For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

• Chicory
• Inulin
• Grapes (table)

ENHANCED BY

• High animal protein diet
• Bile
• Pyruvate
• Milk-derived saturated fat
• High protein diet
• Barley
• High meat diet

PubMed Data

There are over 120+ studies on PubMed.

• Disease:
  • “Differential abundant taxa identified Juvenile Idiopathic Arthritis  patients for the HLA-B27 allele, including Bilophila” [2016]
  • “pediatric multiple sclerosis … had a significant enrichment in relative abundance for members of the Desulfovibrionaceae (Bilophila, ” [2016]
• Diet:
  • “Adding meat back in to a vegan diet caused an immediate increase in the bacteria (Bilophila wadsworthia, Alistipes putredinis and species in the genus Bacteroides) that grow with exposure to bile, which increases when a person eats more fat.” [From Nature]
  • Increases with High saturated fat [2017]
  • 2013 article “Diet rapidly and reproducibly alters the human gut microbiome”,

  • “The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes,Bilophila and Bacteroides) a

• Probiotics:
  • “Lactobacillus plantarum LIP-1 …significantly less lipopolysaccharide-producing bacteria (especially Bilophila, Sutterella and Oscillibacter) ” [2017]
  • “LGG Lactobacillus rhamnosus GG … including decreased abundance of Bilophila wadsworthia ” [2017] [2017]
  • Lactobacillus kefiri LKF01 DSM32079  ..observed a reduction of Bilophila” [2017]
  • “Bifidobacterium longum… absence with animal diet caused a significant increase in the relative abundance of Bilophila,” [2016]
• Antibiotics:
  • “Clindamycin showed antimicrobial activity by all methods,” [1998]
  • ” only metronidazole was uniformly bactericidal” [1993]
  • penicillin resistant [src]

Bottom Line

Avoid:

• High animal protein/meat diet
• Bile
• Milk-derived saturated fat
• Barley

Consume:

• Lactobacillus plantarum
• Bifidobacterium longum.
• Lactobacillus rhamnosus GG
• Lactobacillus kefiri
• Chicory
• Inulin
• Grapes (table) – likely grape seed extract will help

I did a post earlier this year on increasing this genus. As always, some are high and some are low. The working hypothesis is that the high genus are causing many symptoms. CFS have many symptoms — so different high genus are expected. This makes effective treatment more difficult; in theory with uBiome results we can individualize treatment for the person’s uBiome shifts.

For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

• Resistant starch (type IV)
• High fat diet
• Flaxseed
• Omega 3 fatty acids

ENHANCED BY

• Fasting
• Rhubarb
• Grapes (table)
• Daesiho-tang (DSHT)
• Cranberry bean flour
• High protein diet
• Heme
• Pomegranate ellagitannins
• Melatonin
• Lingonberries
• Low processed foods diet
• Cranberry polyphenols
• Resveratrol
• Metformin
• Green tea

