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Stomach issues + metabolism shift years after taking antibiotics - any insight or solutions?

mhealth2 profile image

I've been having stomach issues since late 2017, when I was put on two rounds of back-to-back antibiotics: Augmentin and then Clindamycin. Since then, I have had stomach issues including: going to the bathroom more often, feeling pressure when having to go to the bathroom, occasional mucus in stool, and more recently, bouts of nausea, bloating/cramping, and very smelly gas. Also, it seems my metabolism has shifted after the antibiotics and I gained weight faster than I ever have, and I am still struggling to keep my weight down after making significant diet and lifestyle changes.

Any insight here into the weight gain and/or anything else I could try for the stomach symptoms? I've tried various probiotics and rifaximin. Thank you!

11 Replies

I found this article that may indicate a link between antibiotics and weight gain:

I think this is also down to individual reaction and bodily makeup. For instance since I was on antibiotics last year I'd found it difficult to gain weight. Gut microbes are required to assimilate food and turn it into energy. In my case I believe the reduced ability to gain weight was due to a reduction in the number of microbes.

The article above describes a potential change in enzyme activity leading to weight gain from antibiotic use. One of the overarching points seems to be a potential reduction in bacterial diversity from antibiotics. Bacterial diversity can be achieved by eating a wide variety of foods. I saw one article which stated that if you consume 30 different foods across food groups (carbs, proteins, fruit, veg) concentrating on fruits and vegetables with an array of different colours within 1 week, over time you would have an extremely diverse microbiome. I have seen lots of TV programs about people who've found it difficult to lose weight, were put on a diverse diet plus an exercise regime and found it much easier to lose weight. I've seen in many places the best diet for the microbiome is the Mediterranean diet (pulses, nuts, fruits, vegetables, olive oil, whole grains, oily fish and lean protein such as chicken with protein leaning more towards plant based foods).

The rub with all of the above is that people with IBS can be intolerant to a wide range of foods making gut microbe diversity a challenge which is going to be counterproductive. One potential reason is that in people with IBS there may be an imbalance of gut bacteria - perhaps a bit of overgrowth of bad bugs - this can be the result of antibiotic use or for other reasons such as poor diet or even stress. These bad bugs can produce symptoms such as gas, bloating and disturbed bowel movements. This is a potential reason why the FODMAP diet works for some people with IBS. Some FODMAPs aren't absorbed very well in some people, their waste goes to the colon and the bugs (including bad ones) have a party feeding off of them causing issues.

You say you've previously taken probiotics. I used to take lactobacillus acidopilus & rhamnosus - this helped a bit with my IBS, but I have been doing much better on Alflorex (Bifidobacterium infantis 35624) which has been scientifically studied for IBS - other people do well on Symprove, so it might depend on what probiotics you've taken and whether the specific strains will help your symptoms. I have found that since being on Alflorex I can tolerate far more foods. Eating a greater variety of foods will in turn help to increase microbiome diversity which will have the compounding effect of helping my gut and overall health in the long term. For instance good bacteria can help to reduce inflammation in the gut and help to maintain mucusal barrier of intestinal walls. Once symptoms are under control prebiotics could be considered to help good bacteria to multiply - although when symptomatic they could potentially make symptoms worse. I have only been able to increase my diet very gradually by eating very small amounts to start off with and increasing the amount over time or cutting back and staying on an amount for longer, whilst keeping other aspects of my diet the same and recording symptoms. This allows microbes to proliferate and adapt to what I am eating.

Lastly it's probably best to get a formal diagnosis for your symptoms. You could be diagnosed with IBS by eliminating other issues. Even in lockdown you can be sent a stool sample kit by post from your GP, kick it to one side for 72 hours and then leave it outside your GP surgery for the receptionist to pick up. Once you know what you are dealing with, you should be able to move forward.

mhealth2 profile image
mhealth2 in reply to xjrs

Thank you so much for this detailed reply! Very much appreciate it. I will take a look at that article and see what else I can GI did diagnose me with IBS after discussing symptoms and reviewing previous bloodwork, but I haven't done the stool sample yet. They also said they often don't even run the stool sample if it is solid stool, so not sure how that would work. Thanks again for taking the time to detail all this info!

Hello I don’t know whether this will help at all but I have the IBS for dummies book and it says to avoid all antibiotics where you can , obviously if you need them then take them but it says to avoid taking them for a long time.

The reason to avoid is because the antibiotics kill off the good bacteria which causes the intestines to become thin, vulnerable and easily penetrated which means some nasty new bacteria/organisms can move into the bowel. This may be why you are now experiencing all of your IBS symptoms.

It says when taking antibiotics you need to take other supplements to counter act what the antibiotics are doing to your body. Supplements such as probiotics which are found in some yogurts and has to contain lactobacillus acidophilus and or bifidobacteria.

Moving away from the science and from my personal experience , I really wanted to loose weight and I joined a weight loss group called ‘slimming world” which do cater for IBS sufferers. I live in the UK and I don’t know if it is available world wide but it would definitely be worth a look. I’ve lost nearly 2 stones in 4 months which I never thought would be possible due to my IBS !

I’m always happy to have a chat anytime if you need it.

mhealth2 profile image
mhealth2 in reply to Bethers2000

Thank you so much - I will look into it!

