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The microbiome is the collection of "good" bacteria that reside in the human digestion tract and help digest certain foods. It is sometimes referred to as gut flora. The title "Gut fauna" is a play on words. Fauna means animal life in Latin, and flora means vegetable life. However, in this context flora means bacterial life.
In this comic, Cueball is visiting a doctor (Ponytail) for some unknown problem. The doctor informs him that his gut macrobiome is out of balance, which Cueball responds to with confusion over whether or not she meant the microbiome or macrobiome. A macrobiome, instead of being composed of small organisms such as bacteria, would be composed of larger organisms such as mammals. The phrase "gut fauna" would refer to any animals living inside a gut (as the word fauna refers to animals living in an ecosystem).
Cueball is right to be worried by the doctor's reference to his macrobiome, as normal humans shouldn't have large animals living inside them. This fear is compounded when the doctor prescribes one wolf for Cueball to swallow, which is normally impossible for humans and would, at the very least, result in major interior damage when the wolf resists being swallowed. The choice of a wolf echoes the reintroduction of the animals into the macrobiome of Yellowstone National Park in the United States, where they have improved the balance by, in part, preying on elk and reducing the damage caused by their grazing.
The dialog between the characters ends with the doctor asking the patient whether he needs a glass of water, a typical question asked by health professionals to help patient with swallowing the oral medication being administered. This last phrase further extends the humorous nature of the proposition to swallow the wolf by displaying a confidence of the doctor in her choice of the treatment modality. In reality, of course, drinking a glass of water while attempting to swallow a wolf would make the latter procedure neither easier, nor more feasible.
The title text suggests that swallowing the wolf is not the worst situation that could have occurred, as the doctor refers to "another way" that the wolf could be administered. One typical way that microbiome's are restored is through fecal bacteriotherapy, most easily described as a "poop transfer". The worse "other way" that the doctor is referring to is thus likely the rectal route, which is definitely less preferable than attempting to swallow a live wolf. Both ways, even if they were physically possible, would, however, be likely lethal. 
If we are to take the doctor at her word and there is indeed some sort of macrobiome inside Cueball's gut, then perhaps he has some kind of matter compression ability that would make introducing a live wolf a legitimate therapeutic option.
Randall has referenced wolf reintroduction programs before, in comic 819.
- Doctor: I see the problem. Your gut macrobiome is out of balance. One moment.
- Cueball: I think you mean microbiome... Right?
- Doctor: No. Here, swallow this.
- Cueball: That's a wolf.
- Doctor: Do you need a glass of water?
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I think this comic also contains a pun on macrobiotics. Esp. the wording "out of balance" seems to be a reference to esoteric speech. Knob creek (talk) 09:13, 9 January 2015 (UTC)
In fairy tales (most notably in little red riding hood), the wolf swallows whole its (human) victims. The comic depics an inversion of roles. Do you think it's worth adding this observation in the explanation? 18.104.22.168 (talk) (please sign your comments with ~~~~)
- That's what I took it to mean too, the two options being he swallows the wolf or the wolf swallows him. 22.214.171.124 12:35, 9 January 2015 (UTC)
Another pun might be on the name of a restaurant in Seattle: [How to Cook a Wolf] Araucaria (talk) 15:53, 9 January 2015 (UTC)
- That's so extremely obscure that thinking it intended is difficult. - Equinox 126.96.36.199 16:59, 9 January 2015 (UTC)
- Is a citation really needed?
