Borderline SIBO/IMO? Two GIs disagree on rifaximin + neomycin

Hi all,

I’m trying to understand whether my lactulose breath test really looks like SIBO/IMO, or whether it looks more like a borderline/late rise. I have received two different gastroenterology opinions (one advising for rifaximin + neomycin, while the other one being completely against it) and I’m unsure how to proceed.

In short, I’ve been sick for about 6 months with nausea, poor appetite, weakness, bloating + gas. There have been days where I was so weak I could barely get out of bed. I ended up at urgent care and the ER a few times, but mostly received IV fluids and Zofran/Reglan for nausea.

Low-FODMAP plus gluten-free has helped a lot, but I’m still not feeling normal. I still get episodes if I try new foods, even small amounts of foods that should theoretically be safe.

My fructose breath test was called positive:

Fructose breath test
0 min: H2 2 ppm, CH4 7 ppm
60 min: H2 15 ppm, CH4 15 ppm
120 min: H2 27 ppm, CH4 19 ppm
180 min: H2 32 ppm, CH4 21 ppm

My lactulose breath test is what confuses me:

Lactulose breath test
0 min: H2 3 ppm, CH4 7 ppm
20 min: H2 2 ppm, CH4 6 ppm
40 min: H2 2 ppm, CH4 7 ppm
60 min: H2 2 ppm, CH4 5 ppm
80 min: H2 5 ppm, CH4 7 ppm
100 min: H2 18 ppm, CH4 11 ppm
120 min: H2 33 ppm, CH4 13 ppm
140 min: H2 42 ppm, CH4 15 ppm
160 min: H2 47 ppm, CH4 14 ppm
180 min: H2 55 ppm, CH4 15 ppm

So methane starts at 7 ppm and crosses 10 ppm only at 100 minutes. Hydrogen stays low until about 100 minutes, then rises later.

One gastroenterologist prescribed rifaximin plus neomycin for 14 days for SIBO/IMO.

Another gastroenterologist strongly disagrees. GI2 thinks this may be more of a post-antibiotic dysbiosis/permeability/malabsorption situation, because I had several antibiotic courses shortly before this started, and she thinks more antibiotics could make me worse.

For context, from Aug 2025 to Jan 2026 I had ceftriaxone/Rocephin IM plus 7 days of doxycycline for urethral/urinary symptoms, then 7 days of cephalexin/Keflex for the same thing, then 10 days of amoxicillin after one urgent care center labeled my throat symptoms as strep throat. I was also given topical mupirocin and clotrimazole. My gut symptoms started around Dec 2025, when I was also under a very large amount of stress.

GI2 wants me to first rule out celiac properly with EGD plus duodenal biopsies, then maybe MR enterography if needed.

Other relevant context: colonoscopy with terminal ileum and random biopsies was normal. Fecal calprotectin was elevated at 310.8. Stool analysis showed muscle fibers, starch granules and fat droplets, leading my endocrinologist to think it might be pancreatic. But my fecal elastase is >800. Celiac is not fully ruled out because I’ve been gluten-free, but HLA DQ2/DQ8 is positive. CRP/ESR were normal. MR abdomen/MRCP did not show obstruction, stones or bile duct dilation.

My stool pattern used to be one bowel movement every 1 to 3 days, lately improved to every day. Stool is usually light brown, stickier than normal, and forms soft blobs. I’m usually not clearly constipated and I don’t usually have diarrhea, unless I eat something my gut doesn’t tolerate. Then I feel nauseated for a few days, get diarrhea, and slowly improve again.

With all of this in mind, does this lactulose test look like true SIBO/IMO to you, or more like a late/colonic rise? Would you take rifaximin plus neomycin with this result, or would you work up celiac/small bowel inflammation first?