PubMed Data

There are 330+ studies on PubMed

• Disease:
  • “The intestinal microbiota of patients with constipated-predominant irritable bowel syndrome (C-IBS) …increase of Enterobacteriaceae, Desulfovibrio sp., and mainly Akkermansia muciniphila ” [2016]
  • “Lower numbers of this bacterium have been associated with diabetes, obesity, and IBD (31), and supplying a gluten-free diet to mice increased fecal levels of Akkermansia species (32). In contrast however another study found that levels of A. muciniphila were four times higher in patients with colorectal cancer than in healthy controls (33).”  [2015]
  • “atopic children showed a significant depletion in members of the …Akkermansia muciniphila ” [2012]
  • “decreased abundance of genus Akkermansia … in food allergy” [2017]
  • “we found a significant increase in some taxa such as Akkermansia in untreated multiple sclerosis twins. ” [2017]
  • “Differentially abundant gut microbes, such as Akkermansia, were observed in Parkinson’s disease ” [2017]
  • ” Akkermansia muciniphila, Butyricicoccus pullicaecorum and Clostridium colinum were decreased in ulcerative colitis along with genus Roseburia.” [2017]
  • “Reduced in chronic urticaria ” [2017]
• Diet:
  • “The abundance of specific microbial species known to have anti-inflammatory effects, such as Akkermansia and Desulfovibrio, was increased by whole black raspberries and their residue.” [2017]
  • “a six-week high-protein diet (45% protein) … decreased Akkermansia muciniphila, [2017]
  • ” daily consumption of sweetened dried cranberries (SDC) … an increase in Akkermansia bacteria” [2017]
  • “Pomegranate polyphenols enhanced urolithin and propionate production, as well as Akkermansia” [2017]
  • “Ethanol exposure diminishes intestinal A. muciniphila abundance in both mice and humans” [2017]
  • Anti-obesity Effect of Capsaicin in Mice Fed with High-Fat Diet Is Associated with an Increase in Population of the Gut Bacterium Akkermansia muciniphila [2017].
  • “Melatonin…increase the abundance of mucin-degrading bacteria Akkermansia” [2017]
  • Metformin Is Associated With Higher Relative Abundance of Mucin-Degrading Akkermansiamuciniphila and Several Short-Chain Fatty Acid-Producing Microbiota in the Gut.  – Diabetes drug
  • ” kodo millet whole grain and bran supplementation…promoted … Akkermansia” [2017]
  • “Many of the bacteria,…. Akkermansia …  whose proportions increase with exposure to  bisphenol A (BPA) and ethinyl estradiol (EE), ” [2016]
  • Increased gut microbiota diversity and abundance of Faecalibacterium prausnitzii and Akkermansia after fasting: a pilot study.[2015]
• Prebiotics:
  • “EpiCor fermentate .. a significant increase in Akkermansia muciniphila was observed.” [2017]
  • ” fructooligasaccharide administration showed certain effects on gut microbiota restoration (such as an increase of Akkermansia),” [2017]
  • “Akkermansia muciniphila, belonging to mucin-degrading species, became a dominant species in Verrucomicrobia phylum after treatment with fructo-oligosaccharides and inulin.” [2017]
• Probiotics:
  • Akkenmansia muciniphila probiotic in development [2017] [2017]
  • “The administration of Lactobacillus fermentum  FTDC 8312 also altered the gut microbiota population such as an increase in the members of genera Akkermansia” [2017]
  • “The present Lactobacillus plantarum study demonstrates that Akkermansia muciniphila was significantly enriched ” [2017]
    • ” Lactobacillus plantarum …significantly less… mucosa-damaging bacteria (Bilophila and Akkermansia muciniphila), ” [2017]
    • ” Lactobacillus plantarum — no change” [2013]
  • “B. longum BB536 and L. rhamnosus HN001… the abundance of Akkermansia muciniphila was increased” [2017]
  • “L. rhamnosus hsryfm 1301 …significantly increased the relative abundance of Bacteroides spp., Lactobacillus spp., Butyrivibrio spp., Holdemania spp., Treponema spp. and Akkermansiaspp.  [2014]
• Antibiotics:
  • “Azithromycin induced a modest decline in microbiota richness and a shift in taxonomic composition driven by a reduction in the relative abundance of Proteobacteria and Verrucomicrobia (specifically Akkermansia muciniphila). ” [2017]

Bottom Line

• Inconclusive: Lactobacillus plantarum, (B. longum BB536 and L. rhamnosus HN001 — which one does what?)

Avoid:

• Capsaicin (Chili Peppers)
• Rhubarb
• Grapes (table)
• Daesiho-tang (DSHT)
• Cranberry bean flour
• High protein diet
• Heme
• Pomegranate ellagitannins
• Melatonin
• Lingonberries
• Low processed foods diet
• Cranberry polyphenols
• Resveratrol
• Metformin
• Green tea
• Lactobacillus fermentum
• Lactobacillus rhamnosus
• Akkenmansia muciniphila probiotic (when it becomes available)

Consume

• Resistant starch (type IV)
• High fat diet
• Flaxseed
• Omega 3 fatty acids

I did an earlier post on a member of this genus which was reported high in most CFS patients by Ian Lipkin et al 2017 study .  In this post we can add probiotics to the list of controlling substances instead of just antibiotics.

