How taking antibiotics at the end of pregnancy affected my vaginal microbiome — and what I did to protect my baby’s microbial start

I got bitten by my puppy.

It was my fault. I was trying to pull a chew toy out of her mouth way too deep. Because bites near joints are high-risk, I had to get preventive antibiotics and a tetanus shot.

At the time, I was 36 weeks pregnant, so my immune system was already not operating at full strength. Preventive antibiotics weren’t optional — they were the responsible choice. I was prescribed Augmentin (aka amoxicillin–clavulanate), a broad-spectrum antibiotic.

And immediately I had a few concerns:

  • What will this do to my vaginal microbiome?

  • What will this do to my gut microbiome?

  • And most importantly — what will this mean for my baby, especially if I deliver vaginally?

A mother’s microbiome matters — a lot — during vaginal birth and later during breastfeeding. Antibiotics close to delivery can affect what microbes your baby is first exposed to.

What made this situation unusual is that I already had vaginal microbiome tests on hand, since I give them to customers who want to understand how ZEROTABOOS products affect the microbiome. I used one test right before starting antibiotics, and another two days after finishing the 3-day course of amoxicillin–clavulanate. That gave me a rare, real-world before-and-after snapshot of what actually changed.

Why antibiotics late in pregnancy matter

Antibiotics taken close to delivery don’t just act in one place. They affect several connected systems at once:

  • The vaginal microbiome, which is what a baby first encounters during vaginal birth.

  • The gut microbiome, which influences immune signaling and breastmilk.

  • How many beneficial microbes actually get passed from mother to baby.


What studies show about antibiotic use and vaginal flora.

Research consistently shows that antibiotics (especially broad-spectrum like Augmentin) can shift microbial balance within days, often wiping out protective bacteria and opening the door for less helpful ones.

In longitudinal studies following antibiotic exposure, researchers often see a rapid loss of protective bacteria. Within 3–5 days, Lactobacillus commonly drops to <30%, frequently 10–20%, and sometimes single digits! At the same time, anaerobic bacteria expand aggressively. This is what researchers describe as a BV-like or collapsed profile. The result is a loss of pH control, increased inflammation, and a high risk of symptoms.

What actually happened to my vaginal microbiome (The Real Numbers)

Because I had the tests, I could see exactly how my body responded and how my vaginal suppositories protected my vaginal microbiome.

Before antibiotics (Baseline)

This was a textbook high-resilience microbiome:

  • Total Lactobacillus: 94.47%

  • Lactobacillus crispatus: 81.08%

  • Anaerobic bacteria (total): 5.53%

  • Gardnerella vaginalis: 0%

  • Ureaplasma parvum: 1.35%

  • Candida albicans: Present, asymptomatic

Two days after finishing Augmentin

The microbiome was still protective — but clearly stressed:

  • Total Lactobacillus: 78.03% (Drop of 16.44 percentage points)

  • Lactobacillus crispatus: 62.9% (Drop of 18.18 percentage points)

  • Anaerobic bacteria (total): 21.97% (Nearly 4× increase)

  • Ureaplasma parvum: 9.37% (~7× increase)

  • Gardnerella vaginalis: 6.12% (From 0% → Measurable)

  • Candida albicans: Still present, now with less bacterial competition

How this compares to women whose microbiomes collapsed in studies

This comparison matters enormously because it might seem that vaginal probiotics failed to do their job, but not until you realize how much damage antibiotics inflict typically.

In the studies:

• • Vaginal Lactobacillus is especially sensitive to antibiotics like amoxicillin. A laboratory study of 123 vaginal Lactobacillus isolates reported 100% susceptibility to beta-lactam antibiotics—confirming that amoxicillin-class drugs readily deplete them https://pubmed.ncbi.nlm.nih.gov/25894774/

• • Vaginal Lactobacillus can drop within 3–5 days of antibiotic use, while less-helpful bacteria move in
https://pmc.ncbi.nlm.nih.gov/articles/PMC7355544/

  • Lactobacillus often falls below 30%.

  • Anaerobes often exceed 60–70%.

  • Gardnerella alone can reach 30–60%.

  • The result: The system flips from protective → pathogenic.

In my case:

  • Lactobacillus stayed above 78%.

  • L. crispatus stayed above 60%.

  • Total anaerobes stayed below 22%.

  • Gardnerella stayed low (6%).

  • The result: The core structure did not flip.

So this was not a collapse. It was a partial destabilization — the kind where protective bacteria are weakened but not wiped out, and opportunistic bacteria appear but don’t dominate. That distinction is the difference between a healthy birth environment and a risky one. I attribute the preservation of my vaginal microbiome during antibiotics primarily to the use of vaginal suppositories. 

