How the Covid-19 Vaccine Works: amazing!

It is amazing how the COVID-19 vaccine works (the mRNA vaccines, especially)

It intrigues me how the COVID-19 vaccine works! How effective it is, and how safe it is.

I got mine, #1, as of 12/29/20, and I got my 2nd shot a few weeks later. Update as of 9/7/21: I plan on getting my booster this or next week!

Dr. Donald Thomas gets the COVID-19 vaccine

Dr. Don Thomas, MD getting his COVID-19 vaccine
First: If you have an autoimmune disorder, please consider getting the vaccine when it is your turn

Read my previous post on why lupus patients should get the COVID-19 vaccination

I got my Moderna COVID-19 vaccine on 12/29/20. I’ll post how I do day by day below at the bottom of this post. However, 1st, I’ll go over how this interesting vaccine works!

How the COVID-19 vaccine works “in a nutshell”

​This is fascinating!

– The 2 COVID-19 vaccines available now (Pfizer and Moderna) are RNA vaccines

– It helps to know how RNA works (specifically mRNA)
– Look at the cell above
– We are all born with DNA that codes everything our cells produce. It is responsible for our having blue eyes instead of brown, or black hair instead of blond, or, yes… having funny smelling pee after eating asparagus (or not)
– Our DNA is “transcribed” (think it is as being translated) into RNA, and eventually messenger RNA (mRNA)
– Then, a part of our cells called ribosomes can read this mRNA like a food recipe and produce a particular protein (such as the one responsible for your 2nd toe being shorter, instead of longer, than your big toe)

COVID-19 vaccine contains the COVID-19 mRNA that codes for those spikes
– The COVID-19 vaccines are NOT live virus vaccines. They CANNOT give you COVID-19 (impossible)
– Ingeniously, they contain the virus’ mRNA that codes for those spikes you see on the outside in all the pics
– These spikes look somewhat like a crown. Latin for “crown” is corona, hence, coronavirus
mRNA injected into our bodies as a vaccine: tricks our bodies into producing the spikes, but not the entire virus
– Fascinating!
– The mRNA of the virus (in the vaccine) is injected into your muscle
– It spreads quickly throughout your blood stream and body
– The mRNA is absorbed into our own cells
– Our own cells mistakenly think this mRNA came from our own DNA and instructs those cells to produce this protein
– The protein is the same one found in the spikes of the SARS-CoV-2 coronavirus responsible for COVID-19
– In other words, our cells produce just those pink spikes you see in the pic below, not the entire virus
– The viral spike protein ends up on the surfaces of our cells
– Our very smart T-cells of the immune system actually DO recognize these as being foreign
– They say, “we need to fight this off and protect us”
– They summon other players of the immune system as well to the battle

DaOur B-cells then learn to produce antibodies that quickly recognize those COVID-19 spikes

– The booster shot you get a few weeks later strengthens this memory
– If you were to actually get infected with COVID-19 in the future, your B-cells would recognize those tell-tale spikes
– Those smart B-cells would say, “This is a foreign invader we must destroy”
– They summon the rest of the immune system to attack the virus and protect us

– Note that many people will get a very sore arm, redness, swelling, aches, pains, fever for a few days after the vaccine
– This is actually the immune system learning to mount an attack. Think of it as a sign of the vaccine working
Day #1:
It has just been a few hours since my vaccine
I took some Tylenol and Advil to decrease my chances for the above side effects
If you get the vaccine (which I hope you do), ask your doctor before you consider taking Tylenol and/or Advil or Aleve

Day #2: Woke up with a sore upper arm muscle (deltoid) in the area of the shot. However, I expected this as usual with a good, strong vaccine.  I’ll just take Tylenol plus Advil around the clock today to lower the risk of pain and to lower my risk of a flu-like syndrome reaction.

Day #3: Mild, tolerable arm soreness. I feel great! I am optimistic about getting vaccinated and feeling safer.


Don Thomas, author of “The Lupus Encyclopedia” and “The Lupus Secrets

Lupus and Taking Probiotics: Learn the truth here [Updated]

Lupus and taking probiotics: Should you take probiotics if you have lupus, and what are the best probiotics for autoimmune disease?

Lupus and taking probiotics: My answer in short: “No” to pills; “Yes” to probiotic and prebiotic-rich foods! Lupus Question of the Day:
Probiotic supplements seem to be a real trend these days. Is gut bacteria linked to lupus? If so, is there value in taking probiotic supplements?
My answer:

There are good bacteria in the microbiome that improve our health and bad bacteria that harm us. The microbiome includes all the living organisms inside and on our body (but good ones and bad ones). Probiotics are made up of bacteria that when you consume them in food or supplements, you “hope” that they enter your gut and improve your gut microbiome.

Several bacteria in our microbiome have been shown to be bad for lupus and other autoimmune diseases. They have been linked with making the immune system more active and are associated with inducing the immune system to produce autoantibodies (like anti-SSA) that can attack our body. Others have been shown to protect us and decrease lupus disease activity. Most of these studies have been in lupus mice. However, there are also human studies as well.

