Talk:Microbiome/GA1

GA Review

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Reviewer: Chiswick Chap (talk · contribs) 17:05, 10 November 2021 (UTC)

This is a fascinating article, well-cited and fluently written. It's especially welcome to see the root of a whole tree of articles coming to GA (I was starting to wonder if I was the only editor who'd ever do such a thing with a biology article). I do have quite a few comments but they're mostly quite small things really.

Thank you Chiswick Chap for your prompt, careful and very clear review. I will attempt to address the issues shortly. — Epipelagic (talk) 23:20, 11 November 2021 (UTC)

Lead

The lead section introduces "new" material not in the body of the article. The MoS calls for the lead to summarize the body text. Much of it is currently a detailed analysis of the 'Etymology' of the term and the 'History' of the discipline, which would make good introductory sections near the top of the article. The existing 'Background' would become a subsection of 'History'; the 'Etymology' could be another such subsection actually.

The lead section needs to be rewritten to summarize in 3 or 4 paragraphs what each section of the article says, i.e. each section is mentioned in a sentence. It should begin with a non-technical paragraph, and especially a non-technical first sentence, that says straightforwardly what a microbiome is. The citations should be moved out of the lead so that Mohr and Whipps (etc) are discussed in the body and at most briefly mentioned in the lead.

The current lead image is probably too advanced and too theoretical for its position in the article. It's also visually dull (shades of grey...) and wordy rather than graphic (it looks like a university course PowerPoint slide). Its caption speaks of "the term microbiome", i.e. the thing is defining a word rather than illustrating an encyclopedic subject. If the image is to remain in the article at all, it should be further down (definition section maybe). The little flowering plant of 'Part of a series on Microbiomes' is actually a far better introductory image, so I suggest we simply have that navbox at the top and leave it at that.

'Background'

• See comments on lead for needed reorganisation.

• The timeline is a good idea but it has very small text and even so is a large image and squeezes the text beside it. It would work better as a full-width table with normal-sized text, which could also be wikilinked to allow readers to navigate and to explore any terms they found difficult (what was the Central dogma of molecular biology now... (an odd term, really, if not distinctly dated) ... ). "Important Discoveries" is perhaps verging on the wrong tone, too; it actually heads a 3-column structure of {Date, Discovery, Scientists}. This may be one case where just slotting in CC-by-SA materials isn't really the right answer.

• "Today, we are able to ..." (and "over the past century", "at the beginning of this century", etc.) Two things here: "Today" and similar time-words will soon be out-of-date: which century? (the word means different things in the two instances just quoted). If you mean "By the early 21st century" then say so. Secondly, "we" is not considered encyclopedic in tone; use something like "biologists".

Defining the microbiome

• no need to repeat title "microbiome" in section headings, indeed, better not to do so.

Microbiota – members of the microbiome

• maybe not too bad a heading, but just 'Microbiota' would do, and again, it's probably better.

Microbial networks and interactions

• some terms like "copiotrophic" will not be understood by most readers (even quite a few biologists) so these need to be introduced with a brief gloss.

• The image contains very small text and has a long and complex caption. It should probably be centred and enlarged. If you can simplify (and wikilink) the caption that would be helpful. I'm not sure we actually need to discuss what nodes in network diagrams mean here - if that were important then it should be a full paragraph in the text with a separate real-example image with actual species (etc). The issue I think is that scientific papers try *very* hard to compress information both textually and visually, which is not what we should be doing, so copy-paste even when lawful is often not the right answer. When rewriting the caption, ask yourself "what does the encyclopedia reader need to take home from this?".

• The grey box attributed to Thomas Böttcher is oddly positioned and doesn't instantly relate to the rest of the section. What is it for, who's he, and how does it fit in? Is a lengthy quote what the reader needs here?

• Gone.

Assessing microbial functioning

• This section seems to be misplaced as it's not about the microbiome itself but about the investigation process. We often have an "Interaction with humans" or similar section at the end of an article, so the obvious thing to do is to move this to the end.

• "were binned without culturing the organisms behind." Reword?

• "used to compliment" -> "complement".

