Hypothesis Testing: 16s Results to detect SIBO

I’ve recently added computations for Methane and Hydrogen using KEGG data to Microbiome Prescription. Checking the contributed symptoms, I had over 120 samples with SIBO indicated. So it was time to test the hypothesis.

Charts

15% was 90%ile r over, 10% was expected
Poorer match:: 5% was over 90%ile, 10% expected

What about the old Methane?

The old computation was done on adhoc gathered associations from the literature. It also did not show any patterns.

Bottom Line

With the obvious path being unsuccessful, then time to examine where we did find associations.

ProductNamePattern
(4R,5S)-4,5,6-trihydroxy-2,3-dioxohexanoateBetween 33%ile to 66%ile
cob(II)yrinate a,c diamideBetween 66%ile to 100%ile
D-tagatoseBetween 0%ile to 33%ile
undecaprenyl phosphateBetween 0%ile to 33%ile
EndProductPattern
Vitamin B9 (Folic Acid/Folate)Between 66%ile to 100%ile
Lactic acidBetween 0%ile to 33%ile
2-ButanoneBetween 66%ile to 100%ile
Hydrogen cyanideBetween 66%ile to 100%ile
Methyl thiocyanideBetween 66%ile to 100%ile
PropionateBetween 66%ile to 100%ile
Vitamin KBetween 66%ile to 100%ile
Vitamin B7 (biotin)Between 66%ile to 100%ile
Sialic acidBetween 66%ile to 100%ile
NorepinephrineBetween 66%ile to 100%ile
EnzymeNamePattern
succinyl-CoA:acetate CoA-transferaseBetween 33%ile to 66%ile
phosphoenolpyruvate carboxykinase (GTP)Between 33%ile to 66%ile
Enzymes are a wash — all of focused on typical values
DefinitionPattern
Pentose phosphate pathway (Pentose phosphate cycle)Between 75%ile to 100%ile
Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5PBetween 75%ile to 100%ile
Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5PBetween 75%ile to 100%ile
Serine biosynthesis, glycerate-3P => serineBetween 75%ile to 100%ile
Histidine degradation, histidine => N-formiminoglutamate => glutamateBetween 75%ile to 100%ile
Riboflavin biosynthesis, plants and bacteria, GTP => riboflavin/FMN/FADBetween 75%ile to 100%ile
Tetrahydrofolate biosynthesis, GTP => THFBetween 75%ile to 100%ile
CAM (Crassulacean acid metabolism), lightBetween 75%ile to 100%ile
Lysine biosynthesis, DAP dehydrogenase pathway, aspartate => lysineBetween 75%ile to 100%ile
We find high levels of glutamate, serine, lysine, ribose and ribulose being scents to look at. Unfortunately nothing was found on PubMed
tax_nametax_rankPattern
Blautia hanseniispeciesBetween 33%ile to 66%ile
Filifactor alocisspeciesBetween 66%ile to 100%ile
BacteroidiaclassBetween 66%ile to 100%ile
Bacteroides gallinarumspeciesBetween 66%ile to 100%ile
By bacteria found no strong associations


Last, we look at what studies reported

Tax RankTax NameShiftDistributionCitation Link
genusEnterococcus (NCBI:1350 )HighDistribution   πŸ“š PubMed
genusKlebsiella (NCBI:570 )HighDistribution   πŸ“š PubMed
genusPrevotella (NCBI:838 )HighDistribution   πŸ“š PubMed
genusSalmonella (NCBI:590 )HighDistribution   πŸ“š PubMed
genusStaphylococcus (NCBI:1279 )HighDistribution   πŸ“š PubMed
genusStreptococcus (NCBI:1301 )HighDistribution   πŸ“š PubMed
phylumFirmicutes (NCBI:1239 )LowDistribution   πŸ“š PubMed
speciesAcinetobacter baumannii (NCBI:470 )HighDistribution   πŸ“š PubMed
speciesBacteroides fragilis (NCBI:573 )HighDistribution   πŸ“š PubMed
speciesBifidobacterium longum (NCBI:216816 )LowDistribution   πŸ“š PubMed
speciesEnterococcus faecalis (NCBI:1351 )HighDistribution   πŸ“š PubMed
speciesEnterococcus faecalis (NCBI:1351 )LowDistribution   πŸ“š PubMed
speciesEnterococcus faecium (NCBI:1352 )HighDistribution   πŸ“š PubMed
speciesEscherichia coli (NCBI:562 )HighDistribution   πŸ“š PubMed
speciesEscherichia coli (NCBI:562 )HighDistribution   πŸ“š PubMed
speciesMethanobrevibacter smithii (NCBI:2173 )HighDistribution   πŸ“š PubMed
speciesMethanobrevibacter smithii (NCBI:2173 )HighDistribution   πŸ“š PubMed
speciesPseudomonas aeruginosa (NCBI:287 )HighDistribution   πŸ“š PubMed
We have some agreement, Bacteroidia is HIGH above and FirmicutesΒ  is low.

Looking at the “usual suspect” for SIBO, Methanobrevibacter smithii, a methane producer, we found only 23 samples with any (and all of the labs associated with these samples reports this bacteria so over 100 (80%) of the people reporting SIBO had none appearing)

There is no clear association of this bacteria to SIBO in our samples

Tentatively conclusion, SIBO does not leave any clear tracks in a 16s Sample.

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