How Long Does It Take For Good Bacteria To Restore After Antibiotics?


Antibiotics fight unfriendly bacteria that cause infections, keeping us safe from serious health complications. But these drugs have a dark side. Antibiotics can cause significant damage to the gut microbiome.

How long it takes for good bacteria to restore after antibiotics depends on factors like diet and whether or not you take a probiotic during and after antibiotic use.

The good news is that for most of us, the gut microbiome eventually recovers. But not before going through some major changes.

Phase 1: Gut bacteria under attack

Antibiotics don't distinguish between good and bad microbes. That’s why when you take an antibiotic, the amount of bacteria and the different types of bacteria in your gut —that is, the richness and diversity of your gut microbiome— decrease significantly [1]–[4].

Some species may even disappear, either for a short or long period of time [1], [2].

The drop in richness and diversity depends on different factors. For example, broad-spectrum antibiotics (e.g. ciprofloxacin, cefadroxil) target a wide range of bacteria and have a big impact. Whereas narrow-spectrum antibiotics (e.g. metronidazole, erythromycin) target only a few types of bacteria.

Another important factor is the gut microbiome itself.

As it turns out, the gut microbiome varies considerably among people [5]. Some of us are more resilient to antibiotics than others. One study found that with a 5-day course of antibiotics, most people lost around 10 species, while a few lost around 24 [1].

The good news is that this drop in bacterial numbers is not permanent for most people.

Phase 2: Resistance

When it comes to the gut microbiome, balance is key.

Almost everybody has a small amount of unfriendly bacteria in the gut. And that’s okay. Beneficial bacteria make sure that these not-so-welcome tenants don’t take up much space.

But as we saw in phase 1, antibiotics cause a major drop in the levels of gut microbes, disrupting this healthy balance [1]–[3].

During this phase, there is one specific group of microbes that takes advantage of the decrease in protective bacteria and grows unchecked for a while: drug-resistant bacteria.

Studies have shown that after antibiotics, the number of drug-resistant bacteria and the amount of antibiotic resistance genes increase [1], [2], [4], [6]. This is why our Tiny Health Gut Test looks at these genes and calculates your antibiotic resistance signature.

Your antibiotic resistance signature can help us track the long term side effects of antibiotics.

For some people, one of the unfriendly drug-resistant bacteria that may take the opportunity to grow unchecked are Clostridioides difficile. If present in your gut, these bugs can cause antibiotic-associated diarrhea [7]–[9].

Phase 3: Going back to baseline

Some weeks after an antibiotic course, beneficial bacteria start to repopulate your gut, putting unfriendly bugs in check [2].

But this can be a slow process.

And how long it takes for good bacteria to restore after antibiotics varies from person to person.

For most people, the composition of the gut microbiome returns almost completely to baseline in one to two months. But for a few, things may not go back to the way they were for quite a long period of time. Which is when we may see the long term side effects of antibiotic use.

One study found that 6 months after antibiotics, some individuals only recovered about 63% of the bacterial species they had before the antibiotic treatment [1]. In another study, friendly species such as Bifidobacterium, Coprococcus, and Eubacterium disappeared with antibiotic use. And continued to be undetected from all participants at 6 months post-treatment [2].

Scientists are still not entirely sure why each person responds to antibiotics differently. Some things to consider that may be important factors:

  • The initial composition of the gut microbiome, which varies plenty among individuals [5]
  • An adult gut microbiome with low diversity to begin with
  • A history of antibiotic use, from which the gut didn't fully recover

Is there anything you can do to help restore good bacteria after antibiotics?

Fortunately, you can help to restore good bacteria after antibiotics.

Eating the right foods can promote gut diversity, which is what we want to see. It can also boost the growth of beneficial bacteria.

To support your gut microbiome, try the following:

  • Eat more foods high in fiber and/or polyphenols, such as fruits, vegetables, nuts, legumes, and whole grains
  • Add more fermented foods to your diet. These include yogurt, kefir, sauerkraut, kombucha, and kimchi
  • Try to avoid saturated fats, artificial sweeteners, and processed meats

Can you take probiotics and antibiotics at the same time?

