Comparing Microbiomes from Three Different Providers – Part 1

A reader did Ombre and Thorne from the same physical sample and then processed the Ombre results via Biomeisght resulting in three different reports on the same shit. That is:

  • Ombre (16s) – same digital data used
  • Biomesight (16s) – same digital data used
  • Thorne (MSS)

This is the first of two parts — the bacteria numbers as percentiles and percentages, The second part will look at suggestions from each (and provided documentation for why it was suggested when available).

As a reminder of issues, see the chart below and this earlier post: The taxonomy nightmare before Christmas… [2019]

From The gut microbiome and thromboembolism [2022]

From Standards seekers put the human microbiome in their sights, 2019

My intent is not to suggest/render judgements on the different test results, just show the differences. It should be noted that most studies are done with 16s and not MSS. Conclusions from one study may not be reproduceable using a different lab/software (even with the same digital data).

Pass #1: Percentile Rankings

These are the most likely to be similar between samples. I only looked at those bacteria reported by all three samples.

phylumThryveBiomeSightThorne
Acidobacteria761052
Actinobacteria384665
Bacteroidetes16679
Chloroflexi998888
Cyanobacteria969656
Firmicutes72866
Fusobacteria141078
Proteobacteria271429
Synergistetes46542
Tenericutes776137
Verrucomicrobia818364
classThryveBiomeSightThorne
Actinomycetia465462
Alphaproteobacteria355258
Anaerolineae338453
Bacilli846258
Bacteroidia16680
Betaproteobacteria241315
Caldilineae100791
Clostridia63907
Coriobacteriia768173
Cytophagia205877
Deltaproteobacteria817881
Epsilonproteobacteria687195
Erysipelotrichia182836
Fusobacteriia141078
Gammaproteobacteria473960
Mollicutes786135
Negativicutes90883
Opitutae597860
Synergistia46542
Tissierellia969988
Verrucomicrobiae818163
orderThryveBiomeSightThorne
Acholeplasmatales77624
Acidaminococcales202117
Actinomycetales939545
Alteromonadales169586
Anaerolineales332661
Bacillales904775
Bacteroidales16680
Bifidobacteriales302537
Burkholderiales241314
Caldilineales100791
Campylobacterales687196
Chromatiales459272
Coriobacteriales478411
Corynebacteriales919496
Cytophagales215877
Desulfovibrionales817880
Eggerthellales929496
Enterobacterales292267
Erysipelotrichales182836
Eubacteriales64897
Fusobacteriales141078
Halanaerobiales9410067
Hyphomicrobiales187494
Lactobacillales836761
Micrococcales39992
Micromonosporales741985
Mycoplasmatales878654
Nostocales729725
Oceanospirillales571089
Oscillatoriales958028
Puniceicoccales62161
Rhodospirillales85041
Rickettsiales291049
Selenomonadales858629
Streptosporangiales567876
Synergistales47542
Thermoanaerobacterales221848
Tissierellales959982
Veillonellales969210
