Best Probiotics to Boost Immune System When Taking Antibiotics

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Good bacteria in humans have beneficial effects on basically every system in the body. They regulate our immune system, mood, and may even protect us against certain cancers. Bacteria account for a large proportion of the biomass that we have.

These bacteria are made up of good and bad, and they play a significant role in the host’s body. Unfortunately, overuse of antibiotics is shifting the balance and causing poor health and disease. Taking probiotics after antibiotics is important to keep a healthy balance and to prevent common side effects while using them.

Gut bacteria can change depending on many different factors, such as weight gain or loss, stress, antibiotics, illness, and even simply having a bad diet can change the balance as well. Maintaining good gut health will provide you with many benefits, but these beneficial bacteria can easily be wiped out by overuse of antibiotics. Beneficial bacteria for humans are crucial for proper immune system function.

Many of the foods people consume today are loaded with sugar and devoid of any nutrition.  Good vs bad bacteria is a fight that is constantly ongoing inside the body, and it’s your job to provide the best nutrition and environment for the good bacteria to flourish and colonize so that the bad bacteria don’t get out of control and cause disease.

What Are the Beneficial Bacteria For Humans?

The are many different strains of bacteria which are beneficial for human health, and these include Bifidobacterium Longum, Bifidobacterium Lactis, Lactobacillus Brevis, Lactobacillus Plantarum, and Lactobacillus DDS-1.

There are others which play a role in human health, but these are some of the strain which has a lot of good evidence behind their beneficial effects on the body. Probiotics help restore the balance of improving gut health and thus overall health.

CR and Improved Microbiome

When I began eating healthily, one of the first effects of the diet was on my digestive system. At first, weird things were happening, and I could tell things were changing. All my life I had suffered from a condition known as irritable bowel syndrome and doctors never really suggested anything useful. They never informed me that my diet could be the cause of this problem.

Fast forward a few months after beginning the diet and my gut health was the best it had ever been. I no longer was suffering from any stomach problems, and a host of other issue cleared up as well, including my severe hay fever allergy which I had for years. It wasn’t a coincidence, it was my diet.

Calorie restriction has been found to improve gut bacteria in mice and dogs, whilst studies looking at obesity in humans have shown a negative effect on gut health. A shift towards a better balance of good bacteria is thought to be just one of the reasons calorie restriction extends lifespan. People who live to 100 have very good microbiome ecosystems. Simply put, they have better gut health.

Gut bacteria play a huge role in our health

  • Supplying essential nutrients
  • Aiding digestion and gut health
  • Keeping the immune system healthy
  • Mental health
  • Skin Health
  • Longevity

Taking too many antibiotics

I’ve mentioned before that I have been prone to UTI infections when I was younger, and that once a person gets one, it is 50/50 whether or not you will get another one. I don’t suffer from them anymore, but I did have to take low dose antibiotics for years because of repeated bladder infections, most likely from prostatitis.

At times (especially on high doses of doxycycline) during an active infection, I felt increased anxiety, which seemed to be alleviated by taking probiotics.

It’s not always easy to restore the balance in the gut, but it is possible if you stick to a clean diet and boost the good bacteria with things like kefir or a good probiotic supplement.

These side effects of antibiotics seemed to be prevented once I introduced probiotics into my supplement regimen. And also, the best way to boost the immune system after antibiotics is to take probiotics to put friendly bacteria back into the body.

What is the best probiotic to take after using antibiotics?

I’ve tried out many different probiotics with varying levels of success. The one that I felt made the biggest difference was the probiotic made by Healthy Origins. However, I have come across another probiotic that I like since I originally wrote this article.

How to choose a good probiotic to take?

When choosing a probiotic, you have to make sure that you find one with a decent number of colonies. You typically want numbers in the billions, probably 30 billion and above.

Next, you want to make sure that the strains are acid resistant or if they’re not, then they are coated to resist degradation by stomach acid. Stomach acid will kill all of the good bacteria you swallow,  and you won’t get any benefit from taking them! Which would be a waste of money.

Below are two good probiotics that I recommend. However, I’ve only had limited experience with Captain Biotics. Whereas with the Healthy Origins, I’ve had years of good results. Healthy Origins contains less variety of good bacteria than Captain Biotics does, but they are good quality supplements. So take your pick! 🙂

Healthy Origin is a good brand with excellent quality supplements. It contains many different types of good bacteria, ensuring that you get a diverse range of flora, to help improve overall health.

