Wikipedia talk:WikiProject Microbiology

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Taxonomy in Bacteria

Hello, I am new to WikiProject Microbiology and I have a few questions about adding new taxonomy branches. My first question is if there is a specific source that should be used for bacteria taxonomy. I was comparing what is on Wikipedia with the taxonomy from the National Center for Biotechnology Information and noticed that there were differences. I am also wondering if it in beneficial to add more taxonomic branches if it results in more stubs. Thank you for helping me become a better contributor to the project. From, Coralizzie1 (talk) 05:09, 8 January 2019 (UTC)

@Coralizzie1: can you give an example of differences?Garnhami (talk) 08:54, 8 January 2019 (UTC)

@Coralizzie1: My impression is that the NCBI taxonomy browser is a highly inclusive list. It contains names for anything they have sequence information for (someone correct me if I'm wrong please), even if it's not a widely accepted taxonomic name. It doesn't try to be an authoritative taxonomy source, which is why they include a little disclaimer at the bottom of each page. One very convenient source for bacterial taxonomy is LPSN which contains an "official" list of recognized bacterial taxonomy as well as a citation to the original description paper and any updates to the description that have come since. It's updated very regularly, so will often include species that have been described in the last year. The downside here is that they have more stringent criteria for inclusion and (I think) will only include taxa that have been isolated in culture and described. So that will likely exclude most of life. Also for Cyanobacteria, LPSN basically says "its a mess" and doesn't host much info... For many, the definitive reference text for bacterial taxonomy is Bergey's Manual of Systematics of Archaea and Bacteria. A relatively up-to-date version is hosted online by the publisher, here. You may have access through a school library. If not, just let me know by email and I'm happy to send chapters upon request. The downside of Bergey's is that it's not as regularly updated as LPSN. The upside is that it is a far more detailed reference text, and contains the most widely accepted descriptions of various taxa... The basic problem that you have identified is that there is no official body that dictates bacterial taxonomy that everyone then follows. That said, it's better than eukaryotic microbes, where my impression is that anarchy reigns...

As for your other question of whether its beneficial to add more taxonomic branches etc., I don't think we have broad consensus around here on that. My personal opinion is that adding tiny stub articles on bacteria that few readers will ever search for can be of limited utility. That said there's nothing wrong with stub articles. And we aren't running out of space around here. So if it's something you enjoy doing, that's super! Anyway I'll stop my ramble now. I hope that helps. Happy to be contradicted by others. Happy editing and welcome! Ajpolino (talk) 15:29, 8 January 2019 (UTC)

@Garnhami: Like @Ajpolino: said NCBI includes taxonomic names for anything that has been sequenced, even if it is not widely recognized. One example is on the Chlamydiae wiki page there are only two families from the Chlamydiales tree whereas on the NCBI there are three. Coralizzie1 (talk) 18:29, 8 January 2019 (UTC)

References

Adding infra-specific ranks to Virusbox

I have been working on adding infra-specific ranks to {{Virusbox}}, and would like some views on the questions I've posed at Template talk:Virusbox#Ranks below species. Thanks in advance. Peter coxhead (talk) 12:16, 15 January 2019 (UTC)

Rfc on new classification scheme

Please see Wikipedia talk:WikiProject Tree of Life#Request for comment: new classification scheme for eukaryotes, which asks for comments on how we should deal with a proposed new classification system that has widespread ramifications across the tree of life. Peter coxhead (talk) 09:49, 3 February 2019 (UTC)

Fixing inconsistent ranks in taxonomy templates

Input sought At Wikipedia talk:Automated taxobox system/Archive 1#Fixing inconsistent ranks in taxonomy templates I've suggested some alternative ways of fixing inconsistent ranks in taxonomy templates. They could make it easier to deal with the problem of inconsistent classification systems, e.g. the ones used for birds and dinosaurs, or the ones used for mammals and dinosaurs. Be warned that it's a long post, but it very much needs input, particularly from "old hands" at using the automated taxobox system. Peter coxhead (talk) 15:48, 8 February 2019 (UTC)

New article Chryseobacterium nematophagum

I have made a stub on Chryseobacterium nematophagum which is making the rounds of the lay media. Since I have limited experience in bacteriology, could people take a look? Abductive (reasoning) 13:22, 1 March 2019 (UTC)

Candida blankii

• Find sources: Google (books · news · scholar · free images · WP refs) · FENS · JSTOR · TWL
• Candida blankii (edit|talk|history|links|watch|logs|google) AfD discussion

Our favorite yeast? Probably not. But no pretense of compliance with WP:Before. 7&6=thirteen (☎) 18:50, 24 March 2019 (UTC)