I do not recommend taking a probiotic supplement if you have lupus and taking probiotics. Why? Animal studies show that some bacteria in these supplements actually make some autoimmune diseases worse, while improving others. I recommend the following (instead of taking probiotic pills or capsules). My recommendations regarding lupus and probiotics are below. I also recommend this regarding probiotics for autoimmune disorders such as Sjogren’s and rheumatoid arthritis:

– Eat foods rich in healthy probiotics regularly.

Examples include fermented sauerkraut, live-culture yogurt (I love Siggi’s), kim chee, miso, kombucha, and fermented pickles. Kombucha and lupus have not been studied together. However, I do not see any problems with it theoretically.

– Eat foods rich in prebiotics as well. Particularly “resistant starches” may be beneficial. A lupus mouse study showed decreased lupus disease activity in lupus mice fed a “resistant starch” diet. Examples of resistant starch foods = cooled potatoes that are cold, potatoes starch, cold oatmeal, beans, legumes.

Sea moss and lupus: some of my patients ask me about sea moss. It may provide prebiotics and it appears to be healthy.

Thank you to Kelli of “More than Lupus” for producing the “Ask Dr. T” series!
Go to her blog and Facebook page and join the lupus community!

What are your favorite probiotic and prebiotic foods?
Click COMMENTS above


Don Thomas, MD, author of “The Lupus Encyclopedia” and “The Lupus Secrets

Lupus and Stress Management: How to lessen stress life

Lupus and Stress Management: The Science of Stress and the Immune System

The video below goes over lupus and stress management, while also discussing how stress affects the immune system adversely.The Lupus Foundation of America filed this video of me during their Living and Learning series December 2020 at the height of the COVID-19 epidemic and during the holiday season. Stress can increase lupus onset and lupus flares. Learnhow to lower stress can possibly help decrease the effects of lupus.

– The 1st part of the video goes over some of the science behind how stress abnormally affects the immune system. stress worsens cancer, autoimmune diseases, and cause increased death. Why is it that optimistic people who deal with stress well tend to live longer than pessimistic people who are easily stressed? Stress does have bad effects on our immune systems.

– Then I go over how people who are genetically predisposed to having lupus have a greater chance of developing lupus if they have had major stressors in their life (child abuse, physical abuse, sexual abuse, etc.)

– Then I go over how stress can cause lupus flares.

– Interestingly, easily stressed people can learn to deal with stress better. Some habits are easy and incredibly healthy in many other ways. Examples include exercising regularly, and practicing mindfulness daily.

​- I end the video with practical pointers on how to decrease stress.

Download my free stress management handout from my Lupus Secrets

SHARE with everyone who has an autoimmune disease

COMMENT above: how do you deal with and prevent stress?

​What advice do you have for others?


Don Thomas, MD, author of “The Lupus Encyclopedia” and “The Lupus Secrets

Covid-19 Vaccine for Lupus Patients: Please get your vaccine

Should We be Recommending the COVID-19 Vaccine for Lupus Patients?: Yes!

What I tell my systemic lupus patients as of 12/18/20: 4:00 PM regarding getting a COVID-19 vaccine for lupus patients

The Advisory Committee on Immunization Practices (ACIP) of the CDC made the following recommendations on 12/18/20 regarding vaccination in patients with autoimmune disorders. I’ll first put in verbatim what was said (courtesy of the RheumNow website), then give my recommendations in a nutshell.

The ACIP of the CDC states:
< > = is wording that I inserted

Persons with underlying medical conditions <such as lupus and other autoimmune disorders>:

… the vaccine may be administered to persons with underlying medical conditions who have no contraindications to vaccination. Phase 2/3 clinical trials demonstrated similar safety and efficacy profiles in persons with some underlying medical conditions, including those that place them at increased risk for severe COVID-19, compared to persons without comorbidities.

Immunocompromised persons: Persons with HIV infection, other immunocompromising conditions, or who take immunosuppressive medications or therapies might be at increased risk for severe COVID-19. Data are not currently available to establish vaccine safety and efficacy in these groups. Persons with stable HIV infection were included in phase 2/3 clinical trials, though data specific to this group are not yet available. Immunocompromised individuals may still receive COVID-19 vaccination if they have no contraindications to vaccination. However, they should be counseled about the unknown vaccine safety profile and effectiveness in immunocompromised populations, as well as the potential for reduced immune responses and the need to continue to follow all current guidance to protect themselves against COVID-19.” 

What I will tell my patients:

If you have lupus and just take an antimalarial such as Plaquenil:
– In the clinical trials, patients with underlying medical conditions with no contraindications to vaccines did as well with the COVID-19 vaccine as healthy people.
– This would apply to lupus patients who take hydroxychloroquine (Plaquenil). Plaquenil does not suppress the immune system.

If you take an immunosuppressant:
– Patients who take immunosuppressants (such as prednisone > 7.5 mg a day, mycophenolate, CellCept, azathioprine, Imuran, methotrexate, leflunomide, cyclophosphamide, cyclosporine, tacrolimus, Benlysta, and Rituxan) may get vaccinated if you do not have a contraindication to getting vaccines. However, the safety and effectiveness is unknown. There is always the chance that the vaccine may not work as well (in other words, not 95% effective). Therefore, you can never let your guard down. You must continue to practice strict infection prevention measures (washing hands, disinfecting, mask wearing, social distancing).

