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Probiotics: Quick Fix for Antibiotic Damage?

Last Updated on January 19, 2026 by Will Falconer, DVM

Probiotics: Quick Fix for Antibiotic Damage?

Sound too easy?

I get quite a spectrum of comments on this blog, from the occasional skeptic to a frustrated pet owner who’s getting disrespected by Dr. WhiteCoat, to a handful of drug-enamored folks who aren’t even waiting for the other shoe to drop as they suppress their dog’s symptoms with the latest, greatest from Big Pharma.

But this one caught my eye and got whisked into Evernote, as it’s from a doctor, and it’s dangerously optimistic in an area I have serious concerns about:

The all too common over use of antibiotics.

See what you think:

My dog had erhlichiosis (sic) confirmed on blood test. We gave her doxycycline and she regained use of paralyzed back leg. Just give probiotics and grain free diet to combat the GI effects of meds.

Beep! Beep! Beep!! (the sound of my B.S. detector going off in my head)…

Who’s Living Inside You?

Perhaps you’ve already learned about our amazing microbiome within.

You know, the bazillion and three bacteria and yeasts that live in us that affect not only our digestion and our immune response but even our mood. That whole gut-brain connection is way cool and the sort of important stuff we’re only beginning to understand.

Some recent evidence shows even obesity may be intimately linked to unhealthy gut flora.

In recent years, scientists have discovered that they (microbes) also help control how we store fat, how we balance levels of glucose in our bloodstream and how we respond to hormones that regulate our hunger. There’s even evidence that the particular mix of microbes in our bodies in large part can determine whether we’re slim or overweight 1

We know that giving antibiotics to young chickens, cows and pigs means bigger, fatter animals brought to market. But we are doing pretty much the same thing to our own young, repeatedly dosing them up against all the infections of childhood (many of which do not require antibiotics to resolve). The results of an interconnected series of experiments in Dr. Blaser’s lab, with infant mice fed a variety of antibiotic regimens, lend strong support to the theory that exposure to antibiotics early in life has long-term effects on metabolism, and may contribute to our epidemic of childhood and adult obesity.2

Oh, my. Long term effects on metabolism?

That’s the chemistry within that keeps us alive!

Hence, my concern when that comment came in on my post on Lyme disease and the common overuse of antibiotics to treat dogs with positive Lyme titers who are not sick.

Just give probiotics and a grain free diet and everything will be fixed from those antibiotics?

When it sounds so simple, my BS detector starts beeping.

My biggest concern is just how long does the effect of carpet bombing the gut flora last?

Antibiotics: Indiscriminate Killers

The good guys die off right next to the bad, and that upset in millions and billions of bacteria we depend on?

… it is the hapless bystanders who have suffered the most — not human beings, mind you, but the gazillions of benevolent, hardworking bacteria colonizing our skin and the inner linings of our gastrointestinal tracts. We need these good little creatures to survive, but even a short course of antibiotics can destroy their universe, with incalculable casualties and a devastated landscape. Sometimes neither the citizenry nor the habitat ever recovers.3

That’s a scary thought, isn’t it?

While these organisms within and upon us outnumber our own cells 10 to 1, and we keep discovering new benefits of keeping them happy and healthy…

Well, is it easy to just add probiotics to the mix and the damage will be repaired in short order?

Not so fast. Put those capsules down and back away from the food dish.

A study of adults treated with a powerful broad-spectrum antibiotic, published in Proceedings of the National Academy of Sciences in 2011, revealed that the mix of their internal microorganisms remained disturbed after the 10-month experiment and that the full consequences of this altered state remain unknown 4

Sounds like another place for thinking before “complying” with the all too common antibiotic prescription, doesn’t it?

Let’s Get Practical: What Can I DO?

1. Avoid antibiotics if at all possible

First and foremost, try to avoid antibiotics unless you have no other choice. Unless some rare, life threatening bacterial infection is happening (unlikely), you’ve got time to research alternatives.

You can, instead:

2. Feed probiotics routinely

Regular probiotics help keep your animals’ gut microbiome diverse. That’s always a preventative plus.

I like fresh green tripe for this purpose. If it doesn’t stink and have color, there are no live probiotics in it.

Texas Tripe delivers. Likely someone in your state does, too. Ask the Goog.

Capsules? Yeah, they won’t hurt. But, how much help are they? The jury’s out and it likely depends on the particular cultures and the amount fed.

Think in terms of billions per dose. And, like other things in natural feeding, change up your source periodically.

Variety mimics nature. Always good to compliment Mom Nature by imitating her doings.

3. Damage Repair: FMT

If you’ve got a suspected damaged gut (a dog with overwhelming yeast infections, who smells like a walking bag of Fritos and can’t stop scratching comes to mind), you might consider finding a holistic vet and some healthy dog poop.

Wait. What??

Yes, I’m suggesting FMT, a fecal microbiota transplant. Into the rectum of the sick dog goes a slurry of good guy flora from that healthy dog’s poop.

Some of my colleagues are doing these “transplants” with good success.

Look up Dr. Margo Roman to get started if you’re out East. Find more holistic vets on the AHVMA list on my Resource page. Ask if they’d do this for you. Dr. Roman has a page showing exactly how they can do it.

See the Value, Act Accordingly

Bottom line, we tend to cherish something more when we discover its true value.

We have plenty of info available now to let us honor and respect and care for our gut flora. They truly are important and not to be taken for granted.

It’d be a mistake to play fast and loose with antibiotics and imagine you’d quickly fix any side effects in the gut microbiome by popping some probiotics in.

I’ll end with a quote from those who’ve assessing dysbiosis (the out of balance microbiome) far longer than I:

The functional claim for correcting dysbiosis is poorly supported for most probiotic strains and requires further research.5

We need to know more. Where have I heard that before?

Let us know in the comments if you’ve seen antibiotics set off problems or, better yet, if you’ve seen probiotics or a fecal transplant make a difference.

We’re all ears.

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