Category Archives: Conditions

Unknown's avatar lassesen 10:29 pm on October 29, 2017  

Italian State of the Art Microbiome Report #2 Male

A reader forwarded me two reports, one from a male and one from a female. No notes on the people (I am fine with that). The report appear to be superior to uBiome on two counts:

  • It’s a professional grade report from a clinical laboratory
  • It reports down to the strain level on occasion.

This second post is on the male. (See this post for the female)

  • Low Bifidobacteria
  • No Lactobacillus
  • No E. coli
  • Low Akkermansia muciniphila (less than 1/100 of 1% of typical)

So standard CFS profile on these

ital2

Copying the data to Excel allow me to get similar numbers as I do from uBiome reports.

High Levels

We have a lot more with the male than the female.

Proteobacteria  Haemophilus parainfluenzae 9911% 0.00892
Bacteroidetes Bacteroides ovatus 8200% 0.00574
Proteobacteria  Klebsiella 3000% 0.0003
Firmicutes  Roseburia faecis 1700% 0.00017
Bacteroidetes Bacteroides uniformis 1526% 0.13722
Firmicutes Blautia 1342% 0.24124
Firmicutes  Roseburia 878% 0.04691
Firmicutes  Ruminococcus gnavus 775% 0.01783
Firmicutes  Epulopiscium 720% 0.00036
Firmicutes  Anaerostipes 717% 0.01993
Firmicutes  Lachnospira 561% 0.00185
Firmicutes  Dorea 440% 0.03024
Firmicutes  Bulleidia 361% 0.00231
Firmicutes  Clostridium 341% 0.00133
Firmicutes  Ruminococcus 333% 0.11271
Firmicutes  Oscillospira 271% 0.02044
Actinobacteria Eggerthella lenta 257% 0.00399

The greatest impact (volume of metalites produced) appears to be (in order) from  Blautia, Bacteroides uniformis , Ruminococcus, Roseburia.  I have done just the 8 highest below (for the moment — I may return to expand more in the future).

 

Bottom Line

Combining all of the lists and tossing out things that appear on both side, we have the following lists. There are two genus cited above that I have not done a deep dive into. I have skipped rare bacteria because of the number of over growths found. This was a pretty clean merge — often the same item appeared multiple times in one list or the other.

The lists below are done by merging the lists from the deep dives linked above. Some items may encourage one genus and discourage another genus — those are removed (unless it seems that it strongly predominates on one). The impact on Lactobacillus, Bifidobacterium and E.Coli are intentionally ignored [See this post for the logic]. This is all based on applying logic to the results of studies — thus theoretical. This is an addition (not a replacement) to this overview post.

Avoid

  • Animal-based diet
  • Arabinoxylans
  • Arginine supplements
  • Bacillus probiotics
  • Berberine.
  • Bifidobacterium adolescentis
  • Bifidobacterium Animalis  subsp lactis BB-12
  • Broad beans  and lupin seeds
  • Brown rice
  • Butyrate producing probiotics
  • Chili pepers
  • Cholic acid
  • Dietary fiber
  • Dopamine
  • Favone
  • Fluoroquinolone
  • Fructo-oligosaccharides
  • Gallic acid
  • Glucose foods (fructose [fruit sugar] appears to be fine)
  • Gum arabic
  • Gynostemma pentaphyllum
  • Helminth infections
  • High grain diet
  • Inulin
  • Lactobacillus acidophilus
  • Lactobacillus fermentum
  • Lactobacillus plantarum
  • L-citrulline
  • Metformin
  • N-Acetyl-D-glucosamine
  • Omega 3
  • Polydextrose
  • Polymannuronic acid
  • Resistant maltodextrin.
  • Rosemary
  • Saccharin
  • Saccharomyces boulardii
  • Safflower oil
  • Salt
  • Sodium butyrate
  • Soy
  • Stevia
  • Stress
  • Tannic acid