Yes, I have started to believe that my IBS started after I was prescribed two rounds of back-to-back antibiotics by my dentist, due to gum infections which turned out to be caused by parathyroid problems and not by poor dental hygiene as my dentist thought! I know this because since I had my last parathyroid gland removed in May last year and have been prescribed a weekly, high-dose tablet of Vitamin D3, my gums have been very healthy indeed :-)

But sadly, I am still left with painful IBS, which seems likely to affect me for the rest of my life :-(

mhealth2 profile image
mhealth2 in reply to oldfog

Oh my goodness...yes, I'm in a very similar boat. Hard to believe antibiotics can do so much long-term damage. Sent you a private message!

I had two massive doses of antibiotics to keep me alive around 6 years ago. Two things were accomplished, I'm still alive and I had no good enzymes left in the gut. In the early days one cup of tea would cause a war in the gut within seconds of drinking it. What I have learnt is that firstly it is not easy to repopulate the gut with "good" enzymes and if you do it wrong it only makes the yeast (bad) enzymes that are left more active, exasperating the problem.

After the first does of antibiotics I almost succeeded in repopulating the gut with the good stuff. How I did this was to do a week long fast to weaken the yeast, then took a prebiotic and a probiotic. Make sure that the probiotic you use is alive as most are dead when you buy them through incorrect transport and storage. Most require refrigeration, find one that doesn't and you should be good. Onion happens to be a prebiotic which is what I used.

Had really good success and was able to eat bland foods and was improving. Then a second dose of antibiotics destroyed all the hard work. After trying to repopulate the gut for the second time I gave up unable to get it to work. However I have been able to eat this time around but have now been diagnosed with health issues that preclude some of my regular foods.

Where I'm at now is I don't take salt, sugar, red meat and any spice of herbs. I drink only water and cups of tea, white.

Never any soft drink or soda, definitely not any diet drinks as the sugar substitute also kills kidneys for CKD people. In the case of coke or pepsi the colouring eats your calcium from the bones as it can not be processed through CKD kidneys, the recommended amount of these with 100% functioning kidneys is one small to medium glass per day!

I have to limit the amount of food at the one meal a day I have, as the gut can't process too much food or fluid at one time.

One litre of fluid takes around 5 hours to get to being able to consume anything further. I tend to sip at drinks all day and usually get through around a litre per day. I have a wholemeal bread sandwich with margarine and marmite or sardines on. Either filling is high energy food and slow release so there is not sugar hit for the diabetes I have. Fast food is but a distant memory as are restaurant meals. Basically I eat to survive, I don't enjoy what I eat and some I would prefer not to eat, but the will to survive is stronger than the desire to choose what I eat. I never use processed foods, all fresh and home made.

My dietitian tells me I'm only eating 60% of my daily requirements which is why I have early muscle depletion. It has taken a long time to sort a diet I can get by on and I stick to it religiously for fear of going backwards again. I take Omeprazole sparingly as it kills kidneys for CKD people, 1 on average per month, just as and when required, also not good for kidneys. I get reflux when I'm not careful.

I often wonder if I should have refused the antibiotics in the first place, while I don't have a bad life I honestly can't say it is particularly enjoyable one either. I have taught myself to not crave food and resist it all until the first taste crosses the lips. A bar of chocolate has no chance in the next hour!

My wife tells me I must be fine today because I have been cursing and causing trouble for everyone. When I'm quiet it is a bad day for me, brilliant for others though! I have good days and bad days but the way through has been to keep active doing something to divert the mind from my reality of my health problems. It is interesting that If I do mental work my weight drops quicker than the physical work of pottering around in the workshop. At the end of the day we each have to find our own pathway through or with IBS.

IBS is a catch all term for intestinal problems with no name, hence we each need a different approach to suit ourselves. I found using others ideas a guide to finding my way, not a cure for my IBS.

Apparently I look healthy, even in the mirror I have to agree, so I now tell people I have ducks disease. You know, calm on the water, paddling like hell underneath! Unless you have go it, there is no appreciation of the problems it can cause.

Thanks to who ever set up these forums.

Wow, thanks for sharing your story. So sorry to hear all of's astounding to see the effect that antibiotics can have on our gut/stomach. Glad to hear the medicine saved you, but awful to hear about the adverse effects. :/

At least I know it is possible to recover from a complete good enzyme destruction, if not fully, then enough to get on with life. There are also such things as faecal transfer which works very well. Sadly very expensive here. There is a DIY method but the trick is to be very sure you are not introducing other nasties from the person giving the donations, and it is not an easy process, unlike the professional method.

I have not heard of anyone else having had the same degree of destruction of their gut that I have been through. I have issues with any orally taken medicines now as well, the gut is very sensitive to them, doesn't like them and lets me know without doubt.

The main focus is that I'm alive today, deal with it and don't worry too much about tomorrow.

I have gone from being bloated to extremes that there was no more stretch in the skin and I couldn't bend at the waist, I can empathise with pregnancy, to being able to control flare ups quickly without a lot of discomfort. I was told I would have to live with it by an insensitive moron chief of Gastrology. No way, it is possible to make a changes it just takes time and determination.

Occasionally I break the diet and brother is it good, but then I have to pay the price for the next few days of my rash decision, but it still tasted good!

I guess my message to anyone with health issues is understand your circumstances and deal with it anyway you can. Don't roll over and take it, the brain is a powerful tool, motivate it and fight for something better.

Hi Friends!!

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Do you feel better now? I think i also got the very bad side effect after using augmentin. Got diarrhea for more than a week, it got better for couple of days then it came back again after eating ice cream, cookies and chocolates. Not sure if this is the antibiotics but now had to go to colonoscopy and endoscopy

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