Field of Science

Antibiotics and gut bacteria

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All microbiologists end up writing about gut bacteria at some point. It is the way of things. Disease of the Week is currently doing a whole series on it, and a few weeks ago I covered the interaction of the immune system with gut bacteria (here). However a recent paper came out in Microbiology Today concerning the affect of antibiotics on gut bacteria, which is a topic that I both find interesting and have had some actual experience with.

I've taken antibiotics a few times, and each time I've found that despite the many positive effects it has (i.e I don't die of septicaemia) being on antibiotics tends to make my stomach fairly unhappy. I usually have a good relationship with my stomach - I feed it regularly with plenty of food and in turn it is generally quite accepting of the fact that I don't always wash my hands as much as I should, and occasionally eat things that might be past their sell-by date, or heated up food that isn't exactly the "piping hot" recommended by the label.

Antibiotics however are usually designed to kill off bacteria, and unless the antibiotic in question is very specific that often includes your commensal gut bacteria; the 'friendly' bacteria that yoghurt companies keep mentioning, that hangs around in your gut and prevents other bacteria invading. In the short term this leads too the occasional unhappy stomach but in the long term it can have a more sinister effect, by encouraging antibiotic resistance genes to develop and spread amongst the normal bacteria in your gut.

The diagram below shows a stylised (and not to scale) diagram of what happens to your gut bacteria after a dose of antibiotics. The antibiotic resistant bacteria (in purple) are suddenly at an advantage and can proliferate. As time goes by, the other natural bacteria gradually return to your gut (which is not after all the most sterile of environments) but there will be a higher concentration of antibiotic-resistant bacteria around.

Diagram taken from the reference (below)

It's important to remember that these antibiotic-bacteria are not dangerous in themselves. Unless they move out of the gut for any reason they will remain totally harmless. However they also contain the genes for antibiotic resistance, and if another bacteria manages to survive and get into the gut, they can pass those genes on. As every human carries different gut bacteria, and will take different antibiotics in the course of their lifetime, this study cannot really make any hard and fast rules about what the effect of this might be on any one individual, but it does make the point that many people will be carrying within them a large proportion of bacteria that may have developed a novel form of antibiotic resistance.

It's not always terrible, in some cases the antibiotic resistant bacteria are grossly unfit, and are immediately out-competed as soon as the antibiotic goes away. Those that do survive both the antibiotic and the returning bacteria however, can hang around for a long time, and antibiotic resistance was seen in gut bacteria up to four years after antibiotic treatment had finished. And the intestines are such a wonderful environment for bacteria to share DNA in; there are abundant nutrients, everything is all moist and warm and there are a lot of bacteria in very close contact with each other.

If you have taken antibiotics it's not worth loosing sleep over, but it's something hospitals are starting to be more and more aware of.


Jernberg C, Löfmark S, Edlund C, & Jansson JK (2010). Long-term impacts of antibiotic exposure on the human intestinal microbiota. Microbiology (Reading, England), 156 (Pt 11), 3216-23 PMID: 20705661


Kevin said...

Great post. I think the interaction between commensal flora and human health is probably one of the areas most ripe for amazing discovery.

Anonymous said...

One of the things I was always told by Dr.'s to do during antibiotics was to eat yoghurt to restore the 'good' bacteria. Turns out there's no research to support that but I wonder if the bacteria passing through could provide enough competition to have any effect on the population explosion of antibiotic resistant populations?
Also thanks for linking to us :)

Lab Rat said...

@Kevin: the whole field of bacterial ecosystems is one I find really fascinating, especially when they are in environments such as the stomach, living very close with eukaryotic cells.

@Disease: Oh man, the few times I was on antibiotics I remember heading down to the coop and loading up on yoghurt, yakhult and cranberry juice (to help clear the infection rather than deal with the antibiotics). Any benefit I got was probably more placebo effect than anything, as the evidence for whether ingesting 'good' bacteria help is sketchy at best. They can show that live bacteria come out again, but it's still a mystery as to what, if anything, they do while they're in your stomach.

hat_eater said...

I don't know about youghurt - I heard that live bacteria are unlikely to survive the passage through stomach, despite claims to the contrary by Danone - but I always take the probiotics while on antibiotics and had no problems that are usually associated with gut flora deficiency (diarrhoea). That's of course anecdotal evidence, but surprisingly, Cochrane reviews offer not much more:

Lab Rat said...

@Hat_eater: many of the bacteria in natural (i.e 'live') yoghurt is the same bacteria that is found in the industrial produced probiotics. That's where they get the idea from. if anything *does* survive and benefit (and as you point out the evidence for that is pretty uncertain, thanks for the link to the Cochrane review) the bacteria in yoghurt is one of the more likely things to make it.

hat_eater said...

Ah, but the bacteria in probiotics sold at the pharmacy are protected by the pill shell that doesn't dissolve in acidic environment of the stomach, but only after it passes to the duodenum. The live bacteria in yoghurt have to face the pH=1 environment of the stomach... and I'd pity them if I were more compassionate towards microflora. :)

Second Foundation said...

I've long wanted to push a discipline of "Bio-medical ecology". The antibiotic resistance - as carried on very quickly transferred plasmids between seemingly shamelessly promiscuous bacteria - is a good example of why.
In a hospital situation it is clear that selection pressure for the plasmids and whichever bacteria are carrying them is intense. Thus there can be fast spread of resistant infections and, also, hospitals so easily act as "sumps" for resistance plasmids/bacteria.
Anyone for biomedicalecology?

Lucas Brouwers said...

That's a wonderful diagram!

I've never taken antibiotics myself, but after reading your post, I have a newfound respect for my gut bacteria. Surviving and thriving on student eating/drinking habits? Wow! They really must be hardy little fellows ;).