Some CFS patients have been found to have high glutamate levels. There are two possibilities:
- Bacteria or infections producing too much
- Bacteria that normally consumes it are missing — this I suspect is the more common cause of high levels in CFS.
Glutamate pathways are reported impacted in CFS .
- “These findings suggest that dietary glutamate may be contributing to FM symptoms in some patients.” 
- “patients with FM showed higher levels of glutamate/glutamine (Glx) compounds” 
- “CSF concentrations of substance P and glutamate have been repeatedly found to be increased in fibromyalgia patients [32–34].” 
Now we hit the interesting part of this issue:
- “GI-tract-abundant Gram-positive facultative anaerobic or microaerophilic Lactobacillus, and other Bifidobacterium (Actinobacteria) species such as Lactobacillus brevis and Bifidobacterium dentium are capable of metabolizing glutamate to produce gamma-amino butyric acid (GABA),”  
- “The results revealed that 10 isolates, i.e., Lactobacillus buchneri (2 isolates), Lactobacillus brevis (6 isolates), and Weissella hellenica (2 isolates) had a high GABA–producing ability” out of 53 tested from Japanese foods: aburazushi, narezushi, konkazuke, and ishiru  10/53 or 19%
- “In this paper, we screened our collection of 135 human-derived Lactobacillus and Bifidobacterium strains for their ability to produce GABA from its precursor monosodium glutamate. Fifty eight  strains were able to produce GABA. The most efficient GABA-producers were Bifidobacterium strains (up to 6 g/L)….The genes were found in the following genera of bacteria: Bacteroidetes (Bacteroides, Parabacteroides, Alistipes, Odoribacter, Prevotella), Proteobacterium (Esherichia), Firmicutes (Enterococcus), Actinobacteria (Bifidobacterium). These data indicate that gad genes as well as the ability to produce GABA are widely distributed among lactobacilli and bifidobacteria (mainly in L. plantarum, L. brevis, B. adolescentis, B. angulatum, B. dentium) and other gut-derived bacterial species.”  58/135 = 43%
“GABA metabolism is dependent on the activity of three enzymes: glutamic acid decarboxylase, GABA-transaminase and succinic semialdehyde dehydrogenase. Decreased activity of these enzymes may cause many neurological syndromes, such as stiff-person syndrome, chronic fatigue syndrome, anxiety disorders and seizures.” 
Given any random bifidobacteria or lactobacillus strain, the possibility of it producing GABA from glutamate appears to be between 19% and 43%. The best odds are for
- L. plantarum,
- L. brevis,
- B. adolescentis,
- B. angulatum,
- B. dentium
Given the low levels of bifidobacteria, lactobacillus and E.Coli seen in CFS patients, a high level of glutamate would be expected. It would not effect all because these are not the sole consumers of glutamate.
This model gives a concrete biological process accounting for this shifts seen.