Two-part approach: vaginal + oral probiotics.

I used a two-part approach: fast local support for the birth canal, and slower systemic support for the gut and milk after I was done with antibiotics.

PART 1 — Vaginal probiotics + lactoferrin (Fast, Local Support)

When you are 36 weeks pregnant, timing is everything.

I used ZEROTABOOS Fast Probiotics with lactoferrin.WHILE taking antibiotics. I prioritized vaginal over oral for immediate results.

To understand why I needed vaginal probiotics, you have to look at the "obstacle course" oral probiotics face. Unlike a vaginal suppository that is placed exactly where it needs to be, an oral capsule has to survive a long, hazardous journey:

  1. The Acid Bath (Stomach): Stomach acid (pH ~2.0) is designed to kill bacteria. Many oral probiotics die right here.

  2. The Enzyme Gauntlet (Small Intestine): Next, they are hit with bile salts and digestive enzymes that break down cell membranes. Only the most resilient strains survive this.

  3. Colonization (The Gut): If they survive, they reach the large intestine, where they must compete for space against trillions of existing bacteria.

  4. The "Migration" (The Perineal Path): This is the part that surprises most people—the gut and vagina are not internally connected :). The bacteria must exit the body via the rectum, migrate across the skin of the perineum, and find their way into the vagina.

  5. Integration: Finally, they must attach to vaginal tissue and produce enough lactic acid to change the pH.

This whole process takes 7–10 days for the first "winners" to reach the finish line aka vagina. I didn't have that kind of time.

Vaginal probiotics skip all of that. They’re placed directly in the vagina, which means:

  • faster attachment to the tissue
  • quicker drop in vaginal pH
  • less time for harmful bacteria to take over

What they do:

  • attach directly to vaginal tissue
  • make the environment more acidic (which bad bacteria don’t like)
  • crowd out BV-associated bacteria and yeast
  • lactoferrin helps break down harmful bacterial communities and limits their access to iron

Supporting research:
https://pmc.ncbi.nlm.nih.gov/articles/PMC7355544/
https://www.frontiersin.org/articles/10.3389/frph.2023.1100029/full

Keeping L. crispatus dominant at birth is linked to:

  • lower inflammation
  • lower BV risk
  • better microbial transfer to the baby

Our vaginal probiotics come reinforced with lactoferrin. And this is another crucial component of the defense mechanism:

How lactoferrin reinforces the action of vaginal probiotics

Lactoferrin doesn’t work instead of probiotics — it works with them, and that combination matters. Lactoferrin is an iron-binding glycoprotein naturally present in healthy vaginal secretions. By tightly binding free iron, it starves pathogenic bacteria like Gardnerella and Prevotella, which rely on iron to grow and form biofilms. Lactobacillus species, on the other hand, are far less dependent on free iron, so lactoferrin selectively suppresses the “bad actors” while giving probiotics a competitive advantage.

In addition, lactoferrin has been shown to disrupt Gardnerella-dominated biofilms, which are one of the main reasons BV is hard to clear and easy to relapse. When biofilms are weakened, vaginal probiotics can attach to epithelial cells more effectively, restore low pH faster, and stabilize the ecosystem instead of just temporarily occupying space. This is why lactoferrin + vaginal Lactobacillus often performs better than probiotics alone — especially after antibiotics, when iron availability and biofilm formation tend to increase.

Supporting research:

PART 2 — Oral probiotics (Slower, Systemic Support)

These supported the gut–immune–breastmilk axis. They weren't meant to "fix" the vagina immediately, but to support the long game. If you are interested in more information about these probiotics and why I chose them in context of pregnancy and breastfeeding, check out this post for more details.

I used:

  • Lactobacillus rhamnosus GG (LGG): Helps strengthen the gut lining and increases protective antibodies in breastmilk. (Source)

  • Saccharomyces boulardii: A beneficial yeast that isn’t killed by antibiotics and helps keep Candida in check. (Source)

  • Bacillus coagulans: A hardy probiotic that supports digestion and immune balance. (Source)

Why this mattered for my baby

Because I managed to prevent a total collapse, I delivered with a still crispatus-dominant microbiome.

  • Anaerobes never took over.

  • Harmful bacteria stayed relatively low.

  • Breastfeeding support was stronger due to gut recovery.

  • Lower risk of postpartum dysbiosis (like thrush or mastitis).

Bottom line

Antibiotics late in pregnancy can absolutely destabilize the vaginal microbiome. But collapse is not inevitable.

In my case, the numbers show the difference between temporary stress and full microbial failure. By focusing on timing, diet, and local vaginal support, I was able to preserve resilience — and that difference matters for both mother and baby.

Check out our vaginal test give-away raffle if you are curious about your vaginal microbiome!


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