The Lupus Foundation of America put out additional information below:


The photo above of Covid vaccine comes from the LFA website

How about you? Are you going to get the vaccine?

Share your opinions and comments by clicking “COMMENT” above


Don Thomas, MD, author of “The Lupus Encyclopedia” and “The Lupus Secrets

FDA approves Benlysta for lupus nephritis!

1st drug ever FDA-approved to treat lupus nephritis

​Historic mile-stone!

December 16, 2020: The FDA approved on Wednesday DEC 16, 2020…  Benlysta for lupus nephritis as the first drug ever FDA-approved to treat lupus nephritis (inflammation of the kidneys).
What should lupus patients know about lupus nephritis?

It is common
Lupus nephritis (LN) occurs in approximately 40% – 45% of people who have systemic lupus erythematosus (SLE). It occurs in some ethnicities more than others. For example, while 30% of Caucasian women with SLE will have LN, close to 80% of Caribbean women of African ancestry with SLE will develop LN.  

It can occur at any time 
When we look at people with LN, 1 out of 3 have LN when first diagnosed with SLE. It most commonly develops within the 1st 5 years. However, it can occur at any time, including after having SLE for many years.

It is why rheumatologists ask you for a urine sample every 3 months
It is diagnosed most commonly by finding an increased amount of protein in the urine. We want to catch it at the earliest stages possible when it is easiest to treat. Identifying it quickly increases the chances for remission.

The most common symptoms of lupus nephritis = you feel perfectly normal
Yes, that is correct. Early on with LN, there are no symptoms what-so-ever. By the time you feel any, you already have some significant kidney damage going on. Symptoms of LN once it gets to that more advanced stage include fatigue, swelling of the ankles that gets worse later on in the day (edema), weight gain (fluid retention), urinating more often at night time when in bed, foamy urine (from the increased protein in the urine).

We want to catch it when you feel completely normal. That is why it is so important to see your rheumatologist regularly when you feel great and give us that cup of urine.

Remission can and does happen! Here are the tricks to achieve remission:
– Help your rheumatologist catch it quickly by giving us a urine sample every 3 months.
– Get a kidney biopsy as quick as possible, and begin treatment as soon as possible if the urine sample is abnormal.
– Work hard on maintaining normal body weight.
– Do not smoke cigarettes. (Follow everything else in the Lupus Secrets)
– Take hydroxychloroquine (Plaquenil) religiously. It makes you 3-times more likely to go into remission.
– Take other prescribed medicines religiously (such as mycophenolate and azathioprine)
– If not on an ACE inhibitor or ARB blood pressure medicine, ask your doctor if you should, especially if you have increased protein in your urine.
– Ask your doctor to help you get your BP perfect. Have the top number (systolic) around 110 mmHg; have the bottom number less than 80 mmHg
– Keep your cholesterol perfect (take a statin if it is high)
– Exercise regularly
– Consider eating an anti-inflammatory diet (it has not been proven to put nephritis into remission because it has not been studied. However, there is good data that it can help decrease lupus inflammation in non-renal lupus.)
– Follow-up with your rheumatologist or nephrologist (kidney doctor) regularly. Your goal is to get your urine protein to creatinine ratio below 0.7 g/g (or < 700 mg:mg).

How effective is Benlysta for lupus nephritis?

In the phase III clinical trials, Benlysta IV (intravenous form) was added to the medicines we normally use to treat lupus nephritis (called standard of care, SOC).  Some patients in the study got Benlysta + mycophenolate +/- hydroxychloroquine + steroids, some got Benlysta + cyclophosphamide + steroids +/- hydroxychloroquine, while others got Placebo plus mycophenolate or cyclophosphamide ( plus steroids +/- HCQ).

Results were remarkable. The most important of which is the “complete renal response” meaning marked reduction of protein in the urine close to normal (<0.5 g/g) by week 100 and no worsening of kidney function.

Complete renal response rates at week 100 (bottom left graph):

Placebo + standard of care = 20% complete response
Benlysta + standard of care = 30% complete response

Note that this is a 50% higher amount of complete responses compared to standard of care (30% is 50% greater than 20% mathematically).

That is remarkable. (However, a caveat… we still need better treatments for that other 70% who did not go into complete remission! … read my comments at the bottom of this article for a possibility)

Graphs above come from the BLISS-LN trial published in the NEJM referenced below

How safe was Benlysta?

Benlysta continues to be one of our safest options for treating systemic lupus! There was not any statistically significant differences among side effects between the Benlysta group and the placebo group.

The most common side effects seen in the research studies were infections. However, it is important to remember that all patients were also treated with high dose steroids plus either mycophenolate or cyclophosphamide, which are strong immunosuppressant drugs. Interestingly, 0.7% of the patients who got Benlysta had infections while 1% of those on placebo did. (in other words, the other drugs, such as steroids, played the largest role in this).

Allergic reactions were seen as with any medication, but not common. For example, 0.9% of patients who received the placebo infusion had an infusion reaction, while 1.6% of those who got Benlysta did.

