Author Archives: lassesen

Unknown's avatar lassesen 3:25 am on October 31, 2017  

A CFS Patient since a child – Ubiome Analysis

The short form of the patient history is ” I’m very sick from CFS and MCS and Lyme, I’ve been sick since I was 11 years old, now I’m 34 years old.”

Standard Items

  • Bifidobacterium < 0.01
  • Lactobacillus 0.07x
  • Akkermansia: 0.00x
  • Firmicutes to Bacteroidetes: 1:2, Normal is 2.1:1
  • Biodiversity: 41%ile — much lower than most.

High Bacteria

Bacteria

Ratio
Sutterella: 11.02 X
Barnesiella: 4.16 X
Pseudobutyrivibrio: 3.11 X
Odoribacter: 2.91 X
Butyricimonas: 2.18 X
Kluyvera: 1.91 X
Bacteroides: 1.64 X

Rare Bacteria

Johnsonella Genus 0.5%
Ureaplasma Genus 0.8%
Mycoplasmataceae Family 1.3%
Mycoplasmatales Order 1.3%
Brevundimonas Genus 2.0%
Caulobacteraceae Family 3.0%
Caulobacterales Order 3.0%
Anaerobacter Genus 3.0%
Succiniclasticum Genus 4.0%
Candidatus Saccharibacteria Phylum 4.2%

Bottom Line

Combining all of the lists and tossing out things that appear on both side, we have the following lists. 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.

Working off the overgrowth only (I will revisit the rare bacteria when I have more time). It was interesting that some of the probiotics appeared multiple times for different genus as Avoid or Take — which left me a warm feeling. Two of the “fake sugars” are bad (Aspartame (Nutrasweet) and Stevia) and two are good (Sucralose (Splenda) and Xylitol)

Avoid

Take

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 3:02 am on October 31, 2017  

Reducing Kluyvera Genus

This genus is always associated with disease. It is usually subject to aggressive antibiotic treatment.  It appears to be present is some 20-30% of CFS patient’s uBiome seen so far.

For updated information see Microbiome Prescription

DataPunk.Net Data

“Enterobacteriaceae like Kluyvera are not very friendly and tend to thrive in the inflamed gut. ”

INHIBITED BY

ENHANCED BY

ANTIBIOTIC RESISTANCE

PubMed Data

There are 230+ studies on PubMed — this is just from a select sampling.

Disease

Diet

  • Ineffectual: Lemongrass, Artemesia vulgaris  (wormwood), Nutmeg oil, Selinum wallichianum Essential oil (or) Milk Parsley [2015]
  • study which shows that oil of Mexican oregano works against kluyvera cryocrescens. the active ingredient of Mexican oregano and common oregano are the same, carvacrol. From a reader, Study

Prebiotics

Probiotics

Antibiotics

  • “. Successful treatment options include third-generation cephalosporins, aminoglycosides, betalactams with beta-lactamase inhibitors and carbapenems. ” [2015]
  • “In contrast, the resistance to ampicillin, extended-spectrum penicillins, and first- and second-generation cephalosporins is significant. Kluyvera is a potentially virulent pathogen that deserves aggressive treatment designed with an awareness of the organism’s antimicrobial resistance patterns.” [2001]

Bottom Line

This is a tough genus to reduce without using antibiotics. No known probiotics impacts it.

Avoid

Take

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