• I'm afraid that the "Great plate count anomaly" image doesn't work for me at all. There are nine graphic items, ending with two different kinds of microscope for no obvious reason, and two different grids, where the blue one looks like fewer microbes but apparently means 100 or 1000 times more of them... And why would one dilute water from the environment for microscopic cell counting - really? I could go on. It's very complex, it starts hares running in all directions, and the message is barely conveyed. We'll be better off without it.

• "current estimates predict ... very soon." Better say which year, or this'll be out of date in no time. Paper was 2016 so perhaps it's happened already.

• "archaeal ones are among the least." I've no idea what this means. Physically smallest, maybe? Least well described?

• "Interestingly, primer-free" - let's lose the adverb.

Plant microbiomes

• section is a bit cluttered with the large images, and even so the text embedded in the images is rather small in both cases. Perhaps it'd be best just to "center" both images, and consider making them a bit larger.

• "The diagram on the right → " isn't really ok; apart from being nonstandard (we don't refer to the physical layout of articles) it's a hostage to fortune (someone may center the image!) and it ain't gonna work on mobile devices either.

• "endophyte" is introduced in an image caption. If the term is worth using, and I guess it's used because of that one image/quoted article, then it should be introduced, wikilinked, and explained in the text (plant equivalent of animal microbiome...) so the image is properly tied into the text. "Rhizosphere" and "phyllosphere" are mentioned in the text but not explained, so again some work is needed.

Organisation

• The "Marine microbiomes" is the first place that animal microbiomes are spoken of in any detail. I suppose the sea is not a bad place to start, but coming after plants and with no equivalent "Terrestrial" section it seems a bit unbalanced. The following section "Underlying complexity" is illustrated with a picture of mice, ants, and squid, so it's more balanced; and then we have "Host-microbe coevolution" which talks of "holistic approach" but shows a human, so where are all the other animals and plants then? I think what we need is a bit of rearrangement, to have a chapter (top-level section) called "Types [of microbiome]", and it can contain Plants and Marine and presumably the missing Terrestrial and Human/Gut sections. Taking into account other comments I've made, we'll then have (your mileage may vary):

1. Lead
2. Background
   1. History
   2. Etymology
   3. Definitions
3. Membership
   1. Microbiota
   2. Networks
   3. Coevolution
4. Types
   1. Marine
   2. Terrestrial (new section)
   3. Human/gut
5. Interaction with humans
   1. Assessment (including "Underlying complexity")
   2. Implications (new section)

which I think will be easier to navigate as it reveals the article's structure. The final chapter seems also to be missing some sort of "Implications" section, covering microbiomes and human health/agriculture/surviving climate change/etc. Happy to discuss.

• Done.

Images

I seem to be making the same comment on all the images, so to avoid saying it several more times, here it is: the images are complex, with small text, long words, and elaborate captions. All that makes perfect sense in the context of a paper in Microbiome, but the mix is less good in an encyclopedia. I guess the underlying issue is audience and point of view - here we're simple folk looking down into a vast chasm of seething scientific activity; there, they're white-coated microbiomicists (or whatever they're called) looking up for an overview and a single slide, however cluttered, looks like a marvellous simplification! From the top, however, it just looks like a lot of PowerPoint and words jammed into a box. Sorry for being so direct, but there it is.

Minor comments

• Internal cross-references like "(see diagram at right)" aren't really ok as they are easily broken and don't work on mobile devices where the images are likely to be above or below the text. All instances need to be removed.

• Some of the refs have very long lists of authors. You might like to use "display-authors=" to show a subset of these.

• "Candidatus" should be in italics?

Summary

You'll see I've proposed a bit of reorganisation, some thought to be given to illustrations, a reworking of the lead, and some minor edits. When that's done we'd best read it through again to see if it all works. Chiswick Chap (talk) 12:15, 11 November 2021 (UTC)

• Chiswick Chap - I think I've addressed the remaining issues. Though I'm not sure I've adequately addressed your concerns about the diagrams. — Epipelagic (talk) 07:10, 16 November 2021 (UTC)

• I've realigned one image to look a bit tidier. It certainly seems to me an improvement, and it's great to have major articles brought to GA rather than just sharks and dinosaurs. It's a GA. Chiswick Chap (talk) 08:34, 16 November 2021 (UTC)