How is Benlysta dosed for lupus nephritis?

The IV form is the same as for other lupus problems (10mg/kg given 3 times in the first month; then 1 infusion monthly after that)

Interestingly, the self injectable subcutaneous form is different than for other types of lupus. It is recommended to do 2 injections weekly of 200 mg each (total of 400 mg) for the 1st four weeks. After that, it is just one injection weekly.

My prediction for the near future for lupus nephritis treatments

Voclosporin will probably be the next FDA-approved drug to treat lupus nephritis, and it will probably happen soon. It is a pill taken once a day.

How well did it do?
In the phase III clinical trial:
41% of the voclosporin + standard of care group had a complete response!
23% of the placebo + SOC group had a complete response

That is pretty close to twice as many patients going into remission compared to standard of care.

And voclosporin was safe! It is in the same group of drugs called calcineurin inhibitors (cyclosporine and tacrolimus) and it is safer than those two.

And what would happen if we were to use both voclosporin and Benlysta both together? They work through different mechanisms. We could potentially see even great remission rates.

As you can probably tell. I am pretty excited about the future of better therapies for lupus! They are not possibilities… they are actually happening right now.


Don Thomas, MD, author of The Lupus Encyclopedia and The Lupus Secrets


Furie R, Rovin BH, Houssiau F, Malvar A, Teng YKO, Contreras G, Amoura Z, Yu X, Mok CC, Santiago MB, Saxena A, Green Y, Ji B, Kleoudis C, Burriss SW, Barnett C, Roth DA. Two-Year, Randomized, Controlled Trial of Belimumab in Lupus Nephritis. N Engl J Med. 2020 Sep 17;383(12):1117-1128. doi: 10.1056/NEJMoa2001180. PMID: 32937045.

Lupus Lifestyle Changes Advice: In the anti-Inflammatory diet

Lupus Lifestyle Changes are Important: Read here to learn about important dietary changes

There is more and more evidence that healthy lupus lifestyle changes do make a difference. Read below for practical information regarding diet. 

Lupus lifestyle changes as an anti-inflammatory diet for lupus and autoimmune diseases
There is growing evidence that eating an anti-inflammatory diet benefits lupus patients

​Anti-Inflammatory Diet for Autoimmune diseases

This is the latest handout I give to my own patients. It has information from some of the latest medical research regarding foods to eat and avoid in order to hopefully decrease inflammation in the body. It talks about anti-inflammatory foods to eat, which to avoid, intermittent fasting, prebiotics (such as resistant starches), and probiotics. As per the Lupus Secrets, do this along with taking your medications, exercising regularly, getting at least 8 hours of sleep each night, and protecting yourself from ultraviolet light.

If you find this helpful, please share with others.

There is growing evidence that eating a diet high in foods that decrease inflammation, while avoiding, or minimizing foods that increase inflammation, can help autoimmune diseases such as lupus and rheumatoid arthritis. One of the latest studies from the University of California, San Diego Medical Center showed that rheumatoid arthritis patients had significantly better disease control when sticking to this type of diet. Lupus studies show that diets rich in omega-3 fatty acids and low in omega-6 fatty acids can help disease activity in people with lupus as well as mice with lupus. Lupus mice also have better disease control when they eat a diet rich in “resistant starches.” Resistant starches as discussed in the probiotics section below.  Note that the Mediterranean diet has many of these anti-inflammatory recommendations. You can find information on the internet or ask your doctor for a copy of our Mediterranean diet.

oatmeal and yogurt probiotic foods for lupus lifestyle changes diet
Berries and nuts are high in anti-oxidants; oatmeal is an excellent prebiotic

Eat omega-3 fatty acids. Limit omega-6 fatty acids

Increase intake of:
Omega-3 fatty acids (walnuts, flaxseed, chia seed, salmon, tuna, mackerel, sardines, avocado, sesame seeds, tahini seeds)
Green leaf vegetables (such as arugula, broccoli, cabbage, zucchini, brussel sprouts)
Anti-inflammatory vegetables (onion, carrots, pumpkin; eat garlic in moderation)
Enzymatic fruits (pineapples, mangos, papaya)
Anti-inflammatory spices (turmeric, black pepper)

Decrease intake of:
Omega-6 fatty acids (reduce meat intake to turkey or chicken twice weekly; eat more fish as noted above; avoid or at least limit red meats, fried foods, butter)

Nightshade foods and lupus? Avoid gluten?

Controversial diet changes

Do nightshade foods and lupus mix. Some experts recommend the following changes, while others do not due to insufficient data). Nightshade foods are probably fine to eat when you have lupus. At our 2020 American College of Rheumatology meeting, an anti-inflammatory diet research study was presented that did include nightshades. For example, tomatoes are rich in lycopenes, a strong anti-oxidant (so, it seems like they should be healthy rather than harmful). This is one of those areas that needs more study.:

Decrease the intake of nightshade (solanaceae) vegetables (tomatoes, eggplant, potatoes) if you believe this. Personally, I would still eat them. However, like with any foods, if you predictably flare by eating them, then you should avoid them.

