Antibiotics During Pregnancy & Lactation

by Kristin Dahl 12 min read

Antibiotics During Pregnancy & Lactation

Antibiotics are notoriously over-prescribed, especially in the U.S., where hundreds of millions of prescriptions are doled out annually. Antibiotics are often prescribed for things they cannot treat, such as viral pneumonia (antibiotics can only cure bacterial infections, not viral), and for acute respiratory conditions that could be cured by other means. Taking antibiotics should only be done as absolutely necessary - to kill serious bacterial infections that cannot be treated naturally and that are a true threat to health. And while, when needed, antibiotics do more good than harm, they should truly be viewed as a last resort and avoided as much as possible.

Why? The truth is that the risks of antibiotic use often outweigh the benefits. Antibiotics indiscriminately wipe out much of the bacteria in our delicate microbiomes - not only the “bad” bacteria they’re targeting, but also much of the “good” bacteria that make up the mini-ecosystems that live within each one of us. Our relationship with these bacteria is synergistic, meaning that we benefit from their existence as much as they benefit from having us as a host. Our microbiomes play an important role in our health: they assist with digestion, regulate our immune systems, and even produce certain vitamins. During pregnancy and while breastfeeding, these roles become even more important because mothers pass on their bacteria (or flora) to their new babies, which is the crucial first step in the development of the baby’s immune system.

We’ll explore the role of the microbiome in human health in further detail below, as well as how antibiotics work and their effects on the body. We’ll also discuss natural antibiotic treatments including many herbal remedies that can be used to combat many bacterial infections, and the importance of tuning into your own inner guidance system when it comes to making decisions about antibiotic use. We’ll also look at ways that antibiotics can be used responsibly, when needed, while also making sure to protect and nourish our delicate digestive tracts and our friendly bacteria who reside there.


Your microbiome is the diverse ecosystem of all the bacteria living in and on your body. These bacteria mainly inhabit the gut (i.e. the digestive tract) and mucous membranes (nose, mouth, eyes, vagina, etc.) as well as the skin, and consist of both good and bad bacteria. The balance is essential and we naturally want it to veer more on the side of the good bacteria. These beneficial bacteria are responsible for supporting our health by helping us to digest food, extract and absorb nutrients from our food, balance blood sugar levels, regulate the immune system, modulate energy balance and metabolism, and even balance emotions due to the gut’s direct connection with the brain. Bacteria are also responsible for making certain nutrients that we need, including B vitamins, vitamin K, and short chain fatty acids.

The problem with antibiotics is that they don’t distinguish the good from the bad bacteria - they blindly wipe out all the bacteria in our microbiomes. An imbalance of good to bad bacteria results in a condition called dysbiosis, wherein the colonies of bacteria are imbalanced and unwanted bacteria take over. This can cause digestive issues (such as diarrhea, constipation, excessive gas, heartburn, or nausea), bloating, bad breath, rashes or other skin irritations, fatigue, anxiety, depression, and more.

Dysbiosis can also have a direct impact on growing babies. Babies get their first inoculation of gut flora from the mother's birth canal during childbirth, which is why a mother's use of antibiotics during pregnancy can predispose the child to asthma, allergies, social problems, obesity, and other issues. If a mother's microbiome is abnormal, her baby's microbiome will also be abnormal.

It’s also important to note that antibiotic use creates a vicious cycle. Every time we use antibiotics, pathogenic bacteria look for ways to adapt to them, eventually turning into resistant bacteria which now have the opportunity to grow and thrive, getting free run of your body where they can multiply and pass their resistance on to other bacteria that make your body their home. This leads to even more resistance and possible “superbugs” that don’t respond to antibiotics at all.

We can mitigate antibiotic resistance and the effects of antibiotics on our health by taking care of our microbiome. Supporting healthy gut flora is absolutely essential. When our bodies lack diversity in friendly gut flora, we become much more vulnerable to a whole range of diseases and complications. More on this below!


Before you fill an antibiotic prescription (which, as mentioned above, are often prescribed unnecessarily), you’ll want to ensure it’s a necessity before subjecting your (and your baby’s) fragile microbiome to any drug’s damaging effects. If the antibiotics are absolutely necessary, then yes please do what is best for your health and get that prescription!

