I’ve written a lot on this blog about the many dietary practices that can make gut dysbiosis worse. However, it’s clear from the emails I get that many people trace their gastrointestinal distress to one or more courses of antibiotics. And the reason for this is that the overwhelming majority of these drugs have broad-spectrum effects.
Now, from a certain standpoint this makes a lot of sense in that it can often be difficult for a physician to pinpoint quickly what particular type of bacteria is making their patient sick. And from the standpoint of the pharmaceutical companies producing these drugs, an antibiotic with broad-spectrum capabilities will sell far better than one that targets only one or two types of bacteria.
Unfortunately, this broad-spectrum action works equally well against our own beneficial gut flora; bacteria we all need to stay healthy and happy. Many, including myself, believe this unintended side effect of antibiotic overuse is behind an explosion in a number of chronic disorders.
Scientists are still coming to grips with just how wide and long-lasting these effects are. Today’s post covers a recently published study out of Spain that sought to assess what happens to native gut flora after a short seven-day course of antibiotics in hospitalized adult patients. (1) This study is open access so feel free to download it and read the original if you wish.
The major limitation of this study was the small number of participants in it, 21 in total. However, it echoes, with one notable exception, findings in other studies of this type.
It followed 18 men and 3 women who were admitted to hospital for various aliments ranging from bronchitis to prostatitis. None of these patients had taken antibiotics in the two months before their admission.
A variety of commonly prescribed antibiotics were given these people during their hospital stay, but I’ll spare you the details of what they were because it didn’t affect what these researchers found. To assess changes in microbial populations, stool samples were taken before treatment and on day seven. Samples were subjected to genetic sequencing analysis as well as assessment of bacterial load.
Before antibiotic use, gene sequencing identified 356 unique microbial groups or taxa with an average of 143 taxa per person. At this point, gut microbiota was dominated by phyla from predominantly gram-positive Firmicutes (65%), followed by gram-negative Bacteroidetes (28%), gram-negative Proteobacteria (5%) and gram-positive Actinobacteria at 2%.
As expected, antibiotic treatment significantly reduced bacterial diversity in all patients, with core taxa dropping to 12 from 29. However, the shift was not proportional between gram-positive Firmicutes and gram-negative Bacteroidetes.
Regardless of the antibiotic used, decline in microbial diversity was accompanied by an increase in gram-negative bacteria. While the decline in bacterial diversity dovetails nicely with what’s been observed in previous research, this increase and shift towards gram-negative bacterial groups is a novel and disturbing finding.
As all of you who’ve read this blog for any length of time know, I’ve spent a lot of my time writing about the bacterial cell-wall components of gram-negative bacteria, i.e. lipopolysaccharides (LPSs). In fact, it’s rare for me not to mention how deleterious LPSs can be when they enter systemic circulation and provoke inflammatory immune responses.
Should the results seen in this study be replicated, this shift towards a predominantly gram-negative colonic ecology raises serious concerns. As I wrote in this post:
“A study that tracked the effects of a short course of metronidazole (Flagyl) and clarithromycin (Biaxin) found disturbed effects in both commensal oral and gut communities for up to four years after treatment.”
In other words, short courses of antibiotics are more than capable of having long-term effects on our microbial partners. Nevertheless, is this disturbance in adults a cause for concern? That really depends.
Bacteria, including pathogenic ones, that remain confined to the lumen of the small or large intestine rarely, if ever, cause any problems. The same holds true for a fungus like Candida albicans.
Gram-negative Bacteroidetes exist in everyone, and they are a normal component of a healthy and diverse human microbiome. However, a shift towards a predominantly gram-negative microbial community could initiate a series of events compromising long-term health.
For example, let’s say that during or after a course of antibiotics, intestinal peristalsis or motility is slowed. Compromised peristalsis is a major risk factor for developing small intestinal bacterial overgrowth because it is those wave-like muscular motions that prevent colonic bacteria from migrating into the small intestine.
So let’s envision a scenario where concurrent with, or immediately after, antibiotic treatment a prescription is written for an opioid-based pain medication which always causes slowed gut motility. What then?
Well, we can predict that immobilizing peristalsis allows a colonic gut flora now dominated by gram-negative bacteria to enter a part of the digestive tract—the small intestine—far less capable of containing them then would be the case in the colon.
This will likely elicit a number of events—immune activation, displacement of beneficial lactobacillus organisms, increased intestinal permeability, gas and bloating, etc.—that may be experienced by the patient as irritable bowel syndrome, insomnia, mood disturbances, joint pain, skin rashes and so forth.
What if this same patient is also placed on a corticosteroid medication? This could amplify an increase in endogenous cortisol synthesis due to chronic immune activation. (2) In other words, symptoms of cortisol excess might become obvious.