Yes. And in fact, doing so during and after antibiotic treatment can help protect against infection caused by the overgrowth of drug-resistant bacteria like C. difficile [10]–[12].

Lastly, you would want to track what phase of recovery you’re in after antibiotic use.

You can do this with Tiny Health microbiome testing, which:

  • Gives you the ability to detect antibiotic resistant genes
  • Helps you to gauge responsiveness to antibiotics in the future
  • Shows whether or not you still need probiotic support
  • Reveals any antibiotic signatures that are linked to an increased risk of developing eczema or allergies during pregnancy and a baby’s first year


[1] W. E. Anthony et al., “Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults,” Cell Rep., vol. 39, no. 2, p. 110649, Apr. 2022, doi: 10.1016/j.celrep.2022.110649.

[2] A. Palleja et al., “Recovery of gut microbiota of healthy adults following antibiotic exposure,” Nat. Microbiol., vol. 3, no. 11, pp. 1255–1265, Nov. 2018, doi: 10.1038/s41564-018-0257-9.

[3] J. de Gunzburg et al., “Protection of the Human Gut Microbiome From Antibiotics,” J. Infect. Dis., vol. 217, no. 4, pp. 628–636, Jan. 2018, doi: 10.1093/infdis/jix604.

[4] M. Reyman et al., “Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial,” Nat. Commun., vol. 13, no. 1, p. 893, Feb. 2022, doi: 10.1038/s41467-022-28525-z.

[5] O. Manor et al., “Health and disease markers correlate with gut microbiome composition across thousands of people,” Nat. Commun., vol. 11, no. 1, p. 5206, Oct. 2020, doi: 10.1038/s41467-020-18871-1.

[6] A. J. Gasparrini et al., “Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome,” Nat. Microbiol., vol. 4, no. 12, pp. 2285–2297, Dec. 2019, doi: 10.1038/s41564-019-0550-2.

[7] V. Stevens, G. Dumyati, L. S. Fine, S. G. Fisher, and E. van Wijngaarden, “Cumulative antibiotic exposures over time and the risk of Clostridium difficile infection,” Clin. Infect. Dis. Off. Publ. Infect. Dis. Soc. Am., vol. 53, no. 1, pp. 42–48, Jul. 2011, doi: 10.1093/cid/cir301.

[8] K. A. Brown, N. Khanafer, N. Daneman, and D. N. Fisman, “Meta-analysis of antibiotics and the risk of community-associated Clostridium difficile infection,” Antimicrob. Agents Chemother., vol. 57, no. 5, pp. 2326–2332, May 2013, doi: 10.1128/AAC.02176-12.

[9] CDC, “Most cases of C. diff occur while taking antibiotics or soon after.,” Centers for Disease Control and Prevention, Jul. 12, 2021. (accessed Jan. 20, 2022).

[10] Q. Guo, J. Z. Goldenberg, C. Humphrey, R. El Dib, and B. C. Johnston, “Probiotics for the prevention of pediatric antibiotic-associated diarrhea,” Cochrane Database Syst. Rev., vol. 4, p. CD004827, Apr. 2019, doi: 10.1002/14651858.CD004827.pub5.

[11] H. Szajewska and M. Kołodziej, “Systematic review with meta-analysis: Lactobacillus rhamnosus GG in the prevention of antibiotic-associated diarrhoea in children and adults,” Aliment. Pharmacol. Ther., vol. 42, no. 10, pp. 1149–1157, Nov. 2015, doi: 10.1111/apt.13404.

[12] C. P. Selinger, A. Bell, A. Cairns, M. Lockett, S. Sebastian, and N. Haslam, “Probiotic VSL#3 prevents antibiotic-associated diarrhoea in a double-blind, randomized, placebo-controlled clinical trial,” J. Hosp. Infect., vol. 84, no. 2, pp. 159–165, Jun. 2013, doi: 10.1016/j.jhin.2013.02.019.