In the world of western medicine, many of us have become passive patients rather than active participants in our own health and wellbeing. While we should trust the knowledge of doctors, we need to ask questions and advocate for our ourselves so that we are making decisions together with our health practitioners.

As women and especially as mothers, we must look within and follow our own instincts - especially during pregnancy and lactation. Knowing that our microbiomes have such an essential role in our overall health, and that the gut flora diversity of our babies will set them up for a life of health and wellbeing, we must tread carefully at this delicate time and make wise decisions that best support us.


It’s also prudent to note that steps can be taken to support the immune system in order to avoid infection or sickness in the first place. Prevention is vital, especially for new mothers who cannot waste time and energy being out of sorts, and for whom having a healthy microbiome is essential in order to pass it along to their new babe. When illness or infection does occur, there are also helpful antimicrobial herbs, supplements, and pantry staples that we can turn to before resorting to antibiotics.

Antimicrobial Herbs + Natural Antibiotics

Herbal antimicrobials are often used in place of antibiotics during pregnancy and lactation, or anytime a more natural approach is preferred. Other natural remedies can also be used to support the immune system and to counteract bacterial infections. Try some of the following:

  1. Garlic is a safe antibiotic alternative. It has potent antiviral, antibiotic, and antiseptic properties. Add it to meals & broths, or cut a raw clove into small pieces and consume it with a tsp of honey for a powerful punch.
  2. Ginger is helpful for clearing bacteria and viruses. Make a simple tea by blending raw ginger root with boiling water (make sure your blender has a vent & start on very low speed to prevent explosions!), straining, and adding a touch of lemon.
  3. Dandelion is great for liver cleansing. It can be taken as an infusion as needed.
  4. Cod liver oil can be taken daily for prenatal health + preventative care. It’s a great source of omega 3 fatty acids (EPA and DHA) as well as the antioxidants vitamin A and vitamin D, all of which help to fight inflammation and boost immunity.
  5. Echinacea acts as a surface immune tonic. It should be taken as a tea or tincture at the first signs of sickness.
  6. Cayenne powder has antimicrobial, analgesic (pain-relieving), and expectorant (helping to clear mucus from the respiratory tract) properties. Add it to meals & ginger tea.
  7. Elderberry syrup is a powerful immune booster filled with antioxidants that’s also effective at battling colds and flus. Making your own is best or purchase a local source blended with honey. Recipe below.
  8. Lemon is antibacterial & helps to alkalize the body. It’s also rich in vitamin C, which is a  potent antioxidant. Add freshly-squeezed lemon juice to hot water and sip it throughout the day.
  9. Apple cider vinegar helps to kill viruses. Mix 1-2 tbsps of ACV into water or tea and drink 3 times a day. You can also gargle ACV to soothe a sore throat. Used in a bath, ACV can reduce fever.
  10. Coconut oil is antiviral & antimicrobial. Add it to daily meals or tonics, or take it by the teaspoon-full throughout the day when you’re feeling unwell. You can also mix coconut oil with honey & cinnamon for a delicious combo with increased benefits.
  11. Honey is antibacterial, antimicrobial, and antiseptic, especially raw local honey. Manuka honey is a powerful immune stimulator. Take 1 tsp daily and add to ginger tea. 
  12. Cinnamon has antiviral and antibiotic properties. It can be taken as a tea, used in whole form, or added to meals. Ceylon cinnamon is the best form to purchase.
  13. Thyme is antimicrobial, antibacterial, antiviral, an expectorant, and has astringent properties (meaning that it helps to tone and tighten tissue, which promotes wound healing, tones the digestive tract, and supports mucus membranes in the throat). It’s great for respiratory infections. Mix thyme into meals or steep it with hot water, lemon, and honey for a herbal tea.
  14. Turmeric has anti-inflammatory properties and contains a compound called curcumin that’s effective at fighting certain bacterial strains, such as Helicobacter pylori. Turmeric can be cooked with or added to smoothies or tonics. Take extracts of 400-600 mg throughout the day, 3 times daily, for maximum effect.
  15. Nettle is a great source of vitamin C and rich in minerals. Drink daily as an infusion.
  16. Herbal or bone broths, whether homemade or store-bought, have incredible healing properties and contain nutrients that help boost immunity and heal the gut lining. Broths are rich in minerals and contain gelatin, which helps to soothe the intestinal tract.