Verrucomicrobiales818163
familyThryveBiomeSightThorne
Acholeplasmataceae77624
Acidaminococcaceae212117
Actinomycetaceae939566
Aerococcaceae929860
Akkermansiaceae828569
Anaerolineaceae352661
Atopobiaceae901671
Bacillaceae769897
Bacteroidaceae231555
Bifidobacteriaceae322541
Bradyrhizobiaceae342581
Caldilineaceae100791
Campylobacteraceae686695
Carnobacteriaceae521067
Clostridiaceae879412
Coprobacillaceae Verbarg et al. 201476421
Coriobacteriaceae18847
Corynebacteriaceae909295
Desulfovibrionaceae837880
Dysgonomonadaceae60479
Eggerthellaceae929496
Enterobacteriaceae582367
Enterococcaceae606289
Erysipelotrichaceae192539
Eubacteriaceae927729
Eubacteriales Family XIII. Incertae Sedis959666
Lachnospiraceae809326
Lactobacillaceae897464
Micrococcaceae161391
Microcoleaceae91771
Micromonosporaceae742085
Mycoplasmataceae878654
Odoribacteraceae979477
Oscillospiraceae345417
Paenibacillaceae954796
Peptococcaceae989039
Peptoniphilaceae959982
Peptostreptococcaceae478483
Planococcaceae308078
Porphyromonadaceae552736
Prevotellaceae585250
Puniceicoccaceae63581
Rhodospirillaceae104835
Rickettsiaceae351338
Selenomonadaceae818726
Sporomusaceae863846
Streptococcaceae556673
Streptosporangiaceae682052
Sutterellaceae24149
Syntrophomonadaceae96586
Tannerellaceae292076
Thermoactinomycetaceae858843
Turicibacteraceae Verbarg et al. 2014262722
Veillonellaceae969210
genusThryveBiomeSightThorne
Acetivibrio668614
Acetobacterium988513
Acholeplasma77486
Actinobaculum38833
Actinomyces747953
Actinotignum517162
Akkermansia828569
Alloscardovia93931
Anaerococcus949681
Anaerostipes907341
Arcanobacterium97975
Bacillus219396
Bacteroides261671
Bifidobacterium191844
Bilophila59612
Blautia84944
Brevibacillus418587
Butyricimonas735682
Butyrivibrio948774
Caloramator65607
Campylobacter676796
Clostridium788716
Coprobacillus87491
Coprococcus27422
Corynebacterium909295
Desulfotomaculum827560
Desulfovibrio698487
Dialister979345
Dorea90691
Dysgonomonas60440
Eggerthella757886
Enterococcus266788
Erysipelothrix766717
Escherichia723252
Ethanoligenens993747
Eubacterium925438
Faecalibacterium333221
Filifactor789750
Finegoldia908475
Gemella659718
Hathewaya88771
Helcococcus99876
Lachnospira59388
Lactobacillus896064
Ligilactobacillus581581
Limosilactobacillus242349
Mediterraneibacter868146
Megasphaera919741
Mobiluncus18163
Mogibacterium989631
Mycoplasma888647
Mycoplasmopsis35940
Negativicoccus759224
Odoribacter989858
Paenibacillus959996
Parabacteroides292076
Pectinatus23192
Peptococcus82901
Peptoniphilus959969
Phocaeicola32555
Porphyromonas949597
Prevotella676458
Pseudobutyrivibrio404328
Roseburia696063
Ruminiclostridium76465
Ruminococcus91848
Schaalia361026
Slackia378110
Streptococcus567075
Sutterella461416
Syntrophomonas97202
Thermoclostridium603834
Turicibacter262722
Varibaculum86862
Veillonella608420
Weissella871331