Decrease the intake of gluten products (instead of wheat bread and pasta, switch to rye bread, corn tortillas, quinoa/beet/bean/ or chickpea pasta). However, most experts recommend avoiding gluten only if you truly have celiac sprue (gluten hypersensitivity).
*** NOTE: These recommendations are not for people who have celiac sprue, gluten-sensitive enteropathy, or gluten sensitivity. Though these are lower in gluten than wheat breads and pastas, some (such as rye) can contain gluten.

Intermittent Fasting

Fasting has been shown to decrease inflammation in the body in numerous studies.  Some lupus mice studies also show that fasting decreases lupus disease activity. Numerous animal models show that animals that eat a highly restricted diet live longer.

One easy way to fast is to do something called intermittent fasting. This form of fasting also lowers insulin spikes (so may decrease the risk of diabetes), causes weight loss, and may help extend life span. 
An easy way to do intermittent fasting is to only start eating in the late afternoon, then stop when you go to bed. You only want to eat 8 or less hours a day, complete fasting for at least 16 hours (including your 8 hours of sleep). You are only allowed water, black tea, and black coffee while fasting. Go to YouTube to watch some helpful videos about intermittent fasting.

If you have diabetes, discuss with your doctor before doing intermittent fasting (especially if you are on insulin).
You should also exercise regularly to get the full benefits of intermittent fasting. 
The microbiome in autoimmune diseases:

We have trillions of bacteria living on and inside of us; all together it is called our “microbiome.” The insides of our intestines and gastrointestinal tract contain the largest immune system organ of our body, and the constant interactions of the microbiome bacteria and our immune system can either cause beneficial effects when we have good (beneficial) bacteria in our microbiome, or abnormal effects that can actually cause increase autoimmune disease. Studies of the microbiome and autoimmune diseases such as RA and lupus are in its infancy. Many studies have been performed in animals with lupus and RA, and smaller studies have been done in humans. We have so much to learn, but we do realize that having good bacteria that decrease autoimmunity, and getting rid of bad bacteria that increase autoimmunity are very important. Here are some recommended practices that you can do that may help you.

1. Take great care of your oral health! Poor dental health can actually cause RA and make it worse, and now there is evidence that it can do the same with lupus (in fact, one study showed that treatment of periodontal disease in lupus patients improved their lupus disease activity significantly.  Make sure and do the following:
     – Floss every day (flossing picks are very handy to use)
     – Brush twice a day
     – If you have dry mouth, talk to your doctor about how to improve the much needed saliva in your mouth to increase good bacteria and decrease the bad.
     – DO NOT SMOKE! (this is why smokers lose their teeth at a much younger age than nonsmokers)
     – Chew on gum that contains xylitol (or use Xylimelts, or use mouth wash that contains xylitol eg TheraBreath Maximum Strength)
     – Get your teeth cleaned every 6 months (every 3-4 months if you have dry mouth)

2. Improving the microbiome in the gut has less medical evidence behind it. It is probably important to do, but we lack good large studies in humans. However, increasing the amount of resistant starches in your diet may be beneficial.
– Resistant starches include cold oat meal (eg overnight oats), potato starch, green banana starch, potatoes that are cold after being cooked, and lentils
     – These types of starches aren’t digested well until the get into the large intestine where they begin to ferment. Then beneficial bacteria use these starches for food and interact favorably with the immune system and also decrease the numbers of bacteria that cause immune system problems
     – Including a serving of resistant starches in your diet daily is probably a good idea.

​Probiotics in autoimmune diseases:

Probiotics are live bacteria, touted to have beneficial effects by living within our intestinal system and interacting with our immune system. While probiotic supplements have been shown to have some benefit for gastrointestinal problems (such as irritable bowel syndrome), no human studies have proven benefit for autoimmune disorders yet. In fact, in animal research, some autoimmune disorders improve with some probiotic organisms while others actually worsen. Therefore, we do not recommend any probiotic supplements.  Probiotics may be beneficial for the microbiome as above.

However, many foods are rich in natural probiotics, and thus far, there are no studies suggesting that any of these foods make autoimmune disorders worse. Therefore, you may want to consider the possibility of consuming a daily portion of any of the following probiotic rich foods:

Probiotic rich foods
Greek yogurt
Kimchi (fermented, nonpasteurized)
Kombucha tea
Miso soup (warm, not boilded)
Sauerkraut, fermented, nonpasteurized (warm, not cooked too hot)
Fermented, nonpasteurized pickles
Dark chocolate (just a little, and NOT milk chocolate)
Cold green peas on salads
Natto (very healthy, but takes an acquired taste)
Beet kvass
Fermented beets
Cottage cheese containing live cultures (eg “Good Culture” and “Horizon organic”)
Soft, aged cheeses (especially gouda; but also parmesan, cheddar and swiss; the longer the aging, the higher the probiotic content)

Bustamante MF, et al. Contemp Clin Trials Commun 2020
Guma M, et al. Trial of diet to improve RA and impact on the microbiome. Presented at ACR Convergence 11/9/2020.
Zegarra-Ruiz DF, El Beidaq A, Iñiguez AJ, et al. A Diet-Sensitive Commensal Lactobacillus Strain Mediates TLR7-Dependent Systemic Autoimmunity. Cell Host Microbe. 2019;25(1):113-127.e6. doi:10.1016/j.chom.2018.11.009


written by Donald Thomas, MD
author of “The Lupus Encyclopedia
Arthritis and Pain Associates of PG County

Anti-inflammatory Diet for Autoimmune Disease: New Research (AI Protocol)

The Autoimmune Protocol (AI protocol) is another term for the anti-inflammatory diet. The chart below was shown to help patients with the autoimmune disease rheumatoid arthritis.

