These are some note from reviewing recent studies. I view IBS potentially cascading into IBD, UC or Crohn’s disease is some subset of patients.
- “Findings from epidemiology studies indicate that diets high in animal fat and low in fruits and vegetables are the most common pattern associated with an increased risk of IBD. Low levels of vitamin D also appear to be a risk factor for IBD. …. Unfortunately, omega 3 supplements have not been shown to decrease the risk of relapse in patients with Crohn’s disease. … Although fiber supplements have not been definitively shown to benefit patients with IBD, soluble fiber is the best way to generate short-chain fatty acids such as butyrate, which has anti-inflammatory effects. Addition of vitamin D and curcumin [Turmeric] has been shown to increase the efficacy of IBD therapy. There is compelling evidence from animal models that emulsifiers in processed foods increase risk for IBD.” 
- “viruses, and specially bacteriophages, can play a role in controlling microbial populations in the gastrointestinal tract. This may affect both bacterial diversity and metabolism, but possible implications for IBD still remain to be solved.” 
Good and Bad Bacteria
The ubiome reports earlier had a variety of unusual species. There is a lovely study on Crohn’s disease that covered a major number of families which may be of special interest to those that had their uBiome done. 
NOTE: the OTUID is an identifier for the family/species/strain. Thus you have different Bacteroides associated with remission and active. It is not a matter of having bacteroides or not having bacteroides, but the details of which species and strains.
- “the Bacteroides fragilis group and other anaerobic gram-negative bacilli (AGNB) that were previously included in the Bacteroides genus but are now included in the Prevotella and Porphyromonas genera….Infections due to AGNB are common, yet the specific identification of AGNB in these infections is difficult… are resistant to penicillins… AGNB promote infection through synergy with their aerobic and anaerobic counterparts and with each other….The B fragilis group is almost uniformly susceptible to metronidazole, carbapenems, chloramphenicol, and combinations of a penicillin and beta-lactamase inhibitors.” 
- Note: 80% of CFS patients that tried metronidazole, reported getting better, no one worst.
- “Anti-Saccharomyces cerevisiae antibodies (ASCA) of all IgG subclasses and anti-B. fragilis IgG1 levels were increased in CD patients compared to UC patients and controls.”  Note: B. fragilis was high for active disease above, Saccharomyces is a yeast (brewer yeast)
- “Compared to patients in remission, patients with active IBD had lower abundance of Clostridium coccoides (MD = -0.49, 95% CI: -0.79 to -0.19), Clostridium leptum (MD = -0.44, 95% CI: -0.74 to -0.14), Faecalibacterium prausnitzii (MD = -0.81, 95% CI: -1.23 to -0.39) and Bifidobacterium (MD = -0.37, 95% CI: -0.56 to -0.17). Subgroup analyses showed a difference in all four bacteria between patients with UC classified as active or in remission. Patients with active CD had fewer C. leptum, F. prausnitzii and Bifidobacterium, but not C. coccoides.”