Pass #2: Percentage

phylumThryveBiomeSightThorne
Acidobacteria0.0110.0020.005
Actinobacteria0.6520.3642.117
Bacteroidetes12.52612.63360.723
Chloroflexi0.1830.020.02
Cyanobacteria0.1230.3740.024
Firmicutes82.6182.71727.458
Fusobacteria0.0020.0020.02
Proteobacteria1.1631.5021.894
Synergistetes0.0040.0020.005
Tenericutes0.0490.0480.015
Verrucomicrobia1.9941.9540.627
classThryveBiomeSightThorne
Actinomycetia0.6410.3511.093
Alphaproteobacteria0.0130.0850.171
Anaerolineae0.0020.0110.003
Bacilli2.9310.7290.765
Bacteroidia12.52210.23860.036
Betaproteobacteria0.2660.2630.175
Caldilineae0.1820.0090.001
Clostridia73.50881.68925.405
Coriobacteriia0.6650.5270.989
Cytophagia0.0040.0360.047
Deltaproteobacteria0.7230.7350.875
Epsilonproteobacteria0.0110.0090.275
Erysipelotrichia0.2810.1910.336
Fusobacteriia0.0020.0020.02
Gammaproteobacteria0.1520.1980.359
Mollicutes0.0490.0480.013
Negativicutes3.8393.40.069
Opitutae0.0040.0080.004
Synergistia0.0040.0020.005
Tissierellia1.4683.3520.386
Verrucomicrobiae1.9931.9460.621
orderThryveBiomeSightThorne
Acholeplasmatales0.0230.0330.002
Acidaminococcales0.0080.0070.007
Actinomycetales0.0920.3210.021
Alteromonadales0.0020.0650.021
Anaerolineales0.0020.0020.003
Bacillales0.2310.1470.233
Bacteroidales12.56710.23860.01
Bifidobacteriales0.1640.030.123
Burkholderiales0.2670.2590.127
Caldilineales0.1820.0090.001
Campylobacterales0.0110.0090.273
Chromatiales0.0040.030.013
Coriobacteriales0.1430.5270.025
Corynebacteriales0.1960.2020.81
Cytophagales0.0040.0360.047
Desulfovibrionales0.7160.7270.825
Eggerthellales0.5170.5250.963
Enterobacterales0.0110.0120.157
Erysipelotrichales0.2820.1910.336
Eubacteriales73.71780.55425.38
Fusobacteriales0.0020.0020.02
Halanaerobiales0.0130.2390.004
Hyphomicrobiales0.0020.0080.07
Lactobacillales2.710.3880.525
Micrococcales0.0060.0020.063
Micromonosporales0.0040.0020.006
Mycoplasmatales0.0210.0150.007
Nostocales0.0060.3570.005
Oceanospirillales0.0080.0020.02
Oscillatoriales0.1170.0090.002
Puniceicoccales0.0040.0020
Rhodospirillales0.0020.0690.021
Rickettsiales0.0020.0020.004
Selenomonadales0.0960.3920.02
Streptosporangiales0.0040.0080.007
Synergistales0.0040.0020.005
Thermoanaerobacterales0.0020.0070.019
Tissierellales0.993.4240.267
Veillonellales3.7493.40.041
Verrucomicrobiales21.9460.621
familyThryveBiomeSightThorne
Acholeplasmataceae0.0230.0330.002
Acidaminococcaceae0.0080.0070.007
Actinomycetaceae0.0960.0860.021
Aerococcaceae0.0960.0840.007
Akkermansiaceae2.071.9030.616
Anaerolineaceae0.0020.0020.003
Atopobiaceae0.1410.0020.018
Bacillaceae0.0140.070.085
Bacteroidaceae8.2067.86930.336
Bifidobacteriaceae0.170.030.123
Bradyrhizobiaceae0.0020.0020.011
Caldilineaceae0.1890.0090.001
Campylobacteraceae0.0120.0090.267
Carnobacteriaceae0.0040.0020.007
Clostridiaceae2.45611.8270.304
Coprobacillaceae Verbarg et al. 20140.0510.1380
Coriobacteriaceae0.0060.5270.007
Corynebacteriaceae0.1950.1920.776
Desulfovibrionaceae0.7430.7210.822
Dysgonomonadaceae0.0060.0020.023
Eggerthellaceae0.5370.5250.963
Enterobacteriaceae0.0120.0120.117
Enterococcaceae0.0040.0150.06
Erysipelotrichaceae0.2930.1380.336
Eubacteriaceae8.6370.250.054
Eubacteriales Family XIII. Incertae Sedis0.3770.1880.047
Lachnospiraceae35.55838.81715.522
Lactobacillaceae2.4880.0470.09
Micrococcaceae0.0020.0020.027
Microcoleaceae0.1210.0070.001
Micromonosporaceae0.0040.0020.006
Mycoplasmataceae0.0220.0150.006
Odoribacteraceae1.0280.9550.588
Oscillospiraceae1.60421.9735.153
Paenibacillaceae0.1050.0070.085
Peptococcaceae0.2950.1780.03
Peptoniphilaceae1.0283.4130.261
Peptostreptococcaceae0.1620.0470.81
Planococcaceae0.0060.0060.015
Porphyromonadaceae1.7010.8861.001
Prevotellaceae0.6540.5070.285
Puniceicoccaceae0.0040.0040
Rhodospirillaceae0.0020.0650.012
Rickettsiaceae0.0020.0020.002
Selenomonadaceae0.0780.3880.016
Sporomusaceae0.0220.0040.004