Anti-inflammatory diet for lupus and autoimmune diseases

Autoimmune Protocol (AI Protocol) used in 2020 rheumatoid arthritis study above

The AI protocol slides above and below posted with permission of Dr. Monica Guma, MD (principal investigator of this research study. The reference is at the bottom) At the American College of Rheumatology (ACR) meeting NOV 2020, Dr. Monica Guma of UCSD reported results of using an anti-inflammatory diet in the autoimmune disease, rheumatoid arthritis (rheumatoid arthritis). She used the diet posted above.

This is pertinent for lupus patients because lupus is also an autoimmune disease. Eating an anti-inflammatory diet (AI Protocol) is recommended for lupus patients in “The Lupus Secrets.” Note that there are some anti-inflammatory diet studies in lupus mice and lupus humans that show positive effects. However, we need larger, bigger studies. This study is a step in the right direction (even though it is with RA instead of lupus).

She chose motivated RA patients. They stayed on their medications as well. They followed the above diet. They had to have active RA to enter the study. Disease activity was measured 2 weeks before the study, at the start of the study, then 2 weeks later. The bacteria in their stool (microbiome) was also measured!

Below is an example of a typical day of eating:

How did the RA patients do on this anti-inflammatory diet?

After 2 weeks on the diet, there was improved disease activity (overall) with less tender and swollen joints.
Disease activity (measured by a research tool called the CDAI) was significantly decreased.
Below are the results after 2 weeks on the diet.

​For the scientific minded… note the great “p values” for some of these measurements on the right.

What did their gut microbiome do in response to the anti-inflammatory diet?

After 14 days, those RA patients who did better (had lower RA disease inflammation) on the anti-inflammatory diet ended up with a greater diversity of their microbiome. This suggests that the diet influenced their gut bacteria types as well as improved disease activity.

This adds evidence that we may be able to alter our gut bacteria with diet plus improve disease activity in autoimmune diseases! There is hope that diet could also possibly help other autoimmune diseases, such as lupus, in a similar way.

We absolutely need more research. Thanks to Dr. Guma and her team for helping to pave the way for more research on diet and autoimmune disorders.  Below are her results of the microbiome changes in the study.

What should be in an anti-inflammatory diet for lupus and other autoimmune diseases?

This is my commentary:

Some of the recommendations of Dr. Bustamante (first two pics above) have quite a bit of research supporting their use (eating foods high in omega-3, avoiding omega-6, eating prebiotics) in autoimmune diseases such as lupus.

However, others have significantly less evidence (for example, avoiding solanaceae, which is nightshade plants, and eating gluten-free).

I suspect the latter food groups were included since these changes “may possible reduce inflammation.”

We all look forward to more studies in autoimmune disorders, such as lupus.


Coras R, Martino C, Gauglitz J, Tripathi A, Jarmusch A, Cedola F, Fernandez Bustamante M, Agustín-Perez M, Alharthi M, Lee S, Singh A, Choi S, Rivera T, Nguyen K, Shekhtman T, Holt T, Golshan S, Knight R, Dorrestein P, Guma M. Rheumatoid Arthritis Improvement After Exposure to an Anti-Inflammatory “ITIS” Diet Is Associated with Changes of Gut Microbiome and Systemic Metabolome [abstract]. Arthritis Rheumatol. 2020; 72 (suppl 10). Accessed September 17, 2021.

Comments Welcomed
Click on COMMENTS above

What have you found to be helpful in an anti-inflammatory diet?
What do you recommend for a beginner?
Do you recommend any particular books that you found to be most helpful?


Don Thomas, MD author of “The Lupus Encyclopedia” and “The Lupus Secrets

Bustamante MF, et al. Contemp Clin Trials Commun 2020

Guma M, et al. Trial of diet to improve RA and impact on the microbiome. Presented at ACR Convergence 11/9/2020.

Getting the COVID-19 Vaccine: Now see me excited to get it

What was it like getting the COVID-19 vaccine? … and some advice for lupus patients

A rheumatology researcher becomes a research study participant for the Pfizer COVID-19 vaccine

Dr. Kathryn Dao, a rheumatologist in Dallas, Texas, wrote about what it was like getting vaccinated for COVID-19 as a research study participant. I will include the link to her fascinating story below but will provide a short outline on some important points.

