With CFS, SIBO etc we see no or low Lactobacillus, Bifidobacteria, E. Coli. This means we have diminished production of their end products. The absence of these end products can cause a variety of symptoms.  Imagine a diet where all citric fruit was removed — you could get scurvy; or for Vitamin D sources, rickets; or Iodine, goiter.

Whether symptoms develop often is dependent on DNA/SNPs.

The table below comes from DataPunk.Net and shows the known end products.

Known Supplementation

• γ-Amino butyric acid (GABA)
  • [Gamma-aminobutyric acid–metabolism and its disorders].
    • “s stiff-person syndrome, chronic fatigue syndrome, anxiety disorders and seizures”
• Biotin 
  • A Review of the Use of Biotin for Hair Loss.
• Folate
  • Response to vitamin B12 and folic acid in myalgic encephalomyelitis and fibromyalgia.
• Vitamin B12
  • Response to vitamin B12 and folic acid in myalgic encephalomyelitis and fibromyalgia.
• Riboflavin (Vitamin B2)
  • Vitamin B status in patients with chronic fatigue syndrome.
  • Metabolic features of chronic fatigue syndrome.
• 5-hydroxytryptamine (5-HT, Serotonin)
  • Maintenance of Chronic Fatigue Syndrome (CFS) in Young CFS Patients Is Associated with the 5-HTTLPR and SNP rs25531 A>G Genotype.
  • Selective serotonin reuptake inhibitors for fibromyalgia syndrome.
• Lactic acid
  • There appears to be underproduction of L-Lactic acid and overproduction of D-Lactic acid.
  • Examining clinical similarities between myalgic encephalomyelitis/chronic fatigue syndrome and D-lactic acidosis: a systematic review.
• Lactate
• Acetylcholine
  • Single nucleotide polymorphisms and genotypes of transient receptor potential ion channel and acetylcholine receptor genes from isolated B lymphocytes in myalgic encephalomyelitis/chronic fatigue syndrome patients [2016].
  • Acetylcholine mediated vasodilatation in the microcirculation of patients with chronic fatigue syndrome.
    • “Most diseases are accompanied by a blunted response to acetylcholine but the opposite is true for CFS.”
  • Efficacy of a half dose of oral pyridostigmine in the treatment of chronic fatigue syndrome: three case reports.
    • “We describe three cases who fulfill the criteria of CFS, in whom a defect of neuromuscular transmission and dysautonomia are present and who respond to acetylcholine-esterase inhibition”
• Cadaverine
  • are toxic in large doses.^[2][3]
• Indole
  • The amino acid tryptophan is an indole derivative and the precursor of the neurotransmitter serotonin.^[2]
  • A Brief Historic Overview of Clinical Disorders Associated with Tryptophan: The Relevance to Chronic Fatigue Syndrome (CFS) and Fibromyalgia (FM).
• Methanol
• Pentanol
• Propionate
• Putrescine
  • are toxic in large doses.^[2][3]
• Trimethylamine
• Urolithins
  • They are produced in the human gut, and found in the urine in the form of urolithin B glucuronide after absorption of ellagitannins-containing food such as pomegranate,^[2] strawberries, red raspberries, walnuts or oak-aged red wine.^[3]

Bottom Line

It is interesting to note that various uptake inhibitors have positive effects.  This would be consistent with low levels — the alternative approach would be supplementation to replace the non-production by the missing bacteria.

Several items are toxic in larger amount — I suspect that these items are produced to control other bacteria types (likely the ones that are now overgrown).

What is available as supplements over the counter?

• Acetylcholine (choline) 
  • See this post
• Biotin
• Folate
  • See this post
• GABA
• Indole
• Riboflavin
• 5-hydroxytryptamine (5-HT, Serotonin)
• Vitamin B12
  • See this post

Note: The above shortages will likely have knock-on effects to other chemicals, but they are likely the underpinnings of most of the symptoms seen.

This is strictly informational and no supplementation should be started without first consulting with your knowledgeable medical professionals.