I think that requiring a citation for the lethality of administering a wolf via the mouth or rectum may be going just a bit too far? Reference in the Change history Pmw57 (talk) 10:25, 9 January 2015 (UTC)
- I assume that this is a humorous comment, similar to the citation needed tags in the What-if articles. 188.8.131.52 12:04, 9 January 2015 (UTC)
- Good point, could be a joking reference to xkcd #285 184.108.40.206 (talk) (please sign your comments with ~~~~)
I know an old lady who swallowed a... 220.127.116.11 13:45, 9 January 2015 (UTC)
- https://www.youtube.com/watch?v=KiESiO6tLM8 --RenniePet (talk) 19:54, 9 January 2015 (UTC)
- The strange thing is, I am absolutely certain their is an old Chinese fairy tale but I can't google it at all! It's about a man who swallows a fly and then he has to swallow a frog and then a snake and eventually a (human) hunter. But the latter doesn't kick up a fuss so there the problem ends. What's weird is that I couldn't google that fairy tale at all.18.104.22.168 10:21, 30 March 2015 (UTC)
Is Ponytail actually a Doctor? If you take the lessone from what can be done in 699 - Trimester, and buy a labcoat... RedHillian (talk) 01:55, 10 January 2015 (UTC)
"animals are never found in the human digestive system; all known cases of animals in a human digestive system are causes of disease.)" Technically, couldn't it also be the result of one's choice of food? Admittedly a temporary state of affairs, but there are certainly dishes involving live food. Squornshellous Beta (talk) 07:55, 10 January 2015 (UTC)
- Or for pleasure? 22.214.171.124 17:35, 10 January 2015 (UTC)
- Point(s) taken. I'll make a minor change to fix Djbrasier (talk) 00:08, 12 January 2015 (UTC)
- Actually, I can't get the wording right. Happy to have someone rewrite it to include temporary residence of live organisms in the case of some foods and (apocryphal) tales of gerbilling, etc. Djbrasier (talk) 00:11, 12 January 2015 (UTC)
Poor dog. 126.96.36.199 06:25, 10 January 2015 (UTC)
I'm having a really, really hard time imagining what kind of discussion Randall was involved in that led to his thought processes ending up producing the result we see here. --RenniePet (talk) 02:58, 11 January 2015 (UTC)
- Funny nickname in this context, RenniePet. (btw. Does "inwolved" make any sense here?) 188.8.131.52 10:44, 12 January 2015 (UTC)
- ...My take is that the lycan (spelled this way: a werewolf) would probably also eat fawns (deer) - helping to balance forest overpopulation. If we take "gut" and "fawna" back through German/English, we might have "good" and "to make or be glad" another sense of fawning (perhaps alluding here to self-care, but also especially when applied to dogs). The werewolf is historically described as a shapeshifter so it seems appropriate to shift then to lichen (same pronunciation) which is a symbiotic organism (yet another thematic connection) consisting of an alga and fungus; blue-green algae is often taken to balance out the gut. A dry lichen (the etymology of this word means 'to lick', appropriate for the canine, which is also likely to be dry) will absorb many, many times its weight in water, and lichens (which are often found in forests) are important for soil (a word sometimes used to refer to fecal matter). A final connection is in a medical condition known as "guttate" (having drops, as in a glass of water) lichen"...though I might have chased this rabbit a bit far. Elvenivle (talk)
“However, either way would prove both physically impossible and potentially lethal.” ... Potentially lethal? You mean, there is actually a chance to survive swallowing a wolf? --184.108.40.206 22:42, 11 January 2015 (UTC)
According to the research of the Grimm Brothers, Randall has it all wrong. Wolves do not live in the stomach of people, people live in the stomachs of Wolves. For example, a big bad wolf might told to take two humans and call the doctor in the morning. ((Dan Loeb - 9:24pm ET, 11 January 2015))
how about "hungry like a wolf" and a reference to him missing a good appetite ? transfer of the wolf could thus mean re-vigorating his appetite.((SK - 16:01 CET, Jan 16 January 2015))
"normal humans shouldn't have large animals living inside them with the exception of some parasites such as Helminths or Cestoda" -- was that intended to mean what it says? Normal humans shouldn't have helminths or cestoda in them either! I know people can become infected with parasites, and there are anecdotes of jockeys swallowing a tapeworm egg in order to lose weight for an important race, but I would not have thought you should be recommending the practice. 220.127.116.11 22:11, 10 March 2019 (UTC)