It was Pfizer’s placebo-controlled trial. How could she possible know she got the vaccine and not the placebo?
~ It is because she developed classic vaccine reaction symptoms after getting it
~ Out of interest, the name of the trial was:

the phase 3 trial of the Pfizer/BioNTech mRNA vaccine against SARS-CoV2 (protocol C4591001) 

– How big was the research study and how long is it?
~ The goal was to get 44,193 subjects
~ Subjects are expected to be followed for around 2 years each

About Getting the COVID-19 vaccine

– How was the vaccine given?
     ~ 1st dose followed by a 2nd dose 21 days later

~ What is in the vaccine?
     ~ It contains RNA (ribonucleic acid) from the coronavirus that causes COVID-19
     ~ After the injection, our immune system should see this foreign RNA and learn how to make antibodies against it for future protection
     ~ Then, if this person is exposed to the coronavirus, their immune system will recognize the COVID-19 RNA and can launch an attack against it and hopefully prevent infection

Dr. Dao’s COVID-19 vaccine experience

– What was it like to get the shot?
     ~ The vaccination was given in her left upper arm muscle (like a flu shot). She says it was the easiest shot she ever had: no pain, no blood, not even a red dot.

– So how does she know she got the actual vaccine and not a fake shot (placebo)?
     ~ Just 2 hours later, her muscles ached, and her temperature rose.
     ~ She had trouble sleeping that night due to a painful arm and headache. In the AM her temperature was 100.3
     ~ She felt badly, so she took 400 mg ibuprofen (Motrin) with marked improvement. She took it every 8 hours and felt great. She was able to stop the ibuprofen after 24 hours. 
     ~ For the 2nd shot, she started taking ibuprofen before the shot and every 6-8 hours afterward. She still got a slightly sore arm, mild fever, and headaches. She experimented with acetaminophen (Tylenol). It helped the fever but not the sore arm. She had to keep taking these for several days. Day 4 – she felt amazing! 
     ~ A placebo would not have caused these symptoms, so she knows she got the vaccine. 

– What were the Pfizer study results?
     ~ As of 11/13/20, 41,135 participants received their 2nd shot. Half got placebo, half got the vaccine.
     ~ There were 162 COVID infections in the placebo group
     ~ There were only 8 in the vaccine group!
     ~ The vaccine was 95% effective. This is just amazing!
     ~ The effectiveness was similar among different ages, genders, ethnicities/races.
– What were the side effects of the vaccine?
     ~ Fatigue in 4%
     ~ Headache in 2%
     ~ Side effects were more common in younger adults (note that this is similar to what happens with the Shingrix shingles shot: older people are less likely to get side effects)

Will I get the vaccine?

You better believe it! I will be 1st in line!

I will take both Tylenol and Aleve or Advil (Tylenol works through a different mechanism than Aleve and Advil do. Using them together theoretically may work better)
I’ll advise my patients to do the same (for those who can safely take them)
CAUTION: Do NOT do this without asking your doctor first.

Dr. Thomas will be 1st in line to get the COVID-19 vaccine!

– I’ve had too many patients tell me about their relatives and loved ones who died from it … spouses, siblings, parents, God-children, nieces, nephews, best friends

~ This is real, everyone!
~ We need to have over 75% of us get vaccinated in order to achieve what is called “herd immunity”
~ Please do your part and get vaccinated.
~ If you don’t believe in protecting yourself with vaccines, change your mindset…

​Do it out of love for your loved ones. If you get vaccinated, you lower the chances of spreading it to your loved ones.

– Will I recommend it for my patients who have autoimmune disorders such as lupus, or those who are on immunosuppressant drugs?
~ Probably. However, I will go by what the expert recommended guidelines are.
~ One problem is that they probably did not include people with lupus and who are on drugs that suppress the immune system into the studies.
~ However, I suspect the experts will recommend it since all other non-live vaccines are safe for our patients, and this is not a live vaccine.

Dr. Dao stated, “The relief was something I did not anticipate; it was a glimpse of the end of the pandemic. ” She urged others to follow her footsteps and get the vaccine so we can end this pandemic and get back to a normal life.

Here is a link to Dr. Dao’s very interesting personal account. It is a must read on RheumNow:

Let’s get back to a normal life! We can all do our part!

Please don’t believe all the fake news, and misinformation that you read and see about COVID-19. It just makes me angry to see and hear it. Calling this a hoax when we health care workers see the devastation constantly.

​I wish that everyone who minimizes this, or calls it a hoax were forced to help care for the devastated families so they can see these are real people behind the numbers.

Stay safe everyone … and please get vaccinated when it is available.

Wouldn’t it be nice to shop normally again?

Wouldn’t it be nice to get together with loved ones, hug, kiss, and not have to do Zoom meetings?

​Please comment above, what do you think?


Don Thomas, MD
Author of “The Lupus Encyclopedia” and “The Lupus Secrets

Bacteria in Urine May Increase Lupus Flares

If we prevent bacteria in urine (bacteriuria), could we decrease lupus flares?

Bacteria in urine was found in a study to possibly increase flares in lupus patients. If this is true, then decreasing bacteria in the urine could possibly help lower the risk of lupus flare is people who have systemic lupus erythematosus (SLE).

Bacteria in urine is a common problem in women, so this could be an important problem to address.

Background for this study

– Could bacteria in urine cause lupus flares? Bacteria such as E. coli can infect the urinary tract, such as the bladder. They can produce proteins called “amyloid curli” that can trigger the immune system to become more active. Part of this is through something called “toll-like receptors,” a well-known trigger of increased lupus activity.
(Off topic, Plaquenil, our most important drug for lupus inhibits toll-like receptors- one way it works for lupus).