Planning edits to Borrelia page

Hello! I'm planning on upgrading the Borrelia page for a class project. My changes would include fixing existing citations and adding in more information. If anyone has any comments, advice, or concerns, feel free to reach out. Thanks.Smneu (talk) 17:20, 2 April 2019 (UTC)

For any interested, the thread is here. Ajpolino (talk) 22:10, 2 April 2019 (UTC)

List of Bacteria Genera

The page List of bacteria genera is categorized as start-class but high-importance. It was started in 2008, but hasn't been edited since 2012. As of now, the 'List of Bacteria Genera' page is an alphabetical list. But, for a biologist, this isn't very helpful because it doesn't give an indication of the relationships these genera have to one another. Is there a way to structure the content of the page so that it appears on a circular tree? Is this a change that we feel would be particularly helpful to readers? --Zarina 6022 (talk) 14:53, 4 April 2019 (UTC)

As far as I can tell the only way of implementing a circular tree is using an image, unless wikipedia change policy on embedding SVG graphics. I suspect for something as large as a list of bacteria genera the circular tree wouldn't be too helpful as it would need zooming in to see anything much lower ranking than phyla. I wonder if a list of genera is that useful as the amount of work to complete and update this list is substantial.   Jts1882 | talk  15:12, 4 April 2019 (UTC)

I agree; I'm not convinced that a list like List of virus genera is worthwhile, and even less so for bacteria. There could be one for bacteria like List of virus taxa, I suppose, but it would be a lot of work to create and once the initial enthusiasm has passed, these lists are rarely kept up to data. Peter coxhead (talk) 15:56, 4 April 2019 (UTC)

I also agree that this probably isn't worth the immense amount of work it would take to create and maintain. A knowledgable person would have to be willing to update the tree, and hand it off to a new person as they leave... forever... An encyclopedia is probably just not the right place for a giant cladogram of all bacterial genera (useful and interesting as one may be). Category:Bacteria genera is probably a better place to serve the function of listing genera alphabetically. I'd advocate trashing the list as serving a redundant function to the category. Sorry to be such a downer. Happy editing! Ajpolino (talk) 16:24, 4 April 2019 (UTC)

A new newsletter directory is out!

A new Newsletter directory has been created to replace the old, out-of-date one. If your WikiProject and its taskforces have newsletters (even inactive ones), or if you know of a missing newsletter (including from sister projects like WikiSpecies), please include it in the directory! The template can be a bit tricky, so if you need help, just post the newsletter on the template's talk page and someone will add it for you.

– Sent on behalf of Headbomb. 03:11, 11 April 2019 (UTC)

Proposal to delete the MCB tag option from Template:WikiProject Microbiology

Over at WP:MCB we recently had a problem with one of our autopopulated lists (of articles with unassessed importance) not emptying after a full assessment. We narrowed it down to the MCB tag which is part of the WP:Micro template.

I believe that this tag should be removed from your template because:

1. It causes weird bugs in our lists.

2. It is not well-supported by scripts like Rater which make assessment possible.

3. It does not quickly show users on the talk page that we support the article.

4. It offers no benefit over actually tagging us with our own project template.

I'm looking for a few voices of support here instead of just over at MCB. Plus, the template page is protected. Gonna need help with that. Prometheus720 (talk) 00:59, 12 April 2019 (UTC)

@Prometheus720: I'm not sure if you'll get many voices of support here, but you have my support. WikiProject Microbiology never really got off the ground. I've used the WikiProject Microbiology banner to tag articles on bacteria/prokaryote taxa, which don't have any other appropriate subproject of Wikipedia:WikiProject Tree of Life. @NessieVL: has tagged various non-plant/fungi/animal eukaryotes with the project banner. This is not an active project. The Microbiology banner is being used to tag articles by editors with an organismal focus. Editors focused on a molecular/cellular biology perspective have my best wishes, but I'm happy to excuse them from applying the MCB banner to random unicellular taxa. Plantdrew (talk) 03:17, 12 April 2019 (UTC)

It always seemed an odd coupling to me. Like having a geology project tag on the template for WP Palaeontology. I just assumed others wanted the MCB parameter there, i never really used it. It's not to hard to add the MCB template instead of the parameter, but I don't recall doing either much at all. Get rid of it if it's making a mess of things. --Nessie (talk) 03:33, 12 April 2019 (UTC)