As explained here, glucocorticoids typically depress immune function. This would make it that much harder to clear a gastrointestinal infection, turning what would normally be an acute small bowel infection into a refractory one. This immune suppression would also make it more likely for a fungus like C. albicans to spread resulting in oral thrush and genital rashes.
As I explained in my GERD series, small intestinal bacterial overgrowth will likely elevate the risk of developing disturbances further up the gastrointestinal tract. For example, it may cause a delay in stomach emptying that manifests as recurrent acid reflux.
If the patient is now prescribed a proton-pump inhibitor, a greater portion of swallowed bacteria taken in with food, or normally resident in the oral cavity, survives transit through the stomach. Once that occurs, the risk that other sections of the small bowel will now be colonized by pathogens grows even more.
Would it then be fair to blame the antibiotics for this series of events? Not really, but they did set the stage for what came later, at least in this case.
The period immediately following any course of antibiotics is a critical one. There is no avoiding both a decrease in beneficial bacteria nor, if the results of this study hold true, an increase in gram-negative colonic strains. We must find ways to mitigate the damage and enhance gut flora recovery.
By the way, this will be easier to do if you still have an appendix. After decades in which medicine dismissed this pouch as useless, we now know it’s anything but. The appendix serves as a very important reservoir of beneficial bacteria from which recolonization after illness or antibiotic treatment can occur. (3) If you still have one, consider yourself lucky.
At a minimum, replenishment of beneficial gram-positive lactobacillus and bifidobacteria organisms should be taken concurrently with antibiotics and continued after treatment to correct for these shifts in bacterial communities. That requires ingestion of fermented foods like yogurt or kefir, and/or probiotics. Ingesting soluble prebiotic fiber will also work towards the same goal by causing a bloom of bifidobacteria in the colon.
Nothing that I wrote today should dissuade anyone from taking antibiotics when medically necessary. Given the choice between ending up with gut dysbiosis or suffering paralysis, organ failure or death, I think most would agree that the former option is far preferable to the latter ones. No one cares about the gut flora of a corpse.
However, the key phrase here is “medical necessity.” Physicians are currently facing the prospect of untreatable infections caused by resistant strains due to antibiotic overuse. It’s a prospect that should strike fear into the hearts of us all.
But it is sheer folly to believe that this has been the only cost of abusing these powerful drugs. This study, and many others, continue to document how devastating antibiotics are to our native beneficial bacteria.
Sadly, we can’t leave it to doctors alone to curb their overuse. A recently published study in the Journal of the American Medical Association found that many physicians continue to prescribe antibiotics for acute bronchitis contrary to accepted prescribing guidelines that have been in effect for 15 years. (4) I can assure you this isn’t the only antibiotic-prescribing guideline being flaunted.
It’s been jokingly remarked that we are only the house or condo that our beneficial bacteria happen to live in. And you know what? That’s pretty much on the mark.
This internal community outnumbers our cells by a factor of 10. They carry 100-times more genetic material than was bequeathed to us by our own parents.
It should be clear to anybody who’s been reading this blog that we can’t possibly live a long and healthy life without the active help of these organisms. These are, after all, beings that have co-evolved with us through all the vicissitudes of human existence. Without them there would be no Homo Sapiens. As the slogan at the top of this blog proclaims and will continue to proclaim: “You’re only as healthy as your gut flora.”
It is therefore your responsibility to care and nurture them as they do you. That means not insisting on an antibiotic when your doctor tells you the cause of your ailment is viral or fungal in origin.
That also means questioning your doctor or dentist as to medical necessity when they do prescribe these drugs. Being told “I’m writing this just in case” shouldn’t cut it for any of my readers. It’s you and your family who have to live with the consequences of indiscriminately nuking beneficial gut flora.
“But Ray” I hear many of you exclaiming “I’m no medical expert! How should I know when to take them at their word or not?”
Good question, and one you should ask the medical professional writing the prescription. If a test comes back clearly showing a bacterial infection, well there isn’t much to question, unless the doctor suggests there is little risk in waiting to see if your immune system clears it on its own. Nor is there much to debate if you’ve just undergone surgery and want to prevent wound infections.
But what if no test is done, and you suspect it may not be necessary? Then get a second opinion or query a site like WebMD to see if your doctor or dentist is following scientifically validated prescribing guidelines.
And don’t be surprised if the answer you arrive at is unclear. There are many areas where antibiotic-prescribing guidelines are still somewhat murky, especially in prophylactic use. In those cases, you may decide it best to take an antibiotic because the cost of not doing so is worse. But at least you arrived at this decision after doing some research.
It’s time we all learn to jealously safeguard this amazing microbial community as we do our loved ones. Forsaking them through careless neglect has a potentially terrible cost, one that is ultimately borne by those doing the forsaking.