For updated information see Microbiome Prescription

DataPunk.Net

INHIBITED BY

• β-Glucan
• Jerusalem artichoke
• Resistant starch (type IV)
• Whole-grain barley
• Low carbohydrate diet
• Chicory
• Epicatechin
• (+)-Catechin
• Inulin
• Resveratrol
• Dopamine
• Navy bean (Cooked)

ENHANCED BY

• Epinephrine
• Cranberry bean flour
• Red wine
• Heme
• Berberine
• Cranberry bean flour [parent]
• L-citrulline
• Mediterranean diet
• Flaxseed
• Saccharomyces boulardii
• High carbohydrate diet

ANTIBIOTIC RESISTANCE

• Cephalosproin
• Tetracycline

PubMed Data

There are 4700+  studies on PubMed. A lot of these are associated with oral/dental health.

• Disease:
  • Population-Genomic Insights into Variation in Prevotella intermedia and Prevotellanigrescens Isolates and Its Association with Periodontal Disease. [2017]
  • “Dysbiosis, consisting of enrichment in some Gram-negative taxa (including Veillonella, Prevotella, Haemophilus, Neisseria, Campylobacter, and Fusobacterium), has been reported in association with gastroesophageal reflux disease” [2016]
  • “the study found Veillonella(19%), Prevotella (12%), Neisseria (4%), and Fusobacterium (9%) to be more prevalent in patients with reflux esophagitis and Barrett’s esophagus than in controls.” [2014]
  • “Consistent with the literature linking psychiatric disorders with dysbiosis is that life adversity during childhood and certain temperaments that develop early in life are associated with altered gut microbiota, particularly the Prevotella species. ” [2017]
  • “The P. copri and B. vulgatus species were associated with insulin resistance in previous studies.” [2017]
  • “Subjects with improper levels of total cholesterol were enriched in Prevotella” [2017]
  • ” Women (N = 40) with incident bacterial vaginosis (Nugent 7-10) had significantly lower concentrations of lactobacilli and higher concentrations of Gardnerella vaginalis, Atopobium vaginae, and Prevotella bivia, at the incident visit ” [2017]
  • “We observed the declined abundance of Prevotella_9 and Dialister in Hypothyroid Hashimoto’s thyroiditis , while elevated genera of the diseased group included Escherichia-Shigella and Parasutterella.” [2017]
  • ” genus Prevotella was under-represented in enthesitis-related arthritis patients. ” [2017]
  • “A significant inverse correlation was found between the abundance of Prevotella and the severity of postprandial distress-like symptoms in patients with functional dyspepsia” [2016] – High prevotella means less severe.
  • “A growing number of microbiota constituents such as Prevotella copri, Porphyromonas gingivalis, and Collinsella have been correlated or causally related to rheumatic disease. [2016]
  • Intestinal Dysbiosis and Rheumatoid Arthritis: A Link between Gut Microbiota and the Pathogenesis of Rheumatoid Arthritis [2017].
    • “a marked increase of species belonging to the genus Prevotella”
• Diet:
  • “niacin had a trend to decrease the percentage of Prevotella, and to increase the abundance of Succiniclasticum, Acetivibrio and Treponema. “
  • Antimicrobial Effects of Mastic Extract Against Oral and Periodontal Pathogens[2017].
    • Mastic extract led to significantly (P ≤0.016) increased inhibition of the tested periodontal pathogens((Porphyromonas gingivalis,  Streptococcus oralis, Aggregatibacter actinomycetemcomitans, Fusobacterium nucleatum, Prevotella intermedia, and Prevotella nigrescens) ) compared with H₂O_{2(Hydrogen Peroxide)}. No effect of mastic extract was observed on Streptococcus mutans”.
  • “Dietary advanced glycation end products restriction altered the bacterial gut microbiota with a significant reduction in Prevotella copri and Bifidobacterium animalis relative abundance” [2017]
  • Sialic Acid (R, R2) (higher levels found in red meat and milk)
    • A relative rise in Prevotella
  • “Rosemary Extract …increased the Blautia coccoides and Bacteroides/Prevotella groups and reduced the Lactobacillus/Leuconostoc/Pediococccus group in both types of animals.” [2014]
  • “cooked navy bean (NB) or black bean (BB) similarly altered the fecal microbiota community structure (16S rRNA sequencing) notably by increasing the abundance of carbohydrate fermenting bacteria such as Prevotella, ” [2017] — NOTE: DataPunk states opposite.
