There are a large number of options for treating Lyme disease and the coinfections associated with it. There’s the more traditional approach comprised of long-term antibiotics and some alternative approaches mostly centered around the use of herbs and supplements (of course, some choose to do both at the same time). I’m not qualified to offer advice as to which treatment plan to choose, as that’s something you should discuss with your doctor. What I can do, however, is share the treatment plan I chose.

Note: The photo on this article is the shelves right above my kitchen sink, where I keep the herbs, supplements, and drugs I use during the day.

My diagnosis

The first thing to understand is what I’m actually fighting. My diagnosis was for Lyme disease, bartonella, and babesia. It’s not uncommon for those who have Lyme disease to have two or more additional coinfections. My doctor advised me that the best way to proceed would be to treat the coinfections first and then attack the Lyme disease. Her rationale was that the coinfections are take less time to treat, and it’s very hard to get rid of Lyme while there are other active infections. (This approach also coincides with the research I’ve done.)

So our plan has been to attack the bartonella first, then the babesia, and finally Lyme. The sequencing was based on my symptoms, as she felt my biggest complaints were bartonella symptoms and so wanted to relieve those as soon as possible. If I had come in complaining of babesia symptoms primarily, we would have started there.

We discussed whether I’d like to use antibiotics or herbs. I was a bit squeamish about long-term antibiotic use given my history of digestive issues and the over-prescribing of antibiotics I had as a child. While I initially agreed to use antibiotics, two weeks later I changed my mind and asked to be switch to an herbal protocol instead.

Notes on sourcing

  • I buy a lot of supplements and herbs from Amazon because their prices are competitive and they deliver. I’ve linked some of these supplements to product pages on Amazon. This is simply to show the brand I use. These links have my Amazon Associates tag on them to get credit for the referral.
  • Any of the herbal tinctures that are not linked can be purchased from Woodland Essence. Don’t let their website design fool you, they are a fantastic, reliable resource for herbs. They process and ship orders very quickly and their products are high-quality.


  • I am not a doctor, do not take this post as medical advice. I am just sharing what I’m doing for informational purposes.
  • Do your own research before trying any new supplement or herb, especially if you are on any kind of medication — seek out the advice of a doctor.
  • I highly recommend finding a doctor who is versed in the use and mixing of medications, herbs, and supplements before attempting a protocol similar to mine.

Bartonella protocol

The herbal protocol I’m following is based on Stephen Buhner’s recommendations in, Healing Lyme Disease Coinfections. The primary protocol was recommended by my doctor, and I’ve augmented it with additional herbs and supplements both based on my reading of the book and on the advise of various other people.

Antimicrobials & immunity

  • Japanese knotweed tincture — high levels of resveratrol make this an important part of treatment. It has all kinds of good effects on the body, acting as an antbiotic, reducing inflammation, and interrupting cytokine cascades that make you feel terrible. 1/2 tsp, 3 times a day
  • Cordyceps tincture — exceptionally good at cytokine intervention and boosts immunity. 1/4 tsp, 3 times a day

Protective herbs & supplements

  • Side acuta tincture — specifically protects red blood cells from being invaded by bacteria and viruses (bartonella acts in this manner). 60 drops, 3 times a day
  • Hawthorne tincture — specifically protects the heart from infection and inflammation. 1/2 tsp, 3 times a day
  • EGCG w/ Quercitin — interrupts cytokine cascades and protects endothelial cells (where bartonella like to invade). Note that because EGCG isn’t well-absorbed, it should be taken with Quercitin to increase absorption. 400mg EGCG w/ 600mg Quercitin, 2 times a day
  • L-Arginine — protects and restores endothelial cells from bartonella infection. Reverses the damage to these cells that bartonella causes. 1000mg, 3 times a day

Energy support

  • Rhodiola rosea tincturebattles fatigue and anxiety by regulating the nervous system. 1/4 tsp, 3 times a day
  • Ashwagandha tincture — anti-inflammatory, helps with fatigue, anxiety, and insomnia through calming and modulating the nervous system. Also has some antimicrobial aspects. 1/4 tsp, 3 times a day
  • Vitamin C — strengthens the body and immune system. Some research says vitamin C helps with absorption and utilization of the herbs, but Buhner warns that he’s not 100% sure if that’s true. 1000mg, 3 times a day

Hormone support

  • Pregnenolone— precursor for a number of steroid hormones, improves energy. 50mg in the morning
  • DHEA — steroid hormone that’s important for metabolic processes. 25mg in the morning
  • DIM — improves free testosterone levels in men. 200 mg, 2 times a day
  • Androgel (prescription) — supplemental testosterone to address my chronically low testosterone levels. 1 pump once a day


  • Red root tincture — helps the lymphatic system to flush out debris, opening up the lymph system for proper detoxification. 1/2 tsp, 3 times a day
  • Milk thistle — helps the liver more effectively detoxify. Taken as silymarin standardized extract. 600mg, 3 times a day
  • Liposomal Glutathione — antioxidant that is vitally important for detoxification. This made the biggest difference in my symptoms almost immediately. I use Readisorb brand. Be wary of glutathione pills, as they aren’t absorbed very well (you can also get glutathione injections, but I’ve found the liposomal glutathione to be good enough that the injections are unnecessary). 3tsp per day


The following are things I’ve added either on my own or under the advise of someone else.

