Wikipedia talk:WikiProject Microbiology

WikiProject Microbiology

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This page is within the scope of WikiProject Microbiology, a collaborative effort to improve the coverage of Microbiology on Wikipedia. If you would like to participate, please visit the project page, where you can join the discussion and see a list of open tasks.MicrobiologyWikipedia:WikiProject MicrobiologyTemplate:WikiProject MicrobiologyMicrobiology articles Project This page does not require a rating on the project's quality scale.

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The old LPSN website at http://www.bacterio.net is frequently linked to from Wikipedia. Many of these links target LPSN entries for species. Because all species belong to a genus and because LPSN uses one HTML page per genus name, links to LPSN species names are links to anchors within an LPSN page for the according genus name. For instance, on https://en.wikipedia.org/wiki/Acetobacter_aceti we find the link http://www.bacterio.net/acetobacter.html#aceti to the old LPSN page.

As part of an agreement between the old LPSN maintainer, Aidan C. Parte, and the Leibniz Institute DSMZ, LPSN has been taken over by DSMZ to ensure long-term maintenance (see also announcement here). In the course of this takeover, a new website was created. In contrast to the old LPSN website, the new LPSN website at https://lpsn.dsmz.de (currently https://lpsn-dev.dsmz.de) uses individual pages for species names. We will employ the following mapping:

(1) the domain http://www.bacterio.net is permanently redirected to https://lpsn.dsmz.de;

(2) the page address acetobacter.html is mapped to genus/acetobacter, which is the page for the genus Acetobacter on the new LPSN website.

This means, however, that http://www.bacterio.net/acetobacter.html#aceti is mapped to https://lpsn.dsmz.de/genus/acetobacter and not to https://lpsn.dsmz.de/species/acetobacter-aceti, which is the page for the species on the new LPSN website, as it should be. The reason for this limitation is that the anchor aceti is not even transferred by the browser and thus cannot be processed by the website. While links on https://lpsn.dsmz.de/genus/acetobacter are present that lead to https://lpsn.dsmz.de/species/acetobacter-aceti, it would be more convenient for the user if http://www.bacterio.net/acetobacter.html#aceti was transferred to a link that leads directly to https://lpsn.dsmz.de/species/acetobacter-aceti.

As LPSN URLs are stored in Wikidata (LPSN), this change should be doable task with the help of a bot. Therefore we are kindly asking for help to accordingly modify all Wikipedia links to LPSN species pages as described above. Tobias1984: you did a great job in the past, helping us with BacDive: Is there a chance that you help us again with this issue? --L.C.Reimer

@L.C.Reimer: Thanks for bringing this up! If you don't get an immediate reply here, you could consider posting at Wikipedia:Bot requests. There are usually users there willing and able to help. Thanks! Ajpolino (talk) 16:20, 4 February 2020 (UTC)Reply[reply]

The "Genome" section of the Vibrio cholerae wiki page promises a following section on "pathology and current research" which does not exist in the current version of the page. Did it get deleted by mistake? posted 4:32 PM March 27 2020 — Preceding unsigned comment added by 108.52.207.45 (talk) 20:32, 27 March 2020 (UTC)Reply[reply]

Will someone please either review this draft or decide that it isn't worth reviewing until it has links to existing articles? It has no links to other articles, including the taxa to which the genus belongs, and the taxa that it is said to be a parasite of. In view of the history, I can't be sure whether it was invented, or whether it is simply a genus of multiply incertae sedis that belongs to an anarchic taxonomic barony nullii regni. Thank you. Robert McClenon (talk) 04:26, 10 April 2020 (UTC)Reply[reply]

Thank you, User:RoySmith. Robert McClenon (talk) 04:45, 6 May 2020 (UTC)Reply[reply]

There was are recent move discussion wheremold was moved to Mold (fungus) with this move discussion about fungal mold (or relevant historical usage) wasn't the WP:PRIMARYTOPIC. It has been relisted, and more eyes would be helpful from this project on establishing if/what primary topic exists with the biological terminology. Kingofaces43 (talk) 21:24, 21 April 2020 (UTC)Reply[reply]

Will someone please review this draft? It appears to be a genus, and should be accepted if properly documented. Robert McClenon (talk) 04:46, 6 May 2020 (UTC)Reply[reply]

 Done Accepted and cleaned up. Ajpolino (talk) 15:32, 6 May 2020 (UTC)Reply[reply]