Streptococcaceae0.180.1650.344
Streptosporangiaceae0.0040.0020.003
Sutterellaceae0.2770.2550.028
Syntrophomonadaceae0.0160.0340.001
Tannerellaceae0.3890.5452.972
Thermoactinomycetaceae0.010.0150.004
Turicibacteraceae Verbarg et al. 20140.0040.0040.004
Veillonellaceae3.8923.40.041
genusThryveBiomeSightThorne
Acetivibrio0.0190.4730.007
Acetobacterium0.0150.1960.003
Acholeplasma0.0230.0070.001
Actinobaculum0.0020.0060
Actinomyces0.0150.0140.009
Actinotignum0.0040.0040.005
Akkermansia1.9951.9030.616
Alloscardovia0.0090.0090
Anaerococcus0.4140.4070.073
Anaerostipes4.8390.1440.173
Arcanobacterium0.030.030.001
Bacillus0.0020.0190.052
Bacteroides7.9087.86930.336
Bifidobacterium0.0170.0190.121
Bilophila0.2950.2920.002
Blautia13.00418.7271.315
Brevibacillus0.0020.0040.004
Butyricimonas0.1470.1420.374
Butyrivibrio0.2760.1080.066
Caloramator0.0230.2410.003
Campylobacter0.0110.0090.263
Clostridium1.0063.2040.188
Coprobacillus0.0510.1380
Coprococcus0.1960.0350.277
Corynebacterium0.1880.1920.761
Desulfotomaculum0.0170.0070.006
Desulfovibrio0.4140.4290.813
Dialister2.4482.0750.019
Dorea1.940.5350.001
Dysgonomonas0.0060.0020.006
Eggerthella0.0770.0460.139
Enterococcus0.0020.0130.056
Erysipelothrix0.0080.0190.003
Escherichia0.0110.010.03
Ethanoligenens0.7560.0040.007
Eubacterium8.2140.0390.051
Faecalibacterium6.4948.2614.065
Filifactor0.0080.0430.004
Finegoldia0.1540.0540.041
Gemella0.0060.0990.003
Hathewaya0.0130.3490.001
Helcococcus0.0240.0060.001
Lachnospira0.0047.1224.473
Lactobacillus2.3970.0170.043
Ligilactobacillus0.0060.0020.029
Limosilactobacillus0.0020.0020.003
Mediterraneibacter5.6610.8130.456
Megasphaera0.0360.1960.009
Mobiluncus0.0020.0020.001
Mogibacterium0.1430.1880.007
Mycoplasma0.0210.0150.006
Mycoplasmopsis0.0020.0150
Negativicoccus0.0080.060.002
Odoribacter0.8440.8130.202
Paenibacillus0.0980.0170.072
Parabacteroides0.3890.5452.955
Pectinatus0.0020.0040.001
Peptococcus0.0190.1450.001
Peptoniphilus0.3952.9460.09
Phocaeicola0.0023.92210.611
Porphyromonas0.3520.3351.001
Prevotella0.630.5070.158
Pseudobutyrivibrio0.0040.0760.022
Roseburia2.6752.713.37
Ruminiclostridium1.9950.0080.002
Ruminococcus8.9729.7360.374
Schaalia0.0040.0020.003
Slackia0.0080.1070.003
Streptococcus0.1710.1650.34
Sutterella0.2110.2550.028
Syntrophomonas0.0150.0020
Thermoclostridium0.0040.0060.004
Turicibacter0.0040.0040.004
Varibaculum0.0360.0340.001
Veillonella0.0230.5560.01
Weissella0.0170.0020.003

Bottom Line….

For some bacteria we have the numbers being close, and for others very, very different. Often we see percentage being 10x different between tests! For Percentile, we see one test reforming 91%ile and a different test reporting 1%.

A human analogy: You pick a person off the street and ask “What is this person?” A Canadian? A Swede?

There is usually no clear answer —

  • Their name may indicate Iceland — Guðrún Jónsdóttir
  • Their passport may indicate that they are a Canadian Citizen
  • Their skin color may indicate that they are from Africa
  • Their nose may suggest that are from the Mediterranean
  • Their DNA may suggest that they are part Nigerian, Finnish, Thai, Irish
    • They are mitochondrial Haplogroup K, very common among Jewish People
  • Their eating habits suggests they may be Hindu
  • The way they speak English suggests that they are Haida Gwaii (native tribe on Canada’s west coast)
  • Their music preference (opera) suggests Italian

Bacteria exchange RNA etc constantly — just like our humans! We may want to have definitive answers — we should fix ourselves before complaining about bacteria! ;-). Different tests use different characteristics to give a bacteria a name.

What I am curious about is whether these changes make dramatic changes in suggestions.

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