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.
Not all sources of microbial information have been
. 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
if you have searched for a while and have not found any information about that specific microorganism. It is
better to select
than to annotate wrong data.
The average search time per species can range from
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
option. If you find that the specific feature you are trying to answer does not apply for that microbe, select
If you found that given microbe does not produce biofilm, you should select
If you cannot find whether a given microbe produces biofilm or not, you should select
If you found that certain characteristic does not apply to your group of organisms, such as biofilms in virus, you should select
If your microbe was is unclassified to species level (i.e.
unidentified proteobacterium or - unidentified marine eubacterium
) you select
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
. 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.
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
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
Here you may find the available taxonomy, synonyms, genome availability and some related articles.
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.
is a fungi that was first described as
by Nakase & M. Suzuki in 1988. Later, it was assigned into a different genus and the species name changed to
Finally, in 2015 it was reclassified again and the genus changed to
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.
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
for the missing data.
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
For example, if your assigned microbe is
a genus of gram-positive coccus. When annotating
, you could select “gram-stain positive”. However, when annotating if the microbe is
you should annotate
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
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.
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
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
, 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
workspace. On the contrary, if you have an specific/personal issue you want to discuss, use firstname.lastname@example.org
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.