@Ajpolino: I changed the taxonomy template for Coccidiniales following the algaebase reference you used, which gives Syndiniophyceae (Syndinea) as the parent. This is consistent with Oakes et al (2012) which placed Euduboscquellidae in class Syndiniophyceae and subphylum Syndinea, although they used order Syndiniales. I think using algaebase for the whole sequence is probably the best solution. —  Jts1882 | talk  16:26, 6 May 2020 (UTC)Reply[reply]

@Jts1882: Thank you! Apologies for making a mess. Ajpolino (talk) 16:52, 6 May 2020 (UTC)Reply[reply]

Hi there, I just wanted to bring up something I saw on the individual pages for the various Chryseobacterium species (Chryseobacterium#Species). On the page for the genus Chryseobacterium, the phylum is listed as Bacteroidetes, however on the individual species pages(the article on Chryseobacterium marinum as an example), the phylum is listed as Proteobacteria. What is the correct phylum? Cheers Abstrakt (talk) 05:10, 7 May 2020 (UTC)Reply[reply]

Ah good catch; they're all Bacteroidetes. It's correct at the intermediate taxa pages (e.g. Flavobacteriia). I'll fix the Chryseobacterium species pages. Thanks! Ajpolino (talk) 14:25, 7 May 2020 (UTC)Reply[reply]

My word, there are a lot of Chryseobacterium species. Posting at Wikipedia:AutoWikiBrowser/Tasks for help. Ajpolino (talk) 14:53, 7 May 2020 (UTC)Reply[reply]

If I'd noticed this thread earlier (before it was solved via AWB), I would've taken the opportunity to convert the manual taxoboxes to automatic taxoboxes. Chryseobacterium is already using an automatic taxobox, so the template required for the species has already been created.

Bacteria taxoboxes have a number of inconsistencies. "Bacteria" is given as a domain or a kingdom or both (and either Bacteria or Bacterium is linked). Proteobacteria classes are inconsistently displayed as e.g. Alpha Proteobacteria/Alphaproteobacteria. I'm sure there are cases where taxobox use an outdated classification. Keeping classification consistent is an advantage of automatic taxoboxes.

Most of Wikipedia's article on organisms use automatic taxoboxes. Bacteria use manual taxoboxes more than any other major group of organisms. I don't know if that is from lack of interest in making the s to change manual bacteria taxoboxes to automatic or any genuine objection to using automatic taxoboxes from bacteria-interested ors. Plantdrew (talk) 01:57, 8 May 2020 (UTC)Reply[reply]

I think the poor uptake for bacteria articles is due to a combination of (1) very few ors working on bacteria articles, and (2) the vast majority of bacteria articles are created by a single or Daniel-Brown (who I now see has slowed down after creating thousands of bacteria articles over several years). DB's articles follow a rough template that includes a manual taxobox. If anyone is interested in undertaking an effort to change taxoboxes over to automatic, I'm all in favor and would help out wherever I can. In this case, if I'd have thought about it, I would've requested the AWBer to swap to automatic boxes instead. So mea culpa there. Ajpolino (talk) 15:04, 8 May 2020 (UTC)Reply[reply]

In Aspergillus wentii, there's a mention of "sterile hyphae", in which the link redirects to the DAB page sterility. It's been flagged as {{disambiguation needed}} since January 2019. None of the entries on the DAB page looks relevant; can any expert help solve this puzzle? Narky Blert (talk) 15:37, 31 May 2020 (UTC)Reply[reply]

Any idea why the stub article Coccobacillus is getting over 200 pageviews per day? Is there perhaps a genus named Coccobacillus? Abductive (reasoning) 04:57, 21 June 2020 (UTC)Reply[reply]

Huh, not that I can find. Pardon my technical ignorance, is there any way to see where the views are coming from? Perhaps there's a poorly disambiguated link that leads to coccobacillus that should lead elsewhere? Special:WhatLinksHere/Coccobacillus - it is linked from more pages than I had expected... Ajpolino (talk) 15:20, 21 June 2020 (UTC)Reply[reply]

Ah, a lot of those links are from the navbox {{Bacteria}}. I presume most of its views are not coming from readers uncollapsing that navbox and clicking the link. Any chance there's an easy way to remove those results from the Special:WhatLinksHere results? Ajpolino (talk) 15:23, 21 June 2020 (UTC)Reply[reply]

The results are real pageviews. Note that there appears to be seasonal and weekly structure in the pageviews. Also, Coccobacillus appears to be a former genus: Coccobacillus pfeifferi. Abductive (reasoning) 23:28, 21 June 2020 (UTC)Reply[reply]