Take

  • Bifidobacterium longum BB536
  • Bile acid
  • Epinephrine
  • Flaxseed
  • Fructo-oligosaccharides
  • Galactooligosaccharides
  • Garlic
  • Lactobacillus paracasei (24 billion viable /daily)
  • Lactobacillus casei strain Shirota (Yakult brand)
  • Lactobacillus kefiri LKF01 
  • l-glutamine
  • Low carbohydrate diet
  • Mutaflor (E.Coli Nissle 1917)
  • Oral Iron Supplements
  • Oranges (pectin/flavanones)
  • Polymannuronic acid
  • Proton-pump inhibitors (PPI)
  • Streptococcus probiotics
  • Sucralose (Splenda)
  • Tea Tree Oil
  • Vitamin D3

 

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of CFS. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

 

 

Unknown's avatar lassesen 9:36 pm on October 29, 2017  

Decreasing Roseburia genus

For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

PubMed Data

There are 260+ studies on PubMed

Disease

  • “A lower abundance of Roseburia has been observed in patients suffering from inflammatory bowel disease.” [ubiome]
  • “elevated levels of Roseburia may be associated with weight loss and reduced glucose intolerance.” [ubiome]
  • “whereas the short-chain fatty acid producer, such as, Roseburia spp. and Faecalibacterium prausnitzii, were higher in controls.. then with hypertension” [2017]
  • “Clostridium colinum were decreased in ulcerative colitis along with genus Roseburia” [2017]
  • “The analysis of the microbiota composition revealed a decrease of the relative abundance of Bacteroides, Roseburia-Eubacterium rectale and Bifidobacterium .. with constipated-predominant irritable bowel syndrome [2016]

Diet

  • “Resistant starch (RS) …  Roseburia, Blautia, and Lachnospiracea incertae sedis were decreased.” [2015] [2016][2014]
  • “The barley group had higher abundances of Akkermansia, Ruminococcus, Blautia, and Bilophila. Turicibacter and Roseburia were more abundant in the malt group, and [reduced] Parabacteroides, Dorea” [2015]
  • “The relative abundance of sequences from several genera belonging to the Lachnospiraceae (eg, Ruminococcus, Roseburia, Blautia, and Dorea) was lower in high … vitamin D quartiles. “
  • “Walnuts enriched the microbiota for probiotic-type bacteria including Lactobacillus, Ruminococcaceae, and Roseburia while significantly reducing Bacteroides and Anaerotruncus. ” [2017]
  • “However, a reversible increased abundance of several genera, including Bifidobacterium, Roseburia and Lactobacillus was observed with one or both omega-3 PUFA interventions. ” [2017]
  • “both the low- and high-capsaicin diets, acting in similar ways, significantly increased the Roseburia abundance ” [2017]
  • “In the  grape pomace  treated group, … we observed a decrease of Desulfovibrio, Lactococcus, whereas Allobaculum and Roseburia were increased” [2017]

Prebiotics:

  • “long-chain arabinoxylans (LC-AX) and the well-established prebiotic inulin (IN) were shown to stimulate bacterial groups with known butyrate-producers (Roseburia intestinalis, Eubacterium rectale, Anaerostipes caccae) ” [2011]

Probiotics

  • ” Blautia, Roseburia and Coprococcus were significantly enriched following treatment with hydrolyzed casein formula supplemented with Lactobacillus rhamnosus GG” [2016]
  • “Lactobacillus salivarius Ls-33…Blautia coccoides_Eubacteria rectale group and Roseburia intestinalis, were significantly increased” [2013]
  • “B. longum BB536 and L. rhamnosus …together with a decrease in Roseburia faecis and Ruminococcus gnavus abundance. ” [2017]
  • “we found that Lactobacillus rhamnosus GG enriched those microbes or microbial activities related to short-chain fatty acid production (e.g. Roseburia and Coprococcus), ” [2017]
  • “A significant inhibition in fecal Escherichia coli and increase in Lactobacillus, Bifidobacterium, and Roseburia intestinalis were observed after consumption of  …Lactobacillus paracasei subsp. paracasei ” [2013]
  • “dietary supplementation of Bacillus spp. increased (P < 0.05) abundance of Roseburia spp..” [2017]

