Over the last 2 decades that I have been active in the Chronic Fatigue Syndrome, thyroid issues in patients with CFS has been a common chorus on many forums. I have not had thyroid issues (typically hypothyroidism or thyroiditis – too low levels) but a reader asked me to look at it — particularly from the microbiome aspects and hopefully with some probiotic interventions being possible. This is what I found:
Thyroid and CFS
There are over 60 pub med articles so it is not an incidental thing. Some high lights that I found are:
- ” Detailed analyses showed that thyroid disease (P<0.01) and gynecologic surgery (P<0.05) were significantly more common in FM.” 
- Thyroid autoimmunity may represent a predisposition for the development of fibromyalgia?  ” we observed that the presence of autoimmune thyroid disease worsens fibromyalgia (FM) symptoms … thus suggesting a hypothetical role of thyroid autoimmunity in FM pathogenesis.”
- “Good responders [to B12 and folic acid] had used significantly more frequent injections (p<0.03) and higher doses of B12 (p<0.03) for a longer time (p<0.0005), higher daily amounts of oral folic acid (p<0.003) in good relation with the individual MTHFR genotype, more often thyroid hormones (p<0.02), and no strong analgesics at all, 
- “However, it is also known that iodine deficiency may give rise to clinical symptoms ofhypothyroidism without abnormality of thyroid hormone values…we will focus on the relationship between iodine deficiency and obesity, ” 
- “The prevalence of thyroid dysfunction in women with suspected FM does not differ from that in the general population.” 
- “FM is often associated with other diseases that act as confounding and aggravating factors, such as rheumatoid arthritis (RA), spondyloarthritides (SpA), osteoarthritis (OA) and thyroid disease.” 
- ” This finding support thyroid autoimmunity may influence the development of FM, but the evidence which support that FM is related to autoimmune etiology is not clear,” 
Obesity and Thyroid
This area has been heavily studied with over 1100 articles,
- ” The prevalence (percentage (95% confidence interval)) of thyroid autoimmunity was lower in the individuals with normal weight, 2.9% (2.0-4.2), than in those with overweight, 6.3% (3.9-9.9), and obesity, 5.6% (2.5-11.3) (p=0.02).” 
- ” No differences in thyroid function were observed in both age groups. In the 6-8-year-old group, obese schoolchildren had higher iodine intake than normal-weight children (415.5 vs. 269.1 μg/day, p < 0.05), but no differences in salt intake. In contrast, in the 9-12-year-old group, obese schoolchildren had higher salt intake than normal-weight children (6.2 vs. 3.8 g/day, p < 0.05), but no differences in iodine intake.” 
- Paradoxical relationship between body mass index and thyroid hormone levels; a study using Mendelian Randomization. “Our analysis shows that children with a genetically higher BMI had higher Free tri-iodothyronine (FT3) but not FT4 levels indicating higher BMI/fat mass has a causal role in increasing FT3 levels.”
- Maternal hypothyroxinaemia in pregnancy is associated with obesity and adverse maternal metabolic parameters.
- Microbiome impact on metabolism and function of sex, thyroid, growth and parathyroid hormones. 
Microbiome and Obesity
There are almost 500 articles dealing with probiotics and obesity. As expected, some probiotics increases weight gain and other reduces weight.
- “Experimental studies with gut microbiota transplantations in mice and in humans indicate that a specific gut microbiota composition can be the cause and not just the consequence of the obese state and metabolic disease, which suggests a potential for gut microbiota modulation in prevention and treatment of obesity-related metabolic diseases.” 
- ” L. plantarum FH185 was demonstrated that it has anti-obesity effect in the in vitro and in vivo test”
- “Lactobacillus reuteri GMNL-263 (Lr263) probiotics, which have been shown to reduce obesity and arteriosclerosis in vivo.” 
- ” oral administration of L. rhamnosus and herbs resulted in a significant decrease in the body weight, epididymal fat mass, fasting blood glucose and serum insulin levels.” 
- Anti-obesity effect of Lactobacillus gasseri SBT2055 accompanied by inhibition of pro-inflammatory gene expression in the visceral adipose tissue in diet-induced obese mice.
Or to cite a 2014 review of all of the literature “Analysis of the eligible articles pointed out that Lactobacillus gasseri SBT 2055, Lactobacillus rhamnosus ATCC 53103, and the combination of L. rhamnosus ATCC 53102 and Bifidobacterium lactis Bb12 may reduce adiposity, body weight, and weight gain. This suggests that these microbial strains can be applied in the treatment of obesity” 
Microbiome and Thyroid
- Link between hypothyroidism and small intestinal bacterial overgrowth.  “It has been reported that SIBO may be present in more than half of patients with hypothyroidism. Lauritano et al. studied 90 subjects (hypothyroidism [n = 50] and control [n = 40]) and found that significantly higher numbers of patients (54%) with hypothyroidism have SIBO as demonstrated with positive glucose breath test compared with the control group (5%) (P < 0.001). … A study with probiotic Bacillus clausii also showed promising results in SIBO. “
- DYSMICROBISM, INFLAMMATORY BOWEL DISEASE AND THYROIDITIS: ANALYSIS OF THE LITERATURE. -” The axis dysmicrobism-IBD-autoimmune reaction will be investigated as a possible etiopathogenic mechanism to Autoimmune Thyroiditis. If such is the case, then the employment of specific probiotic strains may represent a useful approach to moderate the immune system.”
- Does microbiota composition affect thyroid homeostasis? 
- Gut microbe analysis between hyperthyroid and healthy individuals.  “decrease of Bifidobacterium and Lactobacillus ((*) P < 0.05), and increase of Enterococcus ((*) P < 0.05) in the hyperthyroid group. “While this is the opposite of hypothyroidism, it does demonstrate that the microbiome plays a role.
- “Further studies are clearly needed to test the hypothesis that the gut commensal microflora represents an important environmental factor triggering Hashimoto’s thyroiditis.” 
Thyroid and Vitamin D
Vitamin D is generally very low with FM and CFS, with symptom decreasing as the level increases. This raise the question whether there is an association of hypothyroidsim and vitamin D levels.
- Vitamin D and thyroid diseases.  “, particularly levels below 12.5 ng/ml should be considered as an additional, but important risk factor for development of thyroid autoimmunity, both chronic autoimmune thyroiditis and Graves´ disease.”
- Low Serum Vitamin D Is Associated with Anti-Thyroid-Globulin Antibody in Female Individuals. 
- The effect of vitamin D on thyroid autoimmunity in non-lactating women with postpartum thyroiditis  ” The study’s results suggest that vitamin D supplementation may bring benefits”
There is significant evidence that hypothyroidism is connected to the microbiome as well as obesity to the microbiome. There are no studies investigating if both are connected to the same shift. The association of a mother with hypothyroidism to a child with hypothyroidism appears to be more connected with the mother’s microbiome being passed along than DNA (which would be expected to connected to both parents). The available literature suggests the following probiotics may improve these conditions (I’ve omitted the stains to simplify matter) – either by known anti-obesity effects OR by addressing SIBO.
- Lactobacillus gasseri,
- Lactobacillus rhamnosus,
- Lactobacillus reuteri
- Bifidobacterium lactis
- Bacillus clausii
Having a combination of these with other probiotics have the risk that the other probiotics may counter-act the benefits.
Additionally, Vitamin D is a clear benefit. If the microbiome is off, the absorption may be low so a rate of 10-15000 IU/day should be discussed with your medical professional.
Supplementing with Iodine is unclear. High levels appears to cause it “Does iodine excess lead to hypothyroidism? Evidence from a case-control study in India. , so any supplementation should be done with care and testing.