– This bacterial amyloid curli is connected to something called extracellular DNA (DNA from the bacteria that sits on the outside of the cell).
Remember, that anti-dsDNA antibodies are very important in lupus disease activity. 

– This bacterial DNA can “mimic” human DNA and potentially trigger the immune system to make autoantibodies to anti-dsDNA, like we see in lupus!

– Research studies showed that when this amyloid curli bound to extracellular DNA (from bacteria) is injected into mice that are genetically predisposed to having lupus, they develop systemic lupus quicker and more often.

Background of bacteria in urine of women who have lupus

Women who have lupus commonly have bacteria in their urine. This is partly due to the urethra of women being so short. This allows bacteria from the vagina and vulva to enter the bladder easier. This is common in all women. Most of the time, these bacteria do not cause infection (urinary tract infection, UTI). 

We get a urine sample from our patients with systemic lupus erythematosus (SLE) every 3 months to make sure they do not have inflammation of the kidneys (lupus nephritis). Many times there are bacteria in the urine when we analyze it.

One of the most common phone calls my medical assistant makes for me is calling up my SLE patients and asking, “are you having any UTI symptoms?” Usually they say “no,” in which case we call it “asymptomatic bacteriuria” (there is bacteria in the urine but the person does not have any symptoms of a UTI).

The standard of medical care is to NOT treat it with antibiotics. Asymptomatic bacteriuria usually does not cause problems. However, an antibiotic has a high risk for side effects (stomach upset, allergic reaction, rash, yeast infection, and so on). So, instead, we ask our patients to drink cranberry juice daily, take a cranberry supplement, and/or take D-Mannose daily. This is based on research where 13 studies with 1616 subjects demonstrated that taking daily cranberry reduced UTIs by approximately 40%. Studies also show that cranberry decreases the ability of urinary bacteria to stick to the walls of the bladder and urethra.

In the past, I always told my patients, “this is common because of your short urethra and is nothing to worry about.” 


Photo above is one possible type of supplement that may decrease the risk of UTIs when taken daily. It contains both cranberry and D-mannose. I am not advocating this particular brand, it is just an example.

This Research Study Showed that Lupus Women with Bacteria in the Urine have more Lupus Flares!

These researchers measured antibodies to these bacteria proteins bound to DNA and they showed:

– 1/3 of SLE women have persistent bacteria in the urine!
– These lupus patients tend to have more active lupus disease than those women without bacteria in the urine
– They were also more likely to have high anti-dsDNA levels and low C3 and C4 complement levels (indicators of active lupus inflammation)
– They also had higher levels of antibodies to this amyloid curli/DNA complexes
– These curli/DNA complexes from the urinary bacteria cross-reacted with lupus autoantigen dsDNA! (suggesting something called molecular mimicry)

MAJOR FINDING: The urinary bacteria’s curli/DNA proteins triggered increased lupus inflammation and lupus flares in women with SLE!

A summary of this research in the highly acclaimed medical journal “Arthritis & Rheumatology” summarized:

“Lupus patients with persistent bacteriuria could be targeted with appropriate antibiotic therapy as adjunct to standard of care.”


I will not start treating all my SLE patients with asymptomatic bacteriuria with antibiotics. The potential risks of side effects from the antibiotics outweigh the potential benefits. I will await the next-step research where someone does a research study treating SLE patients like this with antibiotics and see what happens. However, what I will do…

In SLE patients who have bacteria in their urine (bacteriuria), I will recommend that they consider taking a cranberry supplement and/or D-Mannose supplement daily and stay on it. It is such a safe thing to do with potential significant benefits.

Fascinating study that has the potential for significant positive benefits for our patients. Thank you to the dedicated researchers of Ryan Pachucki, MS, and Roberto Caricchio, MD and their entire team!

Do you get frequent urinary tract infections? Do you notice any relationship to lupus flares? Please comment and share your experience



Don Thomas, MD, author of “The Lupus Encyclopedia” and “The Lupus Secrets

– Wang CH et al. Cranberry-containing products for prevention of urinary tract infections in susceptible populations: a systematic review and meta-analysis of randomized controlled trials. Arch Intern Med. 2012;172(13):988.

– Kranjčec B, Papeš D, Altarac S. D-mannose powder for prophylaxis of recurrent urinary tract infections in women: a randomized clinical trial. World J Urol. 2014 Feb;32(1):79-84. doi: 10.1007/s00345-013-1091-6. Epub 2013 Apr 30. PMID: 23633128.​

– Pachucki RJ, Corradetti C, Kohler L, Ghadiali J, Gallo PM, Nicastro L, Tursi SA, Gallucci S, Tükel Ç, Caricchio R. Persistent Bacteriuria and Antibodies Recognizing Curli/eDNA Complexes From Escherichia coli Are Linked to Flares in Systemic Lupus Erythematosus. Arthritis Rheumatol. 2020 Jun 17. doi: 10.1002/art.41400. Epub ahead of print. PMID: 32840064.