@Plantdrew: I had no idea this project was so inactive. Wow. I've been working through unassessed backlogs for MCB, Micro, and Biology over the past few days and I have tagged probably dozens of articles into WP Micro. That's disappointing to hear, since microbiology is one of my interests in my undergrad. And yes, I've been quite careful not to apply MCB to taxa articles, though there might be exceptions for antibiotic producers like Streptomyces and so on. As I see it, everything in MCB and Micro should be tagged for Bio, but MCB and Micro should only overlap occasionally when talking about aspects of molecular/cellular biology in microbes. Anyway, I'm gonna wait for some more people to comment in both projects before requesting an edit. Your assertion that this project is inactive will likely temper concerns about consensus, as will your support. That goes for you too, Nessie!Thanks for the comments! Oh, and PS—I'm coming to Plants next! Prometheus720 (talk) 03:50, 12 April 2019 (UTC)

I also didn't know it's a zombie project. The "Scope" on the project page does focus on all micro-scale biota though, and not just Bacteria, Archaea, and viruses. --Nessie (talk) 04:18, 12 April 2019 (UTC)

I agree that the MCB parameter should be removed from {{WikiProject Microbiology}}. I assume it's some kind of historical quirk? Seems like the more effective move is always to add the MCB project tag rather than use this weird parameter. Ajpolino (talk) 04:38, 12 April 2019 (UTC)

I also support the removal if it is causing problems. It is clearer if the projects are directly tagged with the project templates. In most of the few remaining uses the pages are redundantly tagged with {{WikiProject MCB}} (see search). The |MCB= parameter is also an option in {{WikiProject Fungi}} although all current uses seem to be in {{WikiProject Micro}}.   Jts1882 | talk  07:34, 12 April 2019 (UTC)

I started a discussion regarding the Fungi template. Feel free to speak up there as well. — Preceding unsigned comment added by Nessie (talk) 16:12, 12 April 2019 (UTC)

I agree with the proposed change. It also ensures that the Article lists tool is accurate. T.Shafee(Evo&Evo)^talk 09:07, 13 April 2019 (UTC)

I am inserting the template edit request for this project only at this point. It's over on the template page. After some people chime in on Fungi I will post one there as well. To whoever answers this, let me know if you need us to remove the parameter from affected pages before the template is edited, and I'll happily do that. — Preceding unsigned comment added by Prometheus720 (talk • contribs) 15:38, 12 April 2019 (UTC)

UPDATE: This request has been concluded and the tag has been successfully deleted. Thank you, everyone, for your prompt and thoughtful responses. We are now waiting on WP:Fungi to answer the request over there (formality, really) and this will then be finished completely. Thanks especially to Nessie for her help! Prometheus720 (talk) 15:56, 13 April 2019 (UTC)

Saccharomyces cerevisiae

I recently added two new sections to the article : about use as a probiotic and about human infections caused by the species. Since I have no training in microbiology, I propose that someone who has could give a look. Эйхер (talk) 11:09, 16 April 2019 (UTC)

Subscribe to new Tree of Life Newsletter!

"I've never heard so much about crinoids!"

Despite the many Wikipedians who edit content related to organisms/species, there hasn't been a Tree of Life Newsletter...until now! If you would like regular deliveries of said newsletter, please add your name to the subscribers list. Thanks, Enwebb (talk) 00:34, 5 May 2019 (UTC)

Difflugia

Could someone take a look at recent edits to Difflugia? This edit expanded the article but also left it without a lead section or any links to other articles (and perhaps other issues too). I've restored the lede and made some other small changes, but don't know anything about the topic so would appreciate more eyes on it. – Arms & Hearts (talk) 23:06, 15 May 2019 (UTC)

A possible Science/STEM User Group

There's a discussion about a possible User Group for STEM over at Meta:Talk:STEM_Wiki_User_Group. The idea would be to help coordinate, collaborate and network cross-subject, cross-wiki and cross-language to share experience and resources that may be valuable to the relevant wikiprojects. Current discussion includes preferred scope and structure. T.Shafee(Evo&Evo)^talk 03:04, 26 May 2019 (UTC)

please improve Legionella -article into a Featured Article

in my short knowledge, there is an incredible amount of unspent data reserves for this pathogen. --2001:14BB:180:17E:D4C2:D526:8FB1:AC1D (talk) 13:49, 14 July 2019 (UTC)

Discussion on merging with WP:VIRUSES

I've started a discussion to gauge interest in merging this project with WP:VIRUSES. Please share your thoughts at the WT:VIRUSES page. Thank you. Ajpolino (talk) 22:52, 6 August 2019 (UTC)

Links to StrainInfo www.straininfo.net

"StrainInfo has permanently been put out of commission and will no longer be available. 1-januari-2019"

Just wanted to direct your attention to this, because I don't know how many links to www.straininfo.net are in Wikipedia articles on microbiology, possibly many. Maybe someone can update Wikipedia articles with such links by programming a bot for that ... ?

Krakatit (talk) 10:49, 22 October 2019 (UTC)