Online version:
http://funguild.org
Databases:
http://stbates.org/funguild_db.php
http://stbates.org/nemaguild_db.php
GENERAL NOTES
The Guilds bioinformatic tool is a two-component system that includes online community annotated databases and a python script that assigns functional information to operational taxonomic units (OTUs) obtained from next generation sequencing of environmental samples. The script is based on an original in-house python script referenced in Branco et al. 2013. PLoS One 8:1–10 (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0078295). It searches taxonomic strings in the user’s OTU table against the online Guilds databases (fungi or nematodes) containing taxonomic keywords and functional metadata. The output is the original OTU table with functional metadata appended, and users also have options to output an assigned OTUs only table and/or a table containing only OTUs for which assignments could not be made.
To run the Guilds bioinformatic tool locally, a current version of Python (https://www.python.org/) must be installed on the user’s local machine before the Guilds script (https://raw.githubusercontent.com/UMNFuN/FUNGuild/master/Guilds_v1.0.py) can be used. The Guilds databases are accessed by the python script remotely and, therefore, they do not need to be loaded to the user’s local machine. However, the script must be able to access the internet to connect with the databases.
An online version of the Guilds bioinformatic tool, the 'assignment application', is also available here:
An example OTU table has been provided in the FUNGuild GitHub repository (https://github.com/UMNFuN/FUNGuild/blob/master/otu_table_example.txt) to demonstrate table formatting.
CONTRIBUTING GUILD INFORMATION TO THE FUNGUILD DATABASE
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Data pertaining to particular fungal or nematode taxa can be submitted to the Guilds databases (FUNGuild_db or NEMAGuild_db) by contacting the database curators (xerantheum@gmail.com or scott.thomas.bates@gmail.com), or via the online submission application (http://www.stbates.org/guilds/entry.php).
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All submitted entries will be reviewed by the database curators prior to being migrated to the main Guilds databases.
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Taxon entries proposed for addition to the databases will be accessable once they have been reviewed by the database curators and migrated to the main database.
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Once migrated, proposed entries will automatically be available to all using the Guilds bioinformatic tool to make annotated assignments to their OTU tables containing fungal or nematode taxa.
Information should be entered into each Guilds database field, in sequence, as follows:
• Taxon: The scientific name (e.g., Ganoderma).
• Taxon Level: A numeral corresponding the correct taxonomic level for the taxon (0 = keyword, 3 = Phylum, 4 = Subphylum, 5 = Class, 6 = Subclass, 7 = Order, 8 = Suborder, 9 = Family, 10 = Subfamily, 11 = Tribe, 12 = Subtribe, 13 = Genus, 15 = Subgenus, 16 = Section, 17 = Subsection, 18 = Series , 19 = Subseries, 20 = Species, 21 = Subspecies, 22 = Variety, 23 = Subvariety", 24 = Form, 25 = Subform, 26 = Form Species).
• Trophic Mode: One of three trophic categories [pathotroph = receiving nutrients at the expense of the host cells and causing disease (e.g., biotroph, parasite, pathogen, etc.); saprotroph = receiving nutrients by breaking down dead host cells (e.g., wood rotters, litter rotters, etc.); symbiotroph = receiving nutrients by exchanging resources with host cells (e.g., ectomycorrhiza, lichens, etc.)]. The concepts presented here are similar to those of Tedersoo et al. 2014. Global diversity and geography of soil fungi. Science 346(6213). DOI: 10.1126/science.1256688 (http://www.sciencemag.org/content/346/6213/1256688).
• Guild: Provide a relevant guild descriptor (e.g., "Algal Parasite", "Animal Gut", "Animal Pathogen", "Arbuscular Mycorrhizal", "Coprophilous", "Dark Septate Endophyte", "Ectomycorrhizal", "Endophyte", "Foliar Endophyte", "Ericoid Mycorrhizal", "Litter Saprotroph", "Lichenicolous", "Lichenized", "Musicolous", "Mycoparasite", "Plant Pathogen", "Soil Saprotroph", "Undefined Saprotroph", "Wood Saprotroph", etc.). New guilds can be erected if necessary.
• Confidence Ranking: "Highly Probable" (= absolutely certain), "Probable" (= fairly certain), "Possible" (= suspected but not proven, conflicting reports given, etc.).
• Growth Form: A basic morphological category such as "Agaricoid", "Boletoid", "Clavarioid", "Cup Fungus", "Facultative Yeast", "Gasteroid", "Hydnoid", " Jelly Fungus", "Phalloid", "Polyporoid", "Pyrenomycete", "Resupinate", "Rust", "Secotioid", "Smut", "Yeast", or "Thallus" should be noted.
• Trait: Other functional or morphological traits such as "Brown Rot", "Hypogeous", "Poisonous", "White Rot" or "Contact Exploration Type" would be appropriate for this field.
• Notes: Any other relevant information related to the taxon (e.g., "Facultative human pathogen causing coccidioidomycosis" for Coccidioides immitis, "Host - Arecaceae - Casuarinaceae, Palmae, Sapotaceae" for Xylaria obovata, or "Syn. Umbilicaria" for Actinogyra).
• Citation/Source: Publication, website, etc. from which the corresponding guild information was derived e.g.:
Costa IPMW et al. 2012. Checklist of endophytic fungi from tropical regions. Mycotaxon 119:26
Esslinger TL. 2014. North Dakota State University (http://www.ndsu.edu/pubweb/~esslinge/chcklst/chcklst7.htm)
James TY et al. 2006. Nature 443:818-822
Kurtzman CP, Fell JW, Boekhout T eds. 2011. The Yeasts, a Taxonomic Study. Fifth Edition. Vols 1-3. Elsevier, San Diego
Tedersoo L, May TW, Smith ME. 2010. Mycorrhiza 20:217-263
Outline of Ascomycota (http://www.fieldmuseum.org/myconet)
http://www.apsnet.org/publications/commonnames/Pages/default.aspx
*Data for taxa that is based on peer-reviewed publications is preferred.