The seasonality corresponds to (Northern Hemisphere) winter and summer school breaks. I'm pretty sure the navbox is responsible for the page views. Diplococcus is also in the navbox and gets a number of pageviews that strikes me as unusually high. If you want to confirm the navbox is the culprit, just comment out the link in the navbox for a few days. I'm not a fan of navboxes in general, but the links in {{Bacteria}} don't seem very well thought out. The navbox could use an overhaul, and perhaps the bacterial shapes should not be included going forward (fringe cancer treatment Coley's toxins certainly doesn't belong in the navbox). Plantdrew (talk) 01:30, 22 June 2020 (UTC)Reply[reply]

I made some adjustments to the template. Let's give a few days to see how it shakes out. Abductive (reasoning) 01:55, 22 June 2020 (UTC)Reply[reply]

Opinions are needed at Talk:Gut flora#Requested move 4 September 2020: Add "human" to the title?. Flyer22 Frozen (talk) 06:04, 4 September 2020 (UTC)Reply[reply]

Hi all! We are a group of 5 univerisity students from the Federico II University in Naples. We are working on our course assignement and we would like to add more content about the characteristics, morphologies, metabolisms, and ecology about the Gammaproteobacteria.

Read more about the course assignments here and here or by visiting our University webpage here Battloglio (talk) 18:26, 15 November 2020 (UTC)Reply[reply]

Hi there, There is a problem, kind of significant. When you try to search HLAR using Wikipedia you are instantly redirected to page of Vancomycin-resistant Enterococcus, which is truly wrong. HLAR - high-level aminoglycoside resistance is not at all an equivalent to VRE. I'd be grateful for correcting this mistake. Sincerely, XYZ — Preceding unsigned comment added by 2A02:A317:E43D:3780:FC3D:AB3D:DAB6:B411 (talk) 19:51, 27 January 2021 (UTC)Reply[reply]

This is not my area of expertise, but it seems that there are two medical terms for HLAR,^[1][2][3] making this ripe for a disambiguation page that would then link to the appropriate topics:

• High level aminoglycoside resistance
• Human Leukocyte Common Antigen-Related Molecule

I am unclear as to what High level aminoglycoside resistance should redirect, but my guess would be the Drug resistance article. Peaceray (talk) 20:48, 27 January 2021 (UTC)Reply[reply]

Sandbox Organiser A place to help you organise your work

Hi all

I've been working on a tool for the past few months that you may find useful. Wikipedia:Sandbox organiser is a set of tools to help you better organise your draft articles and other pages in your userspace. It also includes areas to keep your to do lists, bookmarks, list of tools. You can customise your sandbox organiser to add new features and sections. Once created you can access it simply by clicking the sandbox link at the top of the page. You can create and then customise your own sandbox organiser just by clicking the button on the page. All ideas for improvements and other versions would be really appreciated.

Huge thanks to PrimeHunter and NavinoEvans for their work on the technical parts, without them it wouldn't have happened.

John Cummings (talk) 11:08, 6 February 2021 (UTC)Reply[reply]

Hi, I'm Geoff. I work for the American Society for Microbiology. As such, I have disclosed my Conflict of Interest here, as well as on my Talk page. Per Wikipedia policy for connected contributors, I will not make s directly to articles about ASM or its journals.

I am here today to ask if anyone is interested in reviewing a draft of an article about one of our journals, Microbiology Spectrum? If so, the draft can be found here. I understand that the article is shorter than usual, but I believe it qualifies under notability for academic journals because it is indexed by SCOPUS and Science Citation Index. Many of our journals already have entries on Wikipedia, and our goal here is to offer content that improves the encyclopedia by helping to fill a gap. I'm committed to following community guidelines, and am open to feedback.

Please feel free to reach out with comments and questions here or on my Talk page.

Thanks so much! Geoffhunt3 (talk) 22:04, 1 March 2021 (UTC)Reply[reply]

Hi Geoffhunt3, thanks for bringing this up here. I'll be happy to review the draft this weekend if no one beats me to it. If you don't hear from me (or anyone else) feel free to remind me come Monday. Cheers. Ajpolino (talk) 05:42, 2 March 2021 (UTC)Reply[reply]

@Ajpolino: Thank you for your offer to review. I haven't heard from any other ors, and you're most welcome to offer feedback. Looking forward to seeing your comments. Thanks again, Geoffhunt3 (talk) 23:38, 9 March 2021 (UTC)Reply[reply]

Malassezia, which is within the scope of this WikiProject, has an RFC for possible consensus. A discussion is taking place. If you would like to participate in the discussion, you are invited to add your comments on the discussion page. Thank you.