Check out my article here on good probiotics for a sensitive stomach as well as digestive enzymes to help improve digestion after taking antibiotics.

Symptoms Of An Unhealthy Gut

If you’re unsure whether or not you have an unhealthy gut, here are some of the signs and symptoms that you might have which could indicate that there is a problem.

  • Frequent infections
  • Poor skin
  • Fungus / candida infections
  • Acid Reflux
  • Diarrhea or constipation
  • Anxiety or depression
  • Autoimmune issues and allergies

If you’ve have used antibiotics in the past and you think they might have affected your health in a negative way, then it’s certainly worth trying a probiotic supplement to see if any problems you have to improve once you introduce more healthy bacteria into the microbiome

To help make the probiotics more effective, make sure to include plenty of foods which are prebiotic such as garlic, leeks, onions, almonds. Foods like kimchi, kefir, and yogurts are also great sources of good bacteria aside from probiotic supplements.

In this BBC Article, it was reported that ‘Older people have 1000 times less friendly bacteria in their gut’ – and researchers have since found that probiotics improve immune function in elderly persons.


1. Structural modulation of gut microbiota in life-long calorie-restricted mice

2. Dogs Lived 1.8 Years Longer On Low-Calorie Diet: Gut Flora May Explain It

3. Changes seen in gut bacteria content and distribution with obesity: causation or association?

4. Review on microbiota and effectiveness of probiotics use in older persons

Reviewed and updated: 08/2018

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  • Great post Matt! Juicing helped me get my digestion back on track. It really did, and staying away from processed food and especially SUGAR is so important. No more soft drinks, no more fast food! Thanks Matt!

    • Thank you! 🙂 Oh yeah, sugar is definitely up there for being really bad for health. I was addicted to sugar when I was younger… I would add loads of it to my cereals and tea. I started eating healthily by cutting out sugar first! Cutting out sugar also made a big difference in being able to appreciate the tastes of different foods… = )

  • Great to see some new posts on here, Matt!

    I assume you’re on a vegan diet? As am I, but I’m always curious about protein sources.

    May I ask what some of your staples are? In your diet plan, you make mention of yogurt — is it a milk-based or of a different variant?

    Take care

    • Hey thanks Kile!

      I think I’ve mentioned around here somewhere that I am “mostly” vegan. Jared Leto called it Cheegan? :p I’m vegan about 95% + of the time, but on occasion I will eat a bit of dairy or eggs.

      I avoided being specific on purpose, just because the blog is primarily about calorie restriction, which can mean any kind of diet. I thought it was easy enough to understand one can just substitute dairy for soya or vice versa. 🙂

      I eat a lot of beans, ya lots of beans, peas. Soy milk (hot chocolate). I haven’t been tracking as carefully lately but my protein is usually around 10-12% of my calories. I’m thinking about experimenting a bit by increasing my protein (I’ll explain that in a post). Would like to get my IGF-1 levels tested first, but I don’t think that’s gonna happen. I’ll see if I can though…

      Both, I eat soy and dairy, but the latter, maybe 3 times a month or something. It really depends. As I said I’m not a strict vegan, but I am always vegetarian. 🙂

      I’ll be posting more soon! Please check back. 🙂

      Thanks, you too!

  • Hello, Matt! I just read this article and have a story to tell you: Michael’s youngest brother, David Politi (age 35), had been having all kinds of health issues for years, including IBS, anxiety, migraines, serious weight gain, poor skin, etc. His doctor sent him to a neurologist re: the migraines and that doctor asked David to cut out sugar as much as possible for 3 weeks. Well, magic started to happen! He felt a lot better and lost a couple of pounds, so he decided to stick with it for 3 months, which was very difficult for him, as he was a chocoholic. SO many of his problems either disappeared or lessened substantially, so he just stuck with it. He has now had almost no sugar for over 18 months and has improved his diet in general. He lost 30 pounds, got into exercising (with his beautiful fiancée cheering him on), his gut issues settled down, he has only the occasional fairly mild migraine, his skin cleared and he both looks and feels wonderful. He’s getting married on September 30th in San Francisco, so watch my Facebook page for lots of pictures of the whole family (including the elusive MR). JD 😎

    • Hi!

      Oh wow! That is really great to hear! 😀 It’s amazing the changes that can happen by simply cutting out certain things in the diet. Glad that he has found a way to dramatically improve his life. Wish more people had the ability to make such big changes…. the benefits are totally worth it. Hope you all have a wonderful time at the wedding. I will look out for the photos! 😀

      Thank you for the comment Judith! 🙂

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