterium ) you select N/A

Where to look?

Here we provide some useful books and links. You are free to get information from other sources such as scientific articles, academic books, other microbial databases. You can find this information in

Useful Links⁠

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Table from Useful_Links.xlsx file

Additionally, books are available for microbial species on Dropbox in the following link

The Microbe Directory Resources⁠

. These books are useful to find information about general and specific information about microbial characteristics.

Names of the species

Sometimes you will find the microbe that you are querying has a combination of letters and/or numbers following the species designation (i.e. Abiotrophia defectiva DA5), see figure below. This means that the species has a corresponding strain. A strain is a genetic variant of the microorganism. Since there could be hundreds of strains from the same species, for this project we will be considering any strain information as part of the species.

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Screen Shot 2020-03-05 at 11.25.26 AM.png

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Multiple strains from the same species example

Unidentified or Unclassified Species

Some of the microbes on your weekly tasks might not be taxonomically classified, meaning that when they were analyzed, the taxonomy (or species name) could not be assigned. If your microbes of your weekly tasks are named Unidentified phage/bacterium or Lucinoma aequizonata gill symbiont you will annotate NA to your answers.

Verify your species taxonomy

If you are unsure about the taxonomy of your species, it is recommend it to look on the NCBI taxonomy

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`Home - Taxonomy - NCBI`⁠
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Here you may find the available taxonomy, synonyms, genome availability and some related articles.

Synonym Species

When a microbes are reclassified due to new findings or new technologies, researchers can change the species name based on the new classification. You could use information of the synonym since this is referring to the same species.

For example, Kondoa yuccicola is a fungi that was first described as Sporobolomyces yuccicola by Nakase & M. Suzuki in 1988. Later, it was assigned into a different genus and the species name changed to Bensingtonia yuccicola. Finally, in 2015 it was reclassified again and the genus changed to Kondoa yuccicola. Then, you can annotate information from articles naming any of the synonyms of your assigned species as long as it is not contradicting between synonyms.

http://www.mycobank.org/MB/813091⁠

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Cannot find species information. What to do?

If you have search for a while and you still do not find information about your microbial species. You can annotate data for the genus if available and select Unknown for the missing data. Only annotate data that applies to the genus in general (all the species within the genus share the same characteristic).

Annotating at Genus level

If your microbe is classified to genus level or there is no information for the specific microbial species, you can annotate characteristics that apply to all member of the genus. However, when certain characteristics are specific to the members of the species level, you should annotate NA.

For example, if your assigned microbe is Streptococcus sp., a genus of gram-positive coccus. When annotating gram-stain, you could select “gram-stain positive”. However, when annotating if the microbe is pathogenic, you should annotate NA since there are multiple species on the genus that are and are not pathogenic. You should always base your answers on the available references.

What is the difference between micro and macro (algae/fungi)?

Macro and Microfungi belong to the same taxonomic groups (Basidiomycota or Ascomycota). However, microfungi are distinguished from macrofungi only by the absence of a large, multicellular fruiting body. Macrofungi are large types of fungi that we can see at Naked-eye or without the help of a microscope. Macrofungi include mushrooms, puffballs, hoofed fungi, coral fungi. Microfungi are composed of organisms such as molds, mildews and rusts.

Similar to Fungi, Algae can be also group as macro and microalgae. The key difference between macroalgae and microalgae is that macroalgae are large and multicellular aquatic photosynthetic plant-like organisms while microalgae are small and unicellular aquatic photosynthetic microbes.

How to cite the information

In the KoboToolbox you should write citation for all the microbial information you query from any source such as webpage, article, or book.

Use zoterobib in the following link to generate references and paste citations into the KoboToolbox.

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ZoteroBib⁠

. Zoterobib works with DOI or links from the journals website. Note that it does not work with direct PDF links.

Example, the following links correspond to the same article. The

first link⁠

corresponds to the article link from the journal, while the

second link⁠

corresponds to the PDF link. Only the first link will work.

After using the zoterobib, your citations should look like this:

Kimkes, Tom E. P., and Matthias Heinemann. “How Bacteria Recognise and Respond to Surface Contact.” FEMS Microbiology Reviews, vol. 44, no. 1, Jan. 2020, pp. 106–22. academic.oup.com, doi:10.1093/femsre/fuz029.

Copy your citations into the KoboToolbox reference empty box.

How many microbes do I have to query?

Ten microbial species will be given to you each week. Not less. Not more.

What to do when I finish my weekly task.

As soon as you finish your weekly task you are all set. You will receive new microbes the following week.

Where will I get the species list for my next task.

You will next your next 10 microbial species through the email you provided.

What to do if I do not wish to continue volunteering.

We understand if you no longer want/can continue. You must notify us through email. We appreciate your participation and will acknowledge your work.

What if I have questions?

If you have a questions about microbial information you found or a Kobo general question, please go to Questions file here in Coda, and write your question. Other volunteers might have the same questions too. We will answer as soon as possible.

If you want to share a useful link or an article or book, feel free to use the SLACK workspace. On the contrary, if you have an specific/personal issue you want to discuss, use themicrobedirectory@gmail.com

How to use The Microbe Directory workspace on SLACK

On the microbe directory workspace, you can share information with all the members of the team about such as articles or webpages relevant for the microbe directory. You can do this by using the #general channel.

If you want to ask a microbe related question you can do this by using the frequently ask questions (#microbe_discussion) channel. If you would like to share additional information not directly related to the microbe directory data query, you could do this in the #random channel.

You can also send direct messages to team members on Direct Messages. Please, be aware that we have zero tolerance with bullying, harassment or any other misconduct behavior.

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