You may participate in any of the following

• RfC: Malassezia: D/SD
• RfC: M. restricta spp. 1
• RfC: M. restricta spp. 2 (CD/Colitis)
• RfC: M. globosa spp. - Pancreatic_cancer

AXONOV (talk) ⚑ 19:47, 1 April 2021 (UTC)Reply[reply]

Just wanted to let you know that this is still relevant. AXONOV (talk) ⚑ 21:50, 15 May 2021 (UTC)Reply[reply]

What's the plan for implementing this change of family and name? At first I thought just all the mentions of the old name had to be exchanged, but Template:Gram-positive firmicutes diseases e.g. had me stumped. With the emphasis on differentiation that template seems to build upon, I wondered how in everyday-scientific work the reclassification is handled. Is removing c.diff from lists in articles reasonable when the new family for lack of species is not mentioned or has no own article? --Murata (talk) 00:43, 2 June 2021 (UTC)Reply[reply]

I was just looking at the article for Cupriavidus respiraculi. It’s quite a short article. It is an emerging problem for certain vulnerable populations. Any help improving it would be greatly appreciated. Thank you, Thriley (talk) 06:46, 13 June 2021 (UTC)Reply[reply]

People who have been watching for a while might (or might not) have noticed that I have organized literally thousands of species articles--bacteria, as well as plants and insects--in their categories. In the course of it, I've added hundreds (if not thousands) or "Sortkeys" to make the categories sort more usefully. I've just now seen an article on a brand new species of bacteria in the Myxococcus genus:

Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis

At the moment, there are apparently only about eight species classified in the Myxococcus genus. Wikipedia has articles on two of them; that is one of them. I can't wait until they discover enough new species of Myxococcus to warrant my creating a category for the genus. I'll really enjoy putting in that Sortkey! Uporządnicki (talk) 20:55, 17 October 2021 (UTC)Reply[reply]

@AzseicsoK: wait until they name find something new at Taumatawhakatangihangakoauauotamateaturipukakapikimaungahoronukupokaiwhenuakitanatahu. --awkwafaba (📥) 02:05, 18 October 2021 (UTC)Reply[reply]

Hi all

I've started a discussion on the reliable sources noticeboard about Encyclopedia of Life as a reliable source for Wikipedia, please share your thoughts here. I've added some basic information about EOL at the top of the section to help inform the discussion.

Thanks very much

John Cummings (talk) 20:24, 23 November 2021 (UTC)Reply[reply]

Hi! I work at the American Society for Microbiology, handling public engagement and science communication. Working with our members, I'm planning to organize two separate -a-thons in the upcoming months focused on ing/improving/creating biographies of microbiologists: one on February 25, 2022 focused on Black scientists (as part of Black History Month), and one on March 25, 2022 focused on female scientists (as part of Women's History Month). I wanted to make you all aware and see if you had any advice or guidance, or particular individuals or areas of focus you'd recommend. Please let me know! Thanks! Geoffhunt3 (talk) 18:54, 25 January 2022 (UTC)Reply[reply]

I've been going through "What links here" and replacing links to old (informal) phylum names with links to the new (valid) phylum names (like changing [[Firmicutes]] to [[Bacillota]]). It was brought to my attention that this might create confusion, such as when a cited source refers to "Firmicutes" but the article text and link refer to Bacillota. I think we should collectively decide what is the most appropriate course. Should we let the old nomenclature persist in the article namespace or should we change most of the old nomenclature to the new nomenclature? Or, to put it another way, is it okay that most of the links to the phylum level articles actually point to a redirect? Ninjatacoshell (talk) 02:32, 21 April 2022 (UTC)Reply[reply]

No real idea, but why are you nowiki-ing the links?? Johnbod (talk) 03:40, 21 April 2022 (UTC)Reply[reply]

To show the change in code. Jo-Jo Eumerus' proposal below makes it clear why we need to look at the underlying code rather than the link that is displayed for this discussion. Ninjatacoshell (talk) 03:44, 22 April 2022 (UTC)Reply[reply]

I think I'd prefer if it was [[Bacillota|Firmicutes]]. I see the advantages of updating but I am concerned about people seeing "bacillota" when the source says "firmicutes", especially if the old name and new names don't mean 100% the same thing. Jo-Jo Eumerus (talk) 14:50, 21 April 2022 (UTC)Reply[reply]

Since [[Firmicutes]] now redirects to [[Bacillota]], [[Bacillota|Firmicutes]] is equivalent to [[Firmicutes]]. So, I don't think there's a need to pipe the link if we decide to conserve the use of "Firmicutes". Ninjatacoshell (talk) 03:44, 22 April 2022 (UTC)Reply[reply]

@Kaficek:, @YorkshireExpat:, @Awkwafaba:, @Slonczewski:, @Plantdrew:, @Daniel-Brown: Comments?