Antibiotics

Bottom Line

Avoid

Take

Unknown's avatar lassesen 8:36 pm on October 29, 2017  

Reducing Blautia genus

High blautia has been seen frequently with CFS (see this earlier post and this one with samples)

For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

PubMed Data

Disease:

  • Distinct Microbiome-Neuroimmune Signatures Correlate With Functional Abdominal Pain in Children With Autism Spectrum Disorder[20176]
    • “A significant increase in several mucosa-associated Clostridiales was observed in ASD-FGID, whereas marked decreases in Dorea and Blautia, as well as Sutterella, were evident. “
  • “At the taxonomic level of genus, putative, “anti-inflammatory” butyrate-producing bacteria from the genera Blautia, Coprococcus, and Roseburia were significantly more abundant in feces of controls than Parkinson’s Disease patients” [2015]  i.e. low levels => PD
  • “We observed an increased abundance of Psuedomonas, Mycoplana, Haemophilus, Blautia, and Doreagenera in Multiple sclerosis  patients, [2016]
  • Hints that it may be high with MCS (see this post)
  • “unlike those of healthy infants, feces of Autism Spectrum Disorder infants had significantly higher and lower abundance of genera Faecalibacterium and Blautia, respectively.” [2016]
  • Diabetes: ” Microbiota in the samples was predominantly represented by Firmicutes, in a less degree by Bacteroidetes. Blautia was a dominant genus in all samples. The representation of Blautia, Serratia was lower in preD than in T2D patients, and even lower in those with normal glucose tolerance.”[2016]
  • “Fecal microbial communities were more similar among UC patients than their healthy partners (P = 0.024). ulcerative colitis  individuals had a lower relative abundance of bacteria belonging to the Firmicutes, especially Blautia, Clostridium, Coprococcus and Roseburia (P < 0.05). ” [2017]
  • “. At the species level, butyrate-producing bacterial species, such as Blautia faecis, Roseburia inulinivorans, Ruminococcus torques, Clostridium lavalense, Bacteroides uniformis and Faecalibacterium prausnitzii were significantly reduced in Crohn’s disease  patients ” [2016]
  • “The intestinal microbiota of elderly manifested a reduction in the diversity, characterized by a large interindividual variability, with lower numbers of Firmicutes, Bifidobacteria, Clostridium clusterXIV, Faecalibacterium Prausnitzii, Blautia coccoides-Eubacterium rectal ” [2015]

Diet:

  • “some bile acids have been shown to exhibit antimicrobial activity….bactericidal activities to Blautia coccoides” [2017]
  • “sodium butyrate …. elevated the abundances of the beneficial bacteria Christensenellaceae, Blautia and Lactobacillus.”[2017]
  • “safflower oil…increased abundance of Blautia,[2016]
  • Japanese traditional dietary fungus koji Aspergillus oryzae functions as a prebiotic for Blautia coccoides through glycosylceramide: Japanese dietary fungus koji is a new prebiotic [2016].
  • “Metformin and berberine.…were markedly increased” [2015] [2016]
  • “Resistant starch (RS) …  Roseburia, Blautia, and Lachnospiracea incertae sedis were decreased.” [2015] [2016][2014]
  • “High grain diet …altered the colonic mucosal bacterial communities, with an increase in the abundance of genus Blautia and a decrease in the abundance of genera Bacillus, Enterococcus, and Lactococcus.”
  • “antimicrobial effect observed for the grape seed polyphenols, particularly against Bacteroides, Prevotella and Blautia coccoides-Eubacterium rectale.” [2015]
    • “Subjects with regular consumption of red wine (mean = 100 ml/day) had lower serum concentrations of MDA and lower fecal levels of… blautia”[2015]
  • “positive associations between flavone intake and Blautia,” [2015]
  • “A negative association was found between the intake of pectins and flavanones from oranges and the levels of Blautia coccoides” [2014]
  • “Rosemary Extract …increased the Blautia coccoides and Bacteroides/Prevotella groups and reduced the Lactobacillus/Leuconostoc/Pediococccus group in both types of animals.” [2014]
  • ” All treatments [a daily dose of 60 g of whole-grain barley (WGB), brown rice (BR), or an equal mixture of the two (BR+WGB)] increased microbial diversity, the Firmicutes/Bacteroidetes ratio, and the abundance of the genus Blautia in fecal samples.”
  • “At the end of the 2-week omega-3 rich diet, we identified a striking reduction in Faecalibacterium, and a remarkable increase in Blautia” [2016]
  • “The relative abundance of sequences from several genera belonging to the Lachnospiraceae (eg, Ruminococcus, Roseburia, Blautia, and Dorea) was lower in high … vitamin D quartiles. “ [2015]