  • “Higher relative abundance of Streptococcus sobrinus and Prevotella melaninogenica was observed in plaque samples in the reference group [lower sugar intake]. ” [2017]
  • “At the genus level, strict vegetarians had a higher Prevotella abundance and Prevotella/Bacteroides ratio than the other groups.” [2017]
  • ” However, lipopolysaccharides increased with the reduction of 25(OH)D (p-trend <0.05). Prevotella was more abundant ” [2017]
    • ” Lower level of vitamin D resulted in reduced vitamin D receptor and increased expression of pro-inflammatory genes in the colon at 3 months, lower numbers of colonic Bacteroides/Prevotella ” [2014]
  • “antimicrobial effect observed for the grape seed polyphenols, particularly against Bacteroides, Prevotella and Blautia coccoides-Eubacterium rectale.” [2015]
  • Consumption of different soymilk formulations differentially affects the gut microbiomes of overweight and obese men [2012].
    • low glycinin soymilk (LGS)
      • Bacteroides-Prevotella and Lactobacillus increased
    • conventional soymilk (S)
      • No change in Bacteroides-Prevotella and Lactobacillus
    • bovine milk (M)
      • Bacteroides-Prevotella and Lactobacillus increased
• Probiotics:
  • [Combination of] “Lactobacillus salivarius LI01, Pediococcus pentosaceus LI05, … an increase in …Prevotella,  ” treatment with C. butyricum, B. licheniformis or L. rhamnosus GG did not have a significant effect.”[2017]
  • “Lactobacillus kefiri LKF01 DSM32079 (LKEF) …After one month of probiotic oral intake we observed a reduction of … Prevotella” [2017]
  • “Lactobacillus gasseri… increases prevotella [2016]
  • “Bifidobacterium animalis subsp. lactis (B. lactis) HN019 …lower proportions of …Prevotella intermedia-like species in rats with  experimental periodontitis (EP)” [2017] Note: no change without EP.
  • “Bifidobacterium bifidum strain Bb …  Prevotellaceae (P = 0.041) and Prevotella (P = 0.034) were significantly decreased” [2016]
  • ” Lactobacillus rhamnosus GG…causing an increase in the abundance of Prevotella, ” [2016]
  • “Probiotics [Lactobacillus rhamnosus GG (LGG), viable Escherichia coli Nissle 1917 (EcN), and heat-inactivated VSL#3 (1:1:1). ] shifted the gut microbial community toward certain beneficial bacteria, including Prevotella”
  • “Lactobacillus casei …Prevotella intermedia… showed moderately significant reduction in their numbers.” [2015]
  • “Streptococcus oralis KJ3, Streptococcus uberis KJ2 and Streptococcus rattus JH145 … the salivary Prevotella intermedia counts were significantly lower in the probiotic group.” [2015]
  • “Lactobacillus salivarius Ren (Ren) …increased the amount of Prevotella. ” [2015]
  • ” Lactobacillus reuteri DSM 17938 and PTA 5289 …reduced …. Prevotella maculosa detection. ” [2015]
  • ” a positive correlation between Lactobacillus casei Zhang (LcZ) and Prevotella” [2014]
  • Lactobacillus brevis CD2 inhibits Prevotella melaninogenica biofilm [2014].
  • ” enterotoxigenic Escherichia coli …  led to a reduction in the number of Bacteroides-Prevotella, ” [2014]
• Antibiotics:
  • “a 7-day metronidazole regimen…Along with the decrease in pathogenic bacteria, such as … Prevotella…“
  • “All Prevotella strains tested were susceptible to imipenem and amoxicillin/clavulanate, whereas 78.6% of the pigmented Prevotellaspecies and 46.4% of the non-pigmented species were resistant to penicillin (MIC >0.5 μg/ml).” [2015]
  • “Cefpodoxime was found to be active at concentrations of less than or equal to 0.125 mg/l against Prevotella oralis, Prevotella buccalis” [1991]

Bottom Line

• No Lactobacillus salivarius
• No Lactobacillus gasseri
• No Lactobacillus casei
• No Lactobacillus rhamnosus GG.
• No Rosemary

• Bifidobacterium bifidum strain Bb probiotics
• Streptococcus probiotics
• Lactobacillus reuteri
• Lactobacillus brevis
• E.Coli probiotics
• Vitamin D supplementation
• grape seed extract (Resveratrol)
• Jerusalem artichoke
• Resistant starch (type IV)
• Whole-grain barley
• Low carbohydrate diet
• Chicory
• Inulin

For updated information see Microbiome Prescription

DataPunk.Net

INHIBITED BY

• Bifidobacterium
• Streptococcus
• Clostridium
• Enterobacteriaceae
• Escherichia

PubMed Data

There are about 18+ studies on PubMed.