Use the new name. There are so many times taxa have been renamed, and Wikipedia has not kept a long string of historical taxonomy for every article. If they are confused, there’s a link. --awkwafaba (📥) 12:14, 22 April 2022 (UTC)Reply[reply]

Use the new name and make sure the old name is listed as a synonym. YorkshireExpat (talk) 16:23, 22 April 2022 (UTC)Reply[reply]

I agree. Use the new name, but make sure the old name is listed as a synonym. Sometimes it makes sense to change the text to a wikilinked new name with the old name in parentheses afterwards, e.g "Bacillota (Firmicutes)". It depends on the context. But "[[Bacillota|Firmicutes]]" is unhelpful, in my view. Peter coxhead (talk) 17:01, 22 April 2022 (UTC)Reply[reply]

I have (with the help of others) made a small user script to detect and highlight various links to unreliable sources and predatory journals. Some of you may already be familiar with it, given it is currently the 39th most imported script on Wikipedia. The idea is that it takes something like

• John Smith "Article of things" Deprecated.com. Accessed 2020-02-14. (John Smith "[https://www.deprecated.com/article Article of things]" ''Deprecated.com''. Accessed 2020-02-14.)

and turns it into something like

• John Smith "Article of things" Deprecated.com. Accessed 2020-02-14.

It will work on a variety of links, including those from {{cite web}}, {{cite journal}} and {{doi}}.

The script is mostly based on WP:RSPSOURCES, WP:NPPSG and WP:CITEWATCH and a good dose of common sense. I'm always expanding coverage and tweaking the script's logic, so general feedback and suggestions to expand coverage to other unreliable sources are always welcomed.

Do note that this is not a script to be mindlessly used, and several caveats apply. Details and instructions are available at User:Headbomb/unreliable. Questions, comments and requests can be made at User talk:Headbomb/unreliable.

- Headbomb {t · c · p · b}

This is a one time notice and can't be unsubscribed from. Delivered by: MediaWiki message delivery (talk) 16:01, 29 April 2022 (UTC)Reply[reply]

Just came across Enterococcus aquimarinus. May need some work. CambridgeBayWeather, Uqaqtuq (talk), Huliva 18:51, 1 May 2022 (UTC)Reply[reply]

See "Missing info on "hybrid viral particles" and other (potential) issues from coinfections". This doesn't only relate to the Coinfection article. Prototyperspective (talk) 22:20, 7 December 2022 (UTC)Reply[reply]

National Microbial Pathogen Data Resource looks like it could be an exceptionally useful article to Wikipedia ors (e.g., to help figure out whether a source is reliable). If anyone knows something about this subject, the article could use some attention. WhatamIdoing (talk) 00:08, 9 January 2023 (UTC)Reply[reply]

The List provided here does neither follow NCBI Taxonomy nor LPSN. It looks very like GTDB instead:

• https://gtdb.ecogenomic.org/tree

E. g. there is a phylum Asgardarchaeota with class Lokiarchaeia comprising Lokiarchaeales and Helarchaeales, but not a phylum Lokiarchaeota. Besides of the fact that the list is worthless due to invalid reference, this rises further problems as follows:

Lokiarchaeaceae[]

"Lokiarchaeaceae " could not be veryfied anywehere, even not in GTDB. There is no reference provided for "Lokiarchaeaceae" Vanwonterghem et al. 2016. Is Lokiarchaeaceae eqal to GTDB-family MK-D1? For a discussion of this and the question if "Lokiarchaeaceae" Vanwonterghem et al. 2016 might be equal to GTDB family MK-D1 see Talk:Lokiarchaeota#2 species cultivated now.

A Google lookup returned just hits from russian server in chinese that wanted me to input my crcard dates. Please find a serious source for

"Lokiarchaeaceae" Vanwonterghem et al. 2016

Sigynarchaeales[]

Order "Sigynarchaeales" belongs to pyhlum Sigynarchaeaota (strain SQRJ_234) according to LPSN. This clade is not known to NCBI taxonomy. There is no relation to Lokiarchaota/Lokiarchaeia according to the rfrerenced soureces. Please could anyone fix this? Thanks.

--Ernsts (talk) 07:55, 9 January 2023 (UTC)Reply[reply]