This is a common symptom for both ME/CFS and Long COVID. This is reported often in samples, and thus being examined if it reaches our threshold for inclusion as defined in A new specialized selection of suggestions links. It does, but the degree of association (z-scores) are lower than prior special studies despite having a larger study population.
|Sleep: Unrefreshed Sleep||1041||107|
- Bacteria Detected with z-score > 2.6: found 139 items, highest value was 5.1
- Enzymes Detected with z-score > 2.6: found 208 items, highest value was 5.2
- Compound Detected with z-score > 2.6: found 1 items, highest value was 2.8 – effectively zero when false detection rate is considered.
The highest z-scores above are less than other symptoms despite larger sample size. This indicates that the causes are more diverse and thus less homogeneous bacteria shifts.
Interesting Significant Bacteria
All bacteria found significant had too low levels.
Low Veillonella is reported in some studies associated with sleep issues with it’s consumption of lactic acid(lactate) being cited as a possible factor:
- Gut microbiota in obstructive sleep apnea–hypopnea syndrome: disease-related dysbiosis and metabolic comorbidities 
- “patients with sleep disturbances were characterized by lower bacterial diversities and distinct microbial composition in comparison to those without sleep disturbances. The relative abundances of Salivarius, Veillonella, Klebsiella, and Eubacterium were independent predictors of sleep disturbances in patients.”  for the specific condition studied.
|Bifidobacterium catenulatum subsp. kashiwanohense (subspecies)||321||100||4.8|
|Clostridium cellulovorans (species)||40||17||4.8|
|Bifidobacterium kashiwanohense PV20-2 (strain)||318||100||4.8|
|Actinobacillus porcinus (species)||184||73||4.6|
|Thiobacillus thiophilus (species)||85||26||4.6|
All enzymes found significant had too low levels.
|Enzyme||Reference Mean||Long COVID Mean||Z-Score|
|(1->4)-alpha-D-galacturonan lyase (126.96.36.199)||2453||1074||5.2|
|2-acetylphloroglucinol C-acetyltransferase (188.8.131.522)||185||61||4.6|
|phylloquinone:disulfide oxidoreductase (184.108.40.206)||28||15||4.6|
|[RNA] 5′-hydroxy-ribonucleotide-3′-[RNA fragment]-lyase (cyclicizing; [RNA fragment]-3′- nucleoside-2′,3′-cyclophosphate-forming and hydrolysing) (220.127.116.11)||1596||634||4.5|
|CMP-N-acetyl-beta-neuraminate:beta-D-galactosyl-(1->4)-N-acetyl-beta-D-glucosaminyl-R (2->3)-N-acetyl-alpha-neuraminyltransferase (configuration-inverting) (18.104.22.168)||1682||659||4.5|
|propane-1,3-diol:NAD+ 1-oxidoreductase (22.214.171.124)||811||106||4.5|
|ATP:(Kdo)-lipid IVA 3-deoxy-alpha-D-manno-oct-2-ulopyranose 4-phosphotransferase (126.96.36.199)||1591||645||4.5|
The key take away is that lactate/lactic acid levels appears to be a significant contributor. The reason that it is high is the lack of lactate consumers. Removal of lactate producing probiotics from supplements appears to be a logical first step (i.e. Lactobacillus), followed by taking Vitamin B1 shortly before bed time.
For suggestions on lowering it, see this old post of mine in the ME/CFS context.
The issue may not be lactate by itself, but by the form of lactate (d-lactate –> bad)
Results and conclusion: Administration of L-lactate does not influence sleep-wake cycle of experimental animals. At the same time, its artificial optical analog D-lactate induces the significant (as compared to the control) decrease in wake (34.8% to 26.5%) and increase in slow wave sleep (57.4% to 69.2%). It has been suggested that D-lactate may be the antagonist of one or several L-lactate receptors.[D-lactate as a novel somnogenic factor?] 
“Thiamine (Vitamin B1) replenishment at intravenous doses of 100 mg every 12 h resolved lactic acidosis and improved the clinical condition in 3 patients.” 
“Lactomin[300 mg Lactobacillus acidophilus, 300 mg Bifidobacterium longum] was discontinued, and she was treated with sodium bicarbonate and oral antibiotics. The probiotics the patient had taken were likely the cause of D-lactic acidosis ”