I did a post earlier on a CFS patient whose labs reported high level (a subset, possible very small) and what could be done to reduce a specific strain. Ian Lipkin study found (on average) low levels for:
- Faecalibacterium prausnitzii
- Faecalibacterium cf
Faecalibacterium (formerly Fusobacterium) prausnitzii (1995) is one of the three most abundant species detected in human feces by anaerobic cultivation (1995) and consists of many stains  as shown below. As with all families, there can be some black sheep: Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis .
Items to Increase (take)
- “Rifaximin appeared to influence mainly potentially detrimental bacteria, such as Clostridium, but increasing the presence of some species, such as Faecalibacterium prausnitzii.”  
- “α-glucosidase inhibitor acarbose …48 OTUs increased by 12.8-fold, including Lactobacillaceae (8 of 9 belonging to Lactobacillus), Ruminococcaceae (6 of 11 belonging to Faecalibacterium)” 
- Probiotic appears available for veterinarians   
- “Bacillus coagulans GBI-30, 6086 (BC30); GanedenBC(30)] …increased populations of Faecalibacterium prausnitzii”  - note: this increases histamine also
Enhanced butyrate formation by cross-feeding between Faecalibacterium prausnitzii and Bifidobacterium adolescentis.
- “Bifidobacterium adolescentis L2-32, which produces acetate during fermentation, and Faecalibacterium prausnitzii A2-165, which consumes acetate and produces butyrate.”  so acetate producing probiotics are likely good.
- Enterococcus durans EP1 a Promising Anti-inflammatory Probiotic Able to Stimulate sIgA and to Increase Faecalibacterium prausnitzii Abundance . Note this was the only one of 15 Enterococcus faecium studied that had this effect. — Very strain specific. Researchers are in France.
- “Bifidobacterium pseudocatenulatum in fecal cultures from some individuals accounted for the prevalence of Desulfovibrio and Faecalibacterium prausnitzii,” 
oligosaccharides /fibre or similar
- “The ranking order of butyrate production rates was amylopectin > oat xylan > shredded wheat > inulin > pectin (continuous cultures), and inulin > amylopectin > oat xylan > shredded wheat > pectin (batch cultures). The contribution of external acetate to butyrate formation in these experiments ranged from 56 (pectin) to 90 % (xylan) in continuous cultures”  – Faecalibacterium consumes acetate and produces butyrate.
- “Relative abundance of lactose-fermenting Bifidobacterium, Faecalibacterium, and Lactobacillus were significantly increased in response to short-chain galactooligosaccharide.” 
- “soybean oligosaccharides..increased the diversity of intestinal microflora and elevated (P < .05) the numbers of some presumably beneficial intestinal bacteria 
- “inulin stimulated colonization by Faecalibacterium prausnitzii, which has anti-inflammatory effects,”  10% increase 
- “Kestose[a fructooligosaccharide] efficiently stimulates the growth of this bacterium in the intestine,” 
- “numbers of lactobacilli, bifidobacteria (P<0.001) and Faecalibacterium prausnitzii (P<0.05) were higher in the low-fat/high-fiber pigs than in high-fat/low-fiber pigs,”  
- “Associated growth of levan-degrading (e.g. Bacteroides) and butyric acid-producing (e.g. Faecalibacterium) taxa was observed in levan-supplemented media.” 
- “Potato fibres [PF]…increases in the proportion of Faecalibacterium (not Lactobacillus/Bifidobacterium, as confirmed by qPCR analysis) with increasing dietary PF concentrations suggest that PF is a possible prebiotic fibre.” 
- “Resistant maltodextrin (RM)..was associated with statistically significant increases (P < 0.001) in various operational taxonomic units matching closest to ruminococcus, eubacterium, lachnospiraceae, bacteroides, holdemania, and faecalibacterium, implicating RM in their growth in the gut.” 