DIY Elderberry syrup


  • 1 cup dried black elderberries 
  • 4 cups of water
  • 2 Tablespoons fresh or dried ginger root (fresh is best!)
  • 1 teaspoon ceylon cinnamon powder
  • 1/2 teaspoon cloves
  • 1 cup raw honey 


  1. Add all ingredients (with the exception of honey) to a saucepan.Bring to a boil, then reduce to a simmer for 45 mins-1hr.
  2. Remove from heat, let cool & then mash the berries to extract as much juice as possible.
  3. Strain, then add honey and fully combine/mix in a mason jar.

1 tbsp for adults 1 tsp for kids - 1/4th tsp for babies/toddlers. When sick - use every few hours until symptoms subside & then occasionally/as needed. 


These immune-boosting supplements can be taken to prevent sickness and also to support the body when illness occurs.

Plant-based prenatal vitamins should be taken daily to support both mama & babe.

Probiotics are also great to take daily, as they provide a boost to our microbiomes by supplying healthy bacteria. They’re an important component in maintaining and supporting the long-term health of the immune system. Visit a quality health food store or your health care practitioner for advice in selecting the best one for you.

Vitamin C is a powerful antioxidant. Take 1,000- 2,000 mg daily when you need an immune boost, in divided doses throughout the day. The liposomal form is best.

Vitamin D3 provides benefits to the microbiome, including maintaining the homeostasis of the gut lining and preserving the tight junctions of the intestinal tract (which, when compromised, lead to leaky gut). Lying out in the sun with most of your skin exposed is a great way to boost your vitamin D production and to lift your mood. Most people in the northern hemisphere are vitamin D-deficient, though, so supplementation is wise as well. Most people benefit from about 2,000 to 5,000 IU/day. Off & on. *Continuous supplementation can lead to overdose.

Zinc is critical for proper immune system functioning, and is a common deficiency in North Americans. It can be supplemented in homeopathic lozenges for relief of acute conditions such as colds and flus.

Medicinal mushrooms (such as chaga, maitake, shiitake, and reishi) have antibacterial and antiviral properties, and are powerful immune modulators. Chaga tea can be taken throughout pregnancy to keep immunity strong. The others can be taken at lower doses, as needed.

Adaptogenic herbs (such as ashwagandha, and Holy Basil) are also helpful to supplement with as they modulate the body’s response to stress and enhance immune functioning. The ones listed here are safe to use during pregnancy, but not all adaptogenic herbs are - so make sure to consult your health care practitioner if you’re wondering about other varieties. Holy basil is best in tea form and ashwagandha in tincture or powder both can be taken as needed throughout pregnancy.


Many microbial depleters in the environment can be consciously avoided. For example, it’s important to stay away from antibacterial cleansers and antimicrobial personal care products as they can further damage your and your baby’s microbiomes. In addition, being active, keeping your stress levels in check, and spending plenty of times outdoors will all help you to create a gut environment that’s conducive to a healthy bacterial population, giving you vibrant overall health and a strong immune system that can fend off sicknesses.

Breastfeeding vs. Formula Feeding
Don’t be too quick to wean off breast milk and introduce formula or solid food. Colonization and proliferation of an infant’s microbiota can be distressed when exclusive human-milk feeding is stopped. Formula, especially incorporated into the diet while breastfeeding, can undesirably alter the structure of baby’s gut. Feed as long as possible or until your baby is ready to self-wean.

Keep Stress Levels in Check
Stress prevents healing. It causes inflammation within the body, which can directly impact our gut flora. Whether taking antibiotics or attempting to prevent illness, make sure to get plenty of rest. Antibiotics have the incredible ability to make us feel well very quickly, but there is still a lot going on in the body, so be sure to rest as much as you can. Meditation, deep sleep, and essential oils can all help to lower cortisol levels, which will provide your body the peace it needs to repair. If you’ve fallen ill in the first place, this is often the body’s way of telling us it needs a break. Give your body the rest and support it needs to recover.

Circulation + Regular Exercise
Regular physical activity gets blood pumping, improves circulation in the body, and increases oxygen uptake. This has been shown to have a beneficial effect on gut flora by increasing the number of beneficial microbial species. Getting daily exercise is therefore an effective way to support your microbiome, along with the many other benefits of regular movement. Incorporate a regular activity that you enjoy - whether it’s walking, hiking, cycling, or doing some yoga. As long as it gets your heart rate up, it will be beneficial in preventing sickness and supporting your immune system.