Probiotics:

  • “Bifidobacterium longum BB536 and  Lactobacillus rhamnosus .., a higher abundance of Blautia producta, Blautia wexlerae ” [2017]
  • ” least 24 billion viable Lactobacillus paracasei DG …the Clostridiales genus Blautia (P = 0.036) was decreased;”
  • ” Blautia, Roseburia and Coprococcus were significantly enriched following treatment with hydrolyzed casein formula supplemented with Lactobacillus rhamnosus GG” [2016]
  • “Blautia and Staphylococcus) significantly increased after Lactobacillus plantarum P-8 consumption,” [2015]
  • “Lactobacillus salivarius Ls-33…Blautia coccoides_Eubacteria rectale group and Roseburia intestinalis, were significantly increased” [2013]
  • “Bacillus subtilis…the relative abundance of Alistipes, Odoribacter, Ruminococcus, Blautia and Desulfovibrio were higher” [2016]

Antibiotics:

  • “Ten OTUs indicating fluoroquinolone treatment were associated with Blautia, Subdoligranulum, Adlercreutzia, Clostridium and Ruminococcus.” [2014]

Bottom Line

Avoid

Take

  • Oranges (pectin/flavanones)
  • Grape seed polyphenols,/ Wine
  • 24 billion viable Lactobacillus paracasei  daily
  • Bile acid
  • Flaxseed
  • Vitamin D3
Unknown's avatar lassesen 5:50 am on October 29, 2017  

Italian State of the Art Microbiome Report

A reader forwarded me two reports, one from a male and one from a female. No notes on the people (I am fine with that). The report appear to be superior to uBiome on two counts:

  • It’s a professional grade report from a clinical laboratory
  • It reports down to the strain level on occasion.

Link to site (in Italian) http://www.ospedalebambinogesu.it/genetica-la-super-mappa-del-microbiota-intestinale#.Wf39d2i3xPY

This first post is on the female. (See this post for the male)

  • Low Bifidobacteria
  • No Lactobacillus
  • No E. coli
  • Low Akkermansia muciniphila (less than 1/100 of 1% of typical)

So standard CFS profile on these

italy

Copying the data to Excel allow me to get similar numbers as I do from uBiome reports.

High Levels

Proteobacteria  Haemophilus parainfluenzae 75956% 0.06836
Firmicutes  Ruminococcus torques 11110% 0.00222
Firmicutes Veillonella dispar 1819% 0.01473
Firmicutes  Ruminococcus gnavus 1720% 0.03956
Firmicutes  Epulopiscium dolichum 891% 0.00196
Firmicutes Coprobacillus 880% 0.00044
Firmicutes  Blautia producta 853% 0.00665
Firmicutes  Clostridium 721% 0.00281
Firmicutes  Ruminococcus 268% 0.09076
Firmicutes  Epulopiscium 220% 0.00011

The greatest impact appears to be (in order) from  Ruminococcus, Haemophilus parainfluenzae, Ruminococcus gnavus, Veillonella dispar. Since I have only done deep dives to the genus, not species level, I have borrowed directly from DataPunk.Net

Bottom Line

Combining all of the lists and tossing out things that appear on both side, we have the following lists. There are two genus cited above that I have not done a deep dive into. I have skipped rare bacteria because of the number of over growths found. This was a pretty clean merge — often the same item appeared multiple times in one list or the other.