- “resistant starch… increased the relative abundance of several butyrate-producing microbial groups, including the butyrate producers Faecalibacterium prausnitzii and Megasphaera elsdeni”  
- “arabinogalactan… was associated with a statistically significant increase in the concentration of total bacteria, Bacteroidetes, Faecalibacterium prausnitzii” 
- “Isoflavones[beans] alone stimulated dominant microorganisms of the Clostridium coccoides-Eubacterium rectale cluster, Lactobacillus-Enterococcus group, Faecalibacterium prausnitzii subgroup, and Bifidobacterium genus.” 
- “sodium butyrate increased the relative abundance of Bacteroides and Faecalibacterium”  – Faecalibacterium produces butyrate, so there appears to be a feed back cycle here.
- “after a specific carbohydrate diet, there was an increased representation of Faecalibacterium prausnitzii, an anti-inflammatory commensal.”
- “Subjects with higher adherence to a Mediterranean dietary pattern presented…higher levels of Clostridium cluster XVIa and Faecalibacterium prausnitzii.”  
- “Vegetarian diet was associated with higher ratio (% of group-specific DNA in relation to all bacterial DNA) of Bacteroides-Prevotella, Bacteroides thetaiotaomicron, Clostridium clostridioforme and Faecalibacterium prausnitzii, but with lower ratio (%) of Clostridium cluster XIVa…Up to 4 % of variance in microbial community analyzed .. could be explained by the vegetarian type of diet.” 
- “high high carbohydrate/low glycemic index and high saturated fat diet increased Faecalibacterium prausnitzii” 
- Increased gut microbiota diversity and abundance of Faecalibacterium prausnitzii and Akkermansia after fasting: a pilot study .
- “The relative abundance of Akkermansia and Faecalibacterium, genera associated with healthy gut mucosa and anti-inflammation, was found to increase in response to lingonberry intake.” 
- “cocoa husks …increased the Bacteroides-Prevotella group and Faecalibacterium prausnitzii,” 
- “Broad beans (Vicia faba) and lupin seeds (Lupinus albus) are legumes rich in a wide range of compound … increased significantly (P < 0.05) were Bifidobacterium spp., Lactobacillus-Enterococcus, Atopobium, Bacteroides-Pretovella, Clostridium coccoides-Eubacterium rectale, Faecalibacterium prausnitzii and Roseburia intestinalis.” 
- “ red wine polyphenols significantly increased the number of fecal bifidobacteria and Lactobacillus (intestinal barrier protectors) and butyrate-producing bacteria (Faecalibacterium prausnitzii and Roseburia) at the expense of less desirable groups of bacteria such as LPS producers (Escherichia coli and Enterobacter cloacae).”  i.e. RED Grape Seed Extract
- “dihydroflavonols were directly associated with Faecalibacterium … red wine was the best contributor to Faecalibacterium variation.” 
- “Most F. prausnitzii strains tested grew well under anaerobic conditions on apple pectin…..Many F. prausnitzii isolates were able to utilize uronic acids for growth …Most strains grew on N-acetylglucosamine” 
- “Dietary capsaicin [cayenne peppers] increased the Firmicutes/Bacteroidetes ratio and Faecalibacterium abundance,” 
- “Curcuma longa[turmeric] and Scutellaria baicalensis [Chinese Skullcap] used as feed additives…S. Enteritidis, Faecalibacterium, and Lactobacillus, both bacterial genera with known positive effects on gut health were positively selected” 
- “was more abundant in the raffinose[beans, etc] diet and the chickpea diet” 
- “MSG promoted the colonization of Faecalibacterium prausnitzii” 
- “several experiments involving downshifts to pH 5.5 resulted in Faecalibacterium prausnitzii replacing Bacteroides spp. as the dominant sequences observed.” 