• Disease:
  • “primary sclerosing … was further characterized by decreased abundance of Adlercreutzia equolifaciens” [2017]
  • “In Multiple sclerosis … lower  abundance of Parabacteroides, Adlercreutzia …” [20162016]
  • “Adlercreutzia, Anaerococcus, Ethanoligenens, Gordonibacter, Lactococcus, Parasutterella, and Tissierellawere greatly reduced in prediabetic (Pre-DM) subjects,  compared with healthy subject” [2015]
• Food:
  • “Adlercreutzia, Odoribacter, and Coprococcus were significantly more abundant in group feed microcrystalline cellulose” [2017]
  • ” Gut microbiota was characterized by increased levels of Adlercreutzia, .. within 1 day of acute cold exposure” [2016]
  • “A high-saturated fat diet seems to increase counts of total anaerobic microflora and the relative abundance of Bacteroides and Bilophila. Human studies have not reported that a high-unsaturated fat diet significantly alters the gut bacterial profile; however, mouse studies have reported increases in Actinobacteria(Bifidobacterium and Adlercreutzia), …. Adlercreutzia …were increased in fish-oil-fed mice. ” [2017]
• Probiotics:
  • “revealed there was significantly lower Helicobacter apodemus, Helicobacter mesocricetorum, Allobaculum stercoricanis and Adlercreutzia equolifaciens following both interventions (L. casei Zhang or vitamin K2)” [2017]

Bottom Line

Avoid

• Getting Cold

Take

• Vitamin K2
• Lactobacillus Casei

For updated information see Microbiome Prescription

DataPunk.net Data

ENHANCED BY

• Berberine

PubMed Data

There are 25+ studies on PubMed.

• Body Impact
  • ” Results indicated fecal Ruminococcus and Butyricimonas predicted brain N-acetylaspartate (NAA). Analysis of serum biomarkers indicated Ruminococcus independently predicted serum serotonin and cortisol. ” [2017]
  • “A positive correlation was found between Butyricimonas and mean arterial pressure (MAP).” [2016]  See this page to compute your MAP
• Disease:
  • ” multiple sclerosis ..decreases in Butyricimonas” [2016]
  • “Butyricimonas, and Clostridium XlVb, which were most abundant in the Active major depressive disorder ” [2016]
• Antibiotics:
  • “resistant to vancomycin (5 μg), kanamycin (1 mg) and colistin sulphate (10 μg),….The results showed sensitivity to ampicillin, sulbactam-ampicillin, amoxicillin-clavulanic acid, piperacillin-tazobactam, imipenem, meropenem, clindamycin and metronidazole.” [2015]
  • “Susceptibility testing of the isolate revealed penicillin and ceftriaxone resistance, but susceptibility to metronidazole. ” [2016]
• Probiotics:
  • “Butyricimonas, a butyrate producer (23), and Prevotella, a propionate producer (24), increased the relative abundance more dramatically in the ProPre group… composed of Lactobacillus rhamnosus GG (LGG), viable Escherichia coli Nissle 1917 (EcN), and heat-inactivated VSL#3 (1:1:1).  ” [2016]
  • Bifidobacterium animalis subsp. lactis B-12®) and Lactobacillus rhamnosus (LGG®) … [increased]” [2017]
  • “L. salivarius UCC118 expressing bacteriocin … reduced” [2012]
  • “Clostridium butyricum  … increases” [2015]

Bottom Line

Avoid

• Bifidobacterium animalis subsp.  lactis  B-12®) [See PDF where it was found to increase it 3 fold]
• Clostridium butyricum (i.e. Miyarisan) probiotics

Take

• E.Coli Probioitics
• Lactobacillus salivarius