  • Vitamin D — I was deficient in vitamin D, so I added supplementation. Vitamin D is also important as part of the detoxification process. 3000IU per day
  • Vitamin B6 complex — I was deficient in most B vitamins, and B6 was the most deficient. B vitamins are important for energy and detoxification. The Pure vitamin B6 complex contains the active form of B vitamins, which is important for those with MTHFR gene mutations. 1 pill, 2 times per day
  • NutraSleep — helps me to fall asleep and have a deeper sleep. 1 pill an hour before bed
  • Zinc picolinate — zinc and copper are frequently deficient in those with Lyme (according to Buhner). I have a history of zinc deficiency, so this is a good way to address two issues at once. 25mg (1 pill) once a day
  • Bidens pilosa tincture — I added this as a recommendation from Buhner’s book for persistent dry cough. Within a week, the cough was all but gone and it also helped with my chronic sore throat and scratchy voice. By far, my favorite tincture (note: bidens frondosa is very different, it did nothing for me). 1/4 tsp, three times a day
  • Kudzu tincture — exceptional for brain and central nervous system issues (tingling, numbness, etc.). I added this based on Buhner’s book for nervous system symptoms. 1/4 tsp, three times a day
  • Baikal scullcap tincture — also very good for central nervous system issues. I received my first bottle on a day when I was having a lot of tingling in my hands and arms, and this reduced the symptoms during the course of the day. 1/4 tsp, three times a day
  • Eleuthero tincture — added as a recommendation from Buhner’s book to increase energy and improve overall strength. 1/4 tsp in the morning
  • Sun Chlorella — chlorella is a beneficial micro-algae that improves energy, provides RNA/DNA protection, and has a large of nutrients. It’s generally hard to absorb unless broken down properly, and Sun Chlorella was recommended to me as the best. 3000mg, 3 times a day
  • Magnesium oil — magnesium is important for a large number of body functions including regulating the nervous system, digestion, energy, and sleep. Those with Lyme are frequently magnesium deficient. I had trouble with oral magnesium supplements so I switched to the oil, which you rub into your skin. After a week, I had more energy and was sleeping better. 500mg per day
  • Probiotics — since I still struggle with digestive issues, probiotics are important. Although I’m not on any antibiotics, the mixture of herbs and supplements can cause digestive issues. I take the probiotics as a preventative measure. My favorite so far is Strengtia, but you need to get it directly from a doctor or chiropractor. 2 pills before bed

Babesia protocol

Just this week I started an additional protocol for babesia. This protocol is added to the bartonella protocol:

  • Artemisinin — recommended by Buhner and Zhang, this is a standardized extract of artemesia that has been shown to be effective against protozoan infections like malaria and babesia. 200mg, 3 times a day
  • Cryptolepis sanguinolenta tincture— recommended by Buhner on his website for babesia. Cryptolepsis is a wide-ranging antimicrobial herb that works best on systemic infections such as malaria, babesia, and even sepsis. 1/2 tsp, 3 times a day
  • Hydroxychloroquine (prescription) — this is an old malaria drug that is still effective against babesia. My doctor explained this to me: “It alkalizes the intracellular space. Since babesia needs an acid environment to survive, it aids in killing them off.” 200mg per day for 7 days, then 400mg per day


If you’re unfamiliar with Lyme disease treatment, then the sheer number of different things I’m taking will probably seem a bit overwhelming. That’s because it is. There was definitely an adjustment period, and even so, I spend a lot of time organizing, reordering, and scheduling around everything I have to take.

This is a far cry from the “take this pill for this” world of Western medicine, but I can say without a doubt that this protocol is the first time in my over 15 years of being sick that I’ve had any improvement in my symptoms. Lyme is a complicated enemy and so it requires a complicated attack to defeat. I hope this post helped enlighten you to the battle so many Lyme disease warriors are fighting right now.

Lyme Disease Warrior

Personal experiences about battling Lyme disease

    Nicholas C. Zakas

    Written by

    Creator of @geteslint. Author. Speaker. Philosopher. Boston ex-pat. Currently fighting Lyme disease.

    Lyme Disease Warrior

    Personal experiences about battling Lyme disease

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