Antibiotics and Gut Health: The Damaging Effect of Antibiotics on the Microbiome

Antibiotics. A necessary evil?

What else are you to do in cases of severe infection, when there are no other viable treatment options?

Untreated UTIs can become severe kidney infections, and prolonged chest infections can lead to severe pneumonia if the body fails to fight it off. While viral infections involve the body letting the illness run its course, bacterial infections often require medication to get rid of.

We know antibiotics damage the gut. But, is this damage repairable?

Let us start by saying that, yes, it is possible to at least partially restore the microbiome to its initial bacterial diversity.

However, this is not always the case, especially with prolonged antibiotic treatment, as we see in cases of Lyme disease – or more commonly, short-term repeated antibiotic therapy for UTIs, sinus infections, and ear infections.

Repeated antibiotic usage also puts women at an increased risk of recurrent UTIs that can become more difficult to treat, while triggering yeast infections from imbalance.

Antibiotics Always Alter the Gut Microbiota

Any antibiotic you take, at any concentration or duration, will impact your gut ecosystem.

There are a number of studies that reinforce the complete disruption of the gut microbiome for prolonged periods, up to 2 years after antibiotic treatment (1). Conversely, those with an increased risk for developing IBD or intestinal disorders are those who previously used antibiotics within the last 1-2 years (2).

This isn’t shocking, given the amount of people that experience C. diff infections after long antibiotic courses.

What is shocking is just how much antibiotic use completely rearranges the entire gut ecosystem. A digestive system researcher at University Hospital Vall d’Hebron (Barcelona, Spain) states that “[whenever] you take antibiotics, some bacteria disappear [and] the others overgrow…you [gain] bacteria that are [now] more resistant to antibiotics (3).”

This means any potentially pathogenic strains of bacteria residing within your gut, like certain strains of E. coli, might now not be treatable with the same antibiotics used for a completely different infection. It also means these same pathogenic strains have the ability to overgrow in the absence of protective bacteria.

Research shows that “the gut microbiota naturally enhances local defenses against enteric pathogens.” The probiotic E. coli strain Nissle was isolated in 1917 from the feces of a soldier that did not experience diarrheal sickness, unlike his comrades. It is now used as a therapeutic, and has strong activity against pathogenic bacteria. 

Can Natural Antibiotics Kill Good Gut Bacteria?

When we think about herbal medicine, we may not consider that natural “antibacterial” or “antiviral” herbs can help us to get rid of infections similarly to antibiotics like amoxicillin or azithromycin. 

We would never recommend herbal tincture or homeopathic remedies in cases of severe infection, but herbs do offer a promising alternative worth considering. Many herbal extracts, like oil of oregano, are able to eliminate antibiotic resistant strains of bacteria and difficult-to-treat biofilms (4).

The concern, then, is can these alkaloid or phenol containing plants can actually kill ‘good’ gut flora? If they kill bad bacteria, will they kill good bacteria too?

Can “natural antibiotics” like garlic, colloidal silver, goldenseal, and oil of oregano kill bacterial populations in the gut indiscriminately?

Studies recently reaffirmed that garlic extract, for example, can eliminate both pathogenic bacteria and beneficial bacteria – namely, Bifidobacterium populations (commonly found in probiotics and yogurt) (5).

However, other studies are more conflicting. 

A 2021 study showed oregano oil had the ability to reduce colonization of bacteria like E. coli, Clostridium, and Campylobacter – while still allowing the growth of probiotic strains like Bacillus and Enterococcus (6).

A study looking at male mice given 28 days of colloidal silver, at 100-400 times the effective antimicrobial concentration, found no impact on the indigenous gut microbiome or “good” bacteria in those mice (7).

Generally, we don’t have to worry about herbs nuking the intestinal system in the same way we do with antibiotics – of course, herbs may just not be as effective or suitable.

How to Help the Gut Heal

Taking probiotics after or alongside antibiotics can help to mitigate some of the damage from antibiotic use. That being said, we would recommend waiting several months after finishing up a course of antibiotics before initiating probiotic use.

This is because supplementing with a concentrated probiotic immediately after antibiotics may prevent your natural flora from replenishing from the appendix. The appendix helps to maintain homeostasis with the gut, and can repopulate populations of bacteria that have been decreased from antibiotic usage or illness (8).

The appendix, once deemed useless – actually has a fully functional role in modulating the gut microbiome.

Of course, you need to let the beneficial populations of your gut recover with healthy, whole food. This would be our primary recommendation. Both prebiotics and probiotics can help, with whole plant-food laying the foundation.

Good bacteria need plant fiber to thrive and keep the biome balanced against pathogenic bacteria. Anyone feeling nausea, upset stomach, or acid reflux upon finishing a course of antibiotics should look into probiotic and prebiotics – but should give themselves some time before they jump in.

Instead, they should ease into this transition with a lot of whole food and plant fiber (provided they can digest it). Digestion can be supported with supplements like sodium butyrate or digestive enzymes. These types of supplements ensure you’re properly digesting and absorbing your food, rather than fueling something like SIBO. They’re also extremely safe and well tolerated. 

SIBO is often simply related to an imbalance of bacteria within the gut, and can be addressed slowly through different supplements and dietary changes. 

How Long Until I’m Back to Normal?

Unfortunately, there’s no concrete timeline when it comes to your gut returning to its original state. The reality is that it may never fully heal. While we don’t say this to scare you, it is always important to understand the impact of antibiotics to ensure appropriate use of them.

The gut microbiome is more adaptable than people give it credit for outside of clinical research. Everything you eat, touch, drink, or use on a daily basis can contribute to the formation of beneficial bacteria or pathogenic bacteria, residing within the gut. 

It is important to work to restore gut health after any round of antibiotics, even if you don’t feel immediate after-effects. Not only can antibiotics predispose you to nasty C. diff infections or intestinal disorders like IBD and Ulcerative colitis, they also put you at a greater risk of developing chronic disease later in life.