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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 [1] 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

  1. ^ https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=2&lvl=2&lin=f&keep=1&srchmode=1&unlock

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)

Refs

Candida blankii

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)

"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)

It's used on over 2600 pages. (search). Some have been archived, e.g. Apophysomyces variabilis at archive.org. Not sure if a bot can find the archive links as the links include the data of the archiving. There is a bot that adds archive links but it might need a live page.   Jts1882 | talk  12:10, 22 October 2019 (UTC)

Request for information on WP1.0 web tool

Hello and greetings from the maintainers of the WP 1.0 Bot! As you may or may not know, we are currently involved in an overhaul of the bot, in order to make it more modern and maintainable. As part of this process, we will be rewriting the web tool that is part of the project. You might have noticed this tool if you click through the links on the project assessment summary tables.

We'd like to collect information on how the current tool is used by....you! How do you yourself and the other maintainers of your project use the web tool? Which of its features do you need? How frequently do you use these features? And what features is the tool missing that would be useful to you? We have collected all of these questions at this Google form where you can leave your response. Walkerma (talk) 04:24, 27 October 2019 (UTC)

(HAFNIA ) ( BUILDING REACTIONS)

I BASED FROM THE STUDY IN THE MICROBIOLOGY ESPECIALLY BACTERIA TO UTILIZE MORE AND BE MORE STRONGE FROM TAKING THIER NUTRIENTS WHAT EVER THIER CONSCEQUENCES EVEN IF IT IS REACH TO BE MORE STAGABLE FATAL PATHOGENIC TO THIER SUSCEPTALE HOSTS THROGH THE GENATIC CONGUGATIONS AND IT IS NOT HAVE EVIDENTS TO SAY THAT BUT I NOTICED UNQUALIFICATIONS OR FORCED IGNORANCE OR BLINDENESS OF THE PROFESSORS BUT I MAY NOT CONSIDERED THAT THERE ARE AGENERAL BASIC DEFECTS (OK) IF HAFNIA IS CAPABLE OF RESISTANCE SURELY IT IS CAPABLE OF DOING WHAT THIER LIFE NEEDS AQUIRED AND DONT WRITTE ANY THING BEFORE GIVING AFINAL DESCISIONS BECOUSE THIS WELL BE LOWER YOUR SCORE AND SORRY TO JUDGE THAT YOU DONT HAVE AMIND INSPITE OF IT IS PHYSIOLOGICALLY PRESENT BECOUSE THE GUIDE PROFESSORS AND SCIENTESTS GIVE US ABASIC INFORMATIONS ABOUT THE FAMILY OF THE SAME GENATIC CHACTERS AND SAME PHYSIOLOGICAL CHACTERS . — Preceding unsigned comment added by M00000HAMED (talk • contribs) 16:05, 9 November 2019 (UTC)

What is this? Garnhami (talk) 21:52, 9 November 2019 (UTC)

First annual Tree of Life Decemberween contest

After all the fun with the Spooky Species Contest last month, there's a new contest for the (Northern hemisphere's) Winter holidays at Wikipedia:WikiProject Tree of Life/Contest. It's not just Christmas, but anything festive from December-ish. Feel free to add some ideas to the Festive taxa list and enter early and often. --Nessie (talk) 17:38, 12 November 2019 (UTC)

Archive 10←Archive 12Archive 13Archive 14

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 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)

Missing section on the Vibrio cholerae page

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)

Draft:Haplozoon

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)

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

Mold

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)

Draft:Euduboscquella

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)

 Done Accepted and cleaned up. Ajpolino (talk) 15:32, 6 May 2020 (UTC)
@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)
@Jts1882: Thank you! Apologies for making a mess. Ajpolino (talk) 16:52, 6 May 2020 (UTC)

Possible discrepancy with the pages for Chryseobacterium species

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)

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)
My word, there are a lot of Chryseobacterium species. Posting at Wikipedia:AutoWikiBrowser/Tasks for help. Ajpolino (talk) 14:53, 7 May 2020 (UTC)
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 edits to change manual bacteria taxoboxes to automatic or any genuine objection to using automatic taxoboxes from bacteria-interested editors. Plantdrew (talk) 01:57, 8 May 2020 (UTC)
I think the poor uptake for bacteria articles is due to a combination of (1) very few editors working on bacteria articles, and (2) the vast majority of bacteria articles are created by a single editor 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)

A link to a DAB page

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)

Coccobacillus

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)

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)
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)
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)
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)
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)

Discussion about moving the Gut flora article

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)

Discussion about Gammaproteobacteria article

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)

HLAR – wrong redirection

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)

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)

References

  1. ^ "HLAR – Science & Medicine". Abbreviations and acronyms dictionary. 2021-01-27. Retrieved 2021-01-27.
  2. ^ "HLAR". TheFreeDictionary.com. Retrieved 2021-01-27.
  3. ^ "HLAR". Definition by AcronymFinder. 2021-01-27. Retrieved 2021-01-27.

Wikipedia:Sandbox organiser

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)

Microbiology Spectrum Draft

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 edits 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)

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

Malassezia has an RFC

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

AXONOV (talk) ⚑ 19:47, 1 April 2021 (UTC)

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

Clostridium difficile -> Clostridioides difficile

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)

Cupriavidus respiraculi

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)

Looking forward to a new genus category

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)

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

Reliable sources noticeboard discussion about Encyclopedia of Life

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)

Edit-a-Thons Being Planned for Black History Month and Women's History Month 2022

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 edit-a-thons in the upcoming months focused on editing/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)

Phylum Links—Request for Discussion

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)

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

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

User script to detect unreliable sources

Main page: User:Headbomb/unreliable

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

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)

Enterococcus aquimarinus

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

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