The lists below are done by merging the lists from the deep dives linked above. Some items may encourage one genus and discourage another genus — those are placed in inconclusive. The impact on Lactobacillus, Bifidobacterium and E.Coli are intentionally ignored [See this post for the logic]. This is all based on applying logic to the results of studies — thus theoretical. This is an addition (not a replacement) to this overview post.

Avoid

Take

Note: Taking as a fresh herb may work similar to oil

This is an education post to facilitate discussing this approach with your medical professionals. It is not medical advice for the treatment of CFS. Always consult with your medical professional before doing any  changes of diet, supplements or activity. Some items cites may interfere with prescription medicines.

 

 

Unknown's avatar lassesen 12:30 am on October 29, 2017  

Reducing Enterococcus Genus

If you have high enterococcus reported, please verified that none of the probiotics that you have taken included enterococcus in the prior month. If so, this may be just residue from those probiotics.

“Vancomycin-resistant enterococci (VRE) are both of medical and public health importance associated with serious multidrug-resistantinfections and persistent colonization. Enterococci are opportunistic environmental inhabitants with a remarkable adaptive capacity to evolve and transmit antimicrobial-resistant determinants. The VRE gene operons show distinct genetic variability and apparently continued evolution leading to a variety of antimicrobial resistance phenotypes and various environmental and livestock reservoirs for the most common van genes. Such complex diversity renders a number of important therapeutic options including “last resort antibiotics” ineffective and poses a particular challenge for clinical management. Enterococci resistance to glycopeptides and multidrug resistance warrants attention and continuous monitoring.” [2017]

For updated information see Microbiome Prescription

DataPunk.Net Data

INHIBITED BY

ENHANCED BY

INHIBITED BY

PubMed Data

There are 25000+ studies on PubMed — this is just from a select sampling.

  • ” The incidence of Hirschsprung-associated enterocolitis with/without probiotics [Lactobacillus, Bifidobacterium, Streptococcus, and Enterococcus] was 22.6 and 30.5%, respectively, but this was not statistically different (OR 0.72; 95% CI 0.37-1.39; P = 0.33).” [2017]
  • “L. reuteri strains tested were able to inhibit and displace (P < 0.05) the adhesion of …. Enterococcus faecalis NCDC115. The probiotic strain L. reuteri LR6 showed the strongest adhesion and pathogen inhibition ability among the eight L. reuteri strains tested” [2017]
  • ” Lactobacilli (Lactobacillus plantarum ATCC 8041 and Lactobacillus rhamnosus ATCC 7408 ) had an inhibitory effect on the growth of E. faecalis by agar cup method but not by deferred antagonism test.” [2017]
  • “Lactobacillus strains ((L. gasseri, L. rhamnosus, L. acidophilus, L. plantarum, L. paracasei, L. acidophilus) ) had similar moderate antimicrobial activities against uropathogens.” [2016]
  • ” all the Lactobacillus isolates[Lactobacillus acidophilus, L. paracasei, L. delbrueckii, L. casei, L. helveticus, L. brevis, L. salivarius, L. fermentum, L. rhamnosus, L. animalis, and L. plantarum} displayed antimicrobial activity against 6 out of 7 antibiotic-resistant uropathogens (E. fecalis….),  L. fermentum and L. plantarum strains demonstrated remarkable inhibitory activities against  E. faecalis,” [2016]
  • “No decline in (enterococci) colony counts was seen over time in subjects who received Lactobacillus rhamnosus GG . ” [2015]

Bottom Line

This is a tough genus to reduce — antibiotics are likely to do more harm than good because of the high resistance reported. Many probiotics have only a moderate effect at best.

Avoid

Take

Personally, I tend to use Triphala, Lactobacillus Fermentum, and Licorice as part of my regular maintenance routine.