SIBO / Colon Bacterial Overgrowth (breath test negative)

In April/2015 I had a very stressful period and a flu after which I experienced a major attack of acid reflux but the atypical kind where I felt no heart burn and all of the symptoms were in my throat. My throat literally burnt. Endoscope found nothing and ENT doc diagnosed LPR, and I was placed on a PPI. Within 3 weeks of starting PPI treatment something changed in my stomach/GI. I stopped the PPI after a month and then reluctantly tried a stronger one in September as my GI thought dexilant could be more beneficial. It was NOT. It made things worse and I have not recovered since.

Since April:

-my stomach continues to make growling and roaring noises WITH and WITHOUT food. Some sort of chemical reaction is occurring NON-STOP leading to the production of gas, which bubbles up as vapour/gas and settles in my throat. I'm burping all day as a result and its difficult to swallow salivia because of the gas pressure coming up from the stomach.
-I experience a taste in my mouth that varies from salty to sour and I'm clearing my throat every 20 seconds.
-I'm bloated all day and night because of the constant chemical reaction that is taking place
-I can't seem to fall asleep (circadian rhythm messed up). In the rare cases that I do its a very disturbed and surface sleep where I find myself dreaming but awake periodically.
-for the past few months Im getting frothy/bubbly urine (lab results no infection and no protein)

I initially thought that the GI issues could be SIBO but I had a hydrogen and methane test done which was negative for both. However, the test wasn't a modern test. They made me drink a solution and periodically blow into a series of balloons, which they then sent to the lab for testing. Perhaps the test was accurate but not sure.

I've seen 3 GI docs, an ENT.

-SIBO test in August/2015 before use of Dexilant was negative
-I've had the stool tests done by the GIs for parasites, h.pylori etc (negative)
-CT scan with contrast of abdomen - normal
-Small bowel series - normal
-Barium swallow - normal
-Esophageal manometry - normal
-Gastric emptying study - normal
-TSH is slightly below the normal reading (was 0.24 in my recent test - normal range is 0.30 - 4.00 mIU/L)
-Vitamin B12 = 401 (normal range = 198 - 615 pmol/L)

No one seems to have any idea whats going on in my stomach/GI and with my sleep.

I recently did a comprehensive stool test from Genova and discovered that many of the bacteria are HIGH. The mycology and parasite segment of the test was negative. I'm currently in the middle of a humaworm parasite 30 day course yet the symptoms i describe continue.

Am I wrong to think I have SIBO / Colon Bacterial Overgrowth as the root cause of my LPR despite having a negative hydrogen and methane breath test?

The diversity of my micro biome is LOW.

All of the HIGH = 5th quantile

Bacteroides-Prevotella group = 1.5E9 (normal range = 3.4E6 -1.5E9) = HIGH
Bacteroides vulgatus = 5.2E9 (normal range <=2.2E9) = HIGH
Barnesiella spp = 8.4E8 (normal range <=1.6E8) = HIGH
Odoribacter spp = 2.1E8 (normal range <=8.0E7) = HIGH
Prevotella spp. = 1.5E7 (normal range 1.4E5 -1.6E7)
Anaerotruncus colihominis = 4.8E7 (normal range <=3.2E7) = HIGH
Butyrivbrio crossotus = 1.3E5 (normal range 5.5E3 -5.9E5)
Faecalibacterium prausnitzii = 8.1E9 (normal range 5.8E7 -4.7E9) = HIGH
Pseudoflavonifractor spp. = 4.1E8 (normal range 4.2E5 -1.3E8) = HIGH
Ruminococcus spp. = 5.5E7 (normal range 9.5E7 -1.6E9) = LOW
Collinsella aerofaciens = NONE (normal range 1.4E7 -1.9E9) = LOW
Desulfovibrio piger = NONE (normal range <=1.8E7) = LOW
Fusobacterium spp. = 4.4E5 (normal range <=2.4E5) = HIGH

Firmicutes/Bacteroidetes Ratio = 5 (normal range 12-620) = LOW

The Gastrointestinal Microbiome showed:

Lactobacillus sp = No Growth
Escherichia coli 4+
Bifidobacterium 1+

The DNA PCR results for Lacto and Bifi were:

Lactobacillus spp. = 3.3E8 (normal range 8.3E6 -5.2E9)
Bifidobacterium spp. = 4.5E8 (normal range <=6.4E9)
Bifidobacterium longum = 9.7E7 (normal range <=7.2E8) Tweet