In Ian Lipkin et al 2017 study, high bacteroides fragilis was reported (on average). [Index to all posts on Study] This bacteria is well studied with over 5000 articles on Pub Med. Some antibiotics are effective, but there is increasing resistance [MedScape].
It is also strongly implicated with Alzheimer’s Disease and Parkinson’s (see these posts for details). For the most current list of items that impact this bacteria see my Analysis Site.
It produces butaric acid.
- “Fecal excretion of Bacteroides fragilis, Clostridium perfringens, and clostridial spores decreased after 7 d of consumption of Streptococcus thermophilus and bifidobacterium breve C50″ 
- “the administration of bifidobacterium longum CECT 7347 reduced the numbers of the Bacteroides fragilis group” 
- ” Coculture stimulated the growth of B. longum, retarding that of B. fragilis, with concomitant changes in the production of some proteins and metabolites of both bacteria.” 
- Effect of the oral intake of yogurt containing Bifidobacterium longum BB536 on the cell numbers of enterotoxigenic Bacteroides fragilis in microbiota.
- “Lactobacillus casei Zhang …an increase in Bacteroides fragilis 
- “Lactobacillus casei variety rhamnosus (LCR35)..increased the population of Bifidobacterium, Lactobacilli, Enterococcus and Bacteroides fragilis group” 
- “Lactobacillus acidophilus, Bifidobacterium lactis and Lactobacillus F19 prevent antibiotic-associated ecological disturbances of Bacteroides fragilis in the intestine.” – stopped the drop of b.fragilis seen with taking antibiotics.
- “Mediterranean diet.. reduces”
- “the relative abundance of Bacteroides fragilis was greater than the control from feeding the Chardonnay grape diet.”  Chardonnay are white wine (green-skinned) grapes. In the same study, Cabernet Sauvignon [red wine, purple] grapes did not increase.
- “a strict vegetarian diet (SVD) for 1 month..an increase in commensal microbes such as Bacteroides fragilis” 
- “oat bran…lower numbers of Enterobacteriaceae, Akkermansia and Bacteroides Fragilis” 
- “Population of Bacteroides fragilis significantly decreased after elemental diet” 
- “polydextrose ingestion…species (B. fragilis, B. vulgatus, and B. intermedius) decreased, whereas LACTOBACILLUS: and BIFIDOBACTERIUM: species increased.” 
- “Rats on the all-rice diet had significantly lower faecal concentrations of the main menaquinone-producing bacterial species (Bacteroides fragilis and Bacteroides vulgatus) than animals on either of the other two diets ( a rice + beans diet or a stock diet)” 
- “Tannic acid, propyl gallate and methyl gallate, but not gallic acid, were found to be inhibitory to the growth of intestinal bacteria Bacteroides fragilis ATCC 25285″ 
- “whole-grain barley…decreased the Bacteroides fragilis group, but increased the number of Bifidobacterium only when dietary fat was consumed at a low level.” 
- “Nisin growth curves of an a peptide reducing the growth of the B fragilis” 
- “Inulin …decreased numbers of Bacteroides fragilis,” 
- ” With the exception of selective inhibitory action of n-hexane extract of Nigella orientalis on growth of Bacteroides fragilis (MIC = 0.5 mg/mL),”  — specific seed extract is needed and then only some impact.
- “The fecal levels of B. fragilis were significantly increased by the inclusion of cholesterol(1%) in the diets.” 
- Human fecal flora: variation in bacterial composition within individuals and a possible effect of emotional stress 1976]. Stress increase it. Tetracyclines work on some strains but other strains are resistant.
During my readings, I came across the following results which validate a speculation that I had: individual strains different mixtures produce different chemicals. So starting with hundred of thousands strains, we need to see how each interact with each other…. if we want to be strictly scientific [All of the computer storage in the world would not be enough to store the results]. Alternatively, guided trial-and-error is viable.
- “Therefore, cocultures of Bifidobacterium and Bacteroides can behave differently against fermentable carbohydrates as a function of the specific characteristics of the strains from each species.” 
- “When stressed, overpopulated or pathogenically stimulated, B. fragilis releases a remarkably complex array of endotoxins and exotoxins (such as fagilysin), lipooligosaccahrides (LOS), lipopolysaccharide (LPS), including an extremely proinflammatory B. fragilis LPS (BF-LPS), microRNA-like sncRNA, and a wide variety of bacterial-derived amyloids (9–11, 56, 57, 64–66). ” 
For the most current list of items that impact this bacteria see my Analysis Site.