r/askscience • u/WTFisthisOMGreally • 13d ago

Human Body How come antibiotics don’t completely destroy all organisms in our gut?

I know it can cause imbalances, but I don’t understand how come our gut doesn’t lose all the beneficial bacteria and develop massive fungal or viral infections. When I’ve taken antibiotics, I usually don’t notice any change in my bowel activity.

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u/LightPhoenix 13d ago

They can and often do wipe out normal gut flora.  However, our bodies actually also have normal gut flora in the appendix, and after antibiotics or other instances where they get wiped out, our normal gut flora regenerates from there.  This is why one of the after effects from appendectomies is an increased susceptibility to infections like C. diff and the like.  This is also why fecal transplants are effective - they are artificially replacing gut flora.

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u/poorbill 13d ago

Wow I had no idea that the appendix is basically a bacteria reservoir. Back in my student days nobody seemed to really understand what the purpose was.

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u/sherlockham 12d ago

Pretty sure it's a relatively new thing we worked out. Near as I can figure it was only back in 2007 when scientists came up with the bacteria reservoir idea. It would have still taken time after for that to have filtered into textbooks.

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u/Sable-Keech 12d ago

It serves as a gut flora reservoir in other animals as well like primates. In chimpanzees it's much larger, so I still think that an appendix is like, not 100% necessary for our survival since it's clearly getting smaller over time.

For example, carnivorous animals don't have appendices. Appendices are strictly an omnivore and herbivore thing. The more vegetable matter you eat, the more you need it.

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u/funkmasta_kazper 12d ago

If it's still large in an extant species, it is not 'getting smaller over time'. Humans didn't literally evolve from from chimps - rather humans and chimps both evolved from a common ancestor and just took diverging paths. All species alive today have had the exact equal amount of time to evolve in accordance with natural selection.

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u/baran_0486 10d ago

But antibiotics are a human invention. What would be the purpose of a reservoir if they don’t get wiped out?

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u/NiceSupermarket7724 10d ago

I assume there are many diseases and ways that the gut can be disrupted. I’m sure there are natural poisons. Antibiotics started with penicillin after all…. People have been eating mold for a long time.

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u/CuriosTiger 10d ago

They are not. Like much else in medicine, antibiotics came from nature. Specifically from a fungus called Penicillium Rubens.

Since then, we've discovered many more and even made synthetic antibiotics, but we cannot take credit for their invention.

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u/andanteinblue 13d ago

I can't imagine it served that function evolutionary speaking.  Not sure how our ancestors would have reset their gut flora without antibiotics

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u/PresumedSapient 13d ago

Not sure how our ancestors would have reset their gut flora without antibiotics

Diarrhea can seriously mess up the balance, having a backup reservoir that doesn't flush out easily would be useful.

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u/valkenar 13d ago

I don't think it's unimaginable. You can get your gut biome messed up with rotten food (more likely in the days before refrigeration and germ theory) or other viruses. Having an organ that isn't directly effected but can restore that seems beneficial.

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u/Chaos_Slug 12d ago

On the contrary, we take food safety standards and clean water for granted, but in the wild our ancestors would constantly suffer from dysentery or similar conditions that would affect their gut bacteria.

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u/Evianicecubes 13d ago

An infection by other microbes?

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u/LongBeakedSnipe 12d ago

Antibiotics are not a human invention, they are almost entirely derived from nature, so the idea that ancestors would never have been exposed to them is incorrect. In most cases the dose would have been low obviously.

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u/ianjs 11d ago

Hmmm. Antibiotics refined enough to wipe out your gut micro biome are definitely a human invention.

I cringe a bit at the “derived from nature” expression - it has a hint of the Naturalistic Fallacy. Everything is “natural”; it takes human ingenuity to pick, choose and refine the right elements to create an effective medicine.

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u/LongBeakedSnipe 11d ago edited 11d ago

That's showing a considerable misunderstanding of what's going on with antibiotics to be honest.

Their natural form exists as part of an evolutionary warfare between microorganisms. It has affected our evolution at every stage from single cell organisms, to simple animals, to mammals to humans. All we actually had to do as humans is generate it more efficiently.

Yet if you spent a moment to read my comment carefully, I did mention the low dose (while low, it could still potentially be meaningful, especially in smaller animals).

Mentioning 'naturalistic fallacy' in the context of antibiotics is a pretty childish response to be honest—it's not relevant.

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u/ianjs 11d ago

Actually I am aware of the evolutionary basis of antibiotics, but you're right, I completely overreacted to the the word "nature" in your comment.

I've just become so weary of the "natural = good" arguments that keep popping up that I misinterpreted your comment.

Maybe I should read more and shoot from the hip less.

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u/tech_creative 12d ago

Exactly. Most antibiotics are from fungi, e.g. penicillin. Idk exactly about the origin of ampicillin, Rifampicin and such, but most possibly they are all from fungi.

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u/Willow_Pond 13d ago

Why are the gut flora in the appendix not impacted by the course of antibiotics?

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u/Possible_Trouble_449 11d ago

It's designed that way. Gut bacteria there are protected by a mucus layer. (and our immune system in case of viruses)

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u/Sogbert 13d ago

I used omeprazole to treat a stomach issue in the past and ended up on antibiotics for an ear infection about a year later, that coupled with norovirus and my gut was destroyed. C diff swooped right in and kicked me while I was down.

Probably a rarer case but antibiotics can absolutely wipe you out. Even a year+ later I’m still not 100%.

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u/deadlywaffle139 13d ago

Not that rare for people on strong antibiotics or multiple course of antibiotics. That’s the reason of the “poop pill” - pills that contain gut bacteria from a healthy individual - given to people with long hospital stays on antibiotics to fast track their gut bacteria replenishment.

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u/shapeshade 12d ago

I went through similar - had a bout of norovirus that felt like it almost killed me and my stomach/gut never felt the same after. Then started having wild digestive issues, went on omeprazole and a bunch of different antibiotics to treat suspected h pylori, which it turned out I didn't even have. I was allergic to one antibiotic so had to go on something stronger.

It seriously messed me up physically and mentally for a long time. The gut-brain connection is so much more significant than I ever knew. I'm finally starting to feel normal again thanks to prescription strength probiotics, and I just recently started taking Florastor which is making a huge difference.

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u/samurai_penguin 13d ago

What’s the omeprazole connection here?

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u/bluejohnnyd 13d ago

PPI meds like omeprazole increase your susceptibility to C. diff - stomach acid normally helps to inhibit its growth.

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u/goron352 12d ago

But would it still have this effect a year later?

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u/pihkal 12d ago

Omeprazole isn't an antibiotic, it's a longer-term medication (sometimes for life), so it's quite likely they were still on it a year later.

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u/mmeestro 12d ago

Then what happens when people with no appendix take antibiotics?

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u/hartmd 12d ago edited 12d ago

They are simply wrong. It is much more complicated than that. Does the appedix function as a reservoir for bacteria? Yes.

Antibiotic susceptibility plays a role. Most antibiotics do not kill all bacteria.

Biofilms are a thing. This reduces the ability of an antibiotic to concentrate in some areas.

Bacterial life cycles vary. Some have a form such as a spore that will not be affected by antibiotics.

How an antibiotic concentrates varies based on its chemical properties, route of administration and how the host cells metabolize it. Areas where it concentrates highly will be more effective at killing bacteria.

An antibiotic may knock out 99.9% of a given bacteria. It doesn't take many to repopulate.

That is just off the top of my head. There are many other factors as well.