If it is, for whatever reason, necessary for you to take an antibiotic during pregnancy or while breastfeeding, there are ways that the body can be supported and the damaging effects minimized. From probiotic supplementation to making sure to get enough prebiotics and other nutritional recommendations, all of the following matters when it comes to supporting your overall health.


Ideally, you’ll already be taking a high-quality probiotic before you became pregnant or when you began taking your prenatal multi. If you aren’t, it’s never too late to start. Probiotics of at least 50 billion CFU and 10 different strains should be taken alongside antibiotics to mitigate their negative effects on the microbiome.

The specific strain Saccharomyces boulardii can help with antibiotic recovery. It’s a yeast rather than a bacteria, so it’s particularly useful during antibiotic treatment because the antibiotics can’t kill it. S. boulardii is also preferable under these circumstances because there’s no risk of it harboring genes for antibiotic resistance and later transferring those genes to pathogenic bacteria.

It’s essential to continue taking probiotics daily even after you’re finished your antibiotic course, as it can take an entire year to bring your microbiome back to a state of balance! Keep taking your probiotics for at least one month after antibiotic use, or for up to a year - or indefinitely - for best results.

Nutritional Support

Along with taking a probiotic supplement, probiotic-rich foods should be consumed in greater abundance to further strengthen the microbiome. These foods include apple cider vinegar, cultured dairy products (amasai, kefir, goat milk yogurt, and cultured probiotic yogurt made from raw cow’s milk), fermented vegetables (sauerkraut, kimchi, and kvass), and probiotic beverages (kombucha, terrain herbals, and coconut kefir). It’s best to consume a variety of these probiotic-rich foods (rather than just one source) to increase the variety of beneficial bacteria being introduced to your system. Rotate them daily.

Avoid foods that interfere with antibiotics and lesson their effectiveness. Foods that are known to dilute the potency of antibiotics include citrus fruits (especially grapefruit), dairy, sugar, gluten-containing foods, and high-acid foods like chocolate and tomatoes.

While taking antibiotics, it’s especially important to choose organic and antibiotic-free meat, dairy, fish, and eggs whenever possible.

Focus on: eating plenty of fruits, vegetables, legumes, and whole grains (provided you have no intolerances).

Foods high in selenium can be beneficial to consume in higher quantities while taking antibiotics, as selenium is a powerful antioxidant that is involved in the immune system’s response. Brazil nuts and seafood are great sources of selenium.

Adequate water intake is also very important as hydration supports overall health and immunity. Investing in a high-quality water filter to filter out undesirable contaminants is very worth it. Tap water contains chlorine as well as other harmful additives such as fluoride, lead, aluminum, and other chemicals, all of which are highly damaging to gut flora.


Prebiotics are indigestible (soluble) fibers that feed your good gut bacteria and help them thrive so they can perform optimally to support your health. Keep your friendly microbes happy with a diet high in peeled fruits, root vegetables (especially raw Jerusalem artichoke and both cooked and raw onions), raw garlic, and dandelion root.

Medication Timing (Relative to Probiotic Supplementation & Breastfeeding)

When taking antibiotics, it’s important to spread out the timing of taking your medicine and your probiotics. Since antibiotics destroy any and all bacteria as they make their way through the body, it’s best to wait at least two hours after taking antibiotics before you take your probiotic supplement. This gives the probiotics more time to settle in and set up shop in your gut.

To decrease the amount of antibiotics that make their way into your breast milk, it’s ideal to take the antibiotic immediately after nursing so that the gap between the medication and the next feeding is as long as possible.

With conscious prevention, tuning into your intuition, and supporting your body’s health and microbiome in the case of necessary antibiotic treatment, you can optimally support both your own and your baby’s microbiome and immune system health.

Alaya Naturals Blog and its materials are not intended to treat, diagnose, cure or prevent any disease. All material on the Alaya Naturals Blog is provided for educational purposes only. Always seek the advice of your physician or another qualified healthcare provider for any questions you have regarding a medical condition, and before undertaking any diet, exercise or other health related program.