- “correlation to vacuum cleaning frequency, with an increase in Faecalibacterium prausnitzii for mothers” 
Items with no effect
Items that decrease (avoid)
- :Metronidazole… known to decrease anaerobes such as Faecalibacterium” 
- “This case study investigated changes of gut microbiota with an omega-3 rich diet. Fecal samples were collected from a 45-year-old male who consumed 600 mg of omega-3 daily for 14 days. After the intervention, species diversity was decreased, but several butyrate-producing bacteria increased. There was an important decrease in Faecalibacterium prausnitzii and Akkermansia spp. Gut microbiota changes were reverted after the 14-day washout.” 
- “proton pump inhibitor…was accompanied by a lower abundance of Faecalibacterium spp.” 
- “antibiotics [which ones not specified] most notably a decrease in relative Faecalibacterium spp. numbers (P < 0.001).”  ” in some patients, complete elimination of certain bacterial communities.” 
- “the beneficial commensal Faecalibacterium prausnitzii was sensitive to Essential Oils[Nerolidol, thymol, eugenol and geraniol] similar or even lower concentrations than the pathogens.” 
- “Lactobacillus paracasei DG ..a concomitant decrease 
- “The relative abundance of Faecalibacterium prausnitzii was unaffected except with thymol [Thyme Oil] at 500 p.p.m. of essential oils tested”
- “All strains tested were bile sensitive, showing at least 80% growth inhibition in the presence of 0.5 μg/ml bile salts, “
- ” Faecalibacterium prausnitzii proportions decreased (P = 0.007, P = 0.031 and P = 0.009, respectively) as a result of the gluten-free diet” 
- “was found to be significantly lower in broccoli-fed mice.” 
- “the abundances of Bacteriodes, Prevotella, Peptostreptococcus and Faecalibacterium were lower in dogs fed the meat diet,” 
- “Faecalibacterium prausnitzii… decreased significantly on the low-FODMAP diet as compared to baseline.” 
- “enteral nutrition induced a further decline in diversity, as well as even lower levels of Faecalibacterium prausnitzii”   
- “Malnutrition was associated to the reduction of several taxa, mainly related to the genus Bacteroides, Parabacteroides, Prevotella, Streptococcus, Faecalibacterium,” 
- “High protein diet…associated with reduced concentrations of the Clostridium coccoides and C. leptum groups and Faecalibacterium prausnitzi” 
- ” smokers had lower proportions of Faecalibacterium prausnitzii”  
- “Oral Iron supplements treatment was associated with decreased abundances of operational taxonomic units assigned to the species Faecalibacterium prausnitzii,” 
- “Commensal organisms (Bacteroides thetaiotaomicron VPI-5482 and Faecalibacterium prausnitzii A2-165) and a probiotic strain (Streptococcus thermophilus LMD-9) led to up to 12-fold induction of ferritin[iron] in colon.”  — so taking iron supplements inhibits the bacteria that helps take up iron!
In discussing this post with my wife, she said “WHAT! No Omega-3, No Iron, No gluten Free, No flaxseed, No essential oils, No Flagyl for yeast infections — and now you want me to put MSG on my food and eat tons of beans!!” The results of the review on PubMed had many surprises.
- Oral Iron (but not IV Iron) reduces the bacteria that absorbs iron – “you can’t get there from here“
- Fibre is not a magic general solution — it must be the right fibres and oligosaccharides — time to read the ingredients very carefully!
- A gluten free diet likely have lower amounts of the right fibres.
Some of the above fits common perception: No Smoking, no proton pump inhibitors, no antibiotics. For yeast infections use Rifaximin instead of Metronidazole (Flagyl) — there are studies finding it just as effective.
THIS IS NOT MEDICAL ADVICE — this post is an education summary of what has been reported on PubMed. Always consult with a knowledgeable medical professional before changing diet, supplements and prescription drugs.
To Physicians and the like: Stopping as many of the reducers as is practical and trying to alter the diet towards regular bean soups and de-alcholized red wine; with lingonberries for desert! If there are no histamines issue, Bacillus coagulans.