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).

• Ombre Suggestions Analysis – Failing Grade – 2A
• Biomesight Suggestions Analysis – Good Results – 2B
• Thorne Suggestions Analysis – INCOMPLETE / FAILED – 2C
• Microbiome Prescription Uber-Consensus Analysis – Excellent – 2D
• Comparing standalone suggestions – 2E, a reader wanted to know how similar Microbiome Prescription suggestions were using different data

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.

phylum	Thryve	BiomeSight	Thorne
Acidobacteria	76	10	52
Actinobacteria	38	46	65
Bacteroidetes	16	6	79
Chloroflexi	99	88	88
Cyanobacteria	96	96	56
Firmicutes	72	86	6
Fusobacteria	14	10	78
Proteobacteria	27	14	29
Synergistetes	46	5	42
Tenericutes	77	61	37
Verrucomicrobia	81	83	64

class	Thryve	BiomeSight	Thorne
Actinomycetia	46	54	62
Alphaproteobacteria	35	52	58
Anaerolineae	33	84	53
Bacilli	84	62	58
Bacteroidia	16	6	80
Betaproteobacteria	24	13	15
Caldilineae	100	79	1
Clostridia	63	90	7
Coriobacteriia	76	81	73
Cytophagia	20	58	77
Deltaproteobacteria	81	78	81
Epsilonproteobacteria	68	71	95
Erysipelotrichia	18	28	36
Fusobacteriia	14	10	78
Gammaproteobacteria	47	39	60
Mollicutes	78	61	35
Negativicutes	90	88	3
Opitutae	59	78	60
Synergistia	46	5	42
Tissierellia	96	99	88
Verrucomicrobiae	81	81	63

order	Thryve	BiomeSight	Thorne
Acholeplasmatales	77	62	4
Acidaminococcales	20	21	17
Actinomycetales	93	95	45
Alteromonadales	16	95	86
Anaerolineales	33	26	61
Bacillales	90	47	75
Bacteroidales	16	6	80
Bifidobacteriales	30	25	37
Burkholderiales	24	13	14
Caldilineales	100	79	1
Campylobacterales	68	71	96
Chromatiales	45	92	72
Coriobacteriales	47	84	11
Corynebacteriales	91	94	96
Cytophagales	21	58	77
Desulfovibrionales	81	78	80
Eggerthellales	92	94	96
Enterobacterales	29	22	67
Erysipelotrichales	18	28	36
Eubacteriales	64	89	7
Fusobacteriales	14	10	78
Halanaerobiales	94	100	67
Hyphomicrobiales	18	74	94
Lactobacillales	83	67	61
Micrococcales	39	9	92
Micromonosporales	74	19	85
Mycoplasmatales	87	86	54
Nostocales	72	97	25
Oceanospirillales	57	10	89
Oscillatoriales	95	80	28
Puniceicoccales	62	16	1
Rhodospirillales	8	50	41
Rickettsiales	29	10	49
Selenomonadales	85	86	29
Streptosporangiales	56	78	76
Synergistales	47	5	42
Thermoanaerobacterales	22	18	48
Tissierellales	95	99	82
Veillonellales	96	92	10
Verrucomicrobiales	81	81	63

family	Thryve	BiomeSight	Thorne
Acholeplasmataceae	77	62	4
Acidaminococcaceae	21	21	17
Actinomycetaceae	93	95	66
Aerococcaceae	92	98	60
Akkermansiaceae	82	85	69
Anaerolineaceae	35	26	61
Atopobiaceae	90	16	71
Bacillaceae	76	98	97
Bacteroidaceae	23	15	55
Bifidobacteriaceae	32	25	41
Bradyrhizobiaceae	34	25	81
Caldilineaceae	100	79	1
Campylobacteraceae	68	66	95
Carnobacteriaceae	52	10	67
Clostridiaceae	87	94	12
Coprobacillaceae Verbarg et al. 2014	76	42	1
Coriobacteriaceae	18	84	7
Corynebacteriaceae	90	92	95
Desulfovibrionaceae	83	78	80
Dysgonomonadaceae	60	4	79
Eggerthellaceae	92	94	96
Enterobacteriaceae	58	23	67
Enterococcaceae	60	62	89
Erysipelotrichaceae	19	25	39
Eubacteriaceae	92	77	29
Eubacteriales Family XIII. Incertae Sedis	95	96	66
Lachnospiraceae	80	93	26
Lactobacillaceae	89	74	64
Micrococcaceae	16	13	91
Microcoleaceae	91	77	1
Micromonosporaceae	74	20	85
Mycoplasmataceae	87	86	54
Odoribacteraceae	97	94	77
Oscillospiraceae	34	54	17
Paenibacillaceae	95	47	96
Peptococcaceae	98	90	39
Peptoniphilaceae	95	99	82
Peptostreptococcaceae	47	84	83
Planococcaceae	30	80	78
Porphyromonadaceae	55	27	36
Prevotellaceae	58	52	50
Puniceicoccaceae	63	58	1
Rhodospirillaceae	10	48	35
Rickettsiaceae	35	13	38
Selenomonadaceae	81	87	26
Sporomusaceae	86	38	46
Streptococcaceae	55	66	73
Streptosporangiaceae	68	20	52
Sutterellaceae	24	14	9
Syntrophomonadaceae	96	58	6
Tannerellaceae	29	20	76
Thermoactinomycetaceae	85	88	43
Turicibacteraceae Verbarg et al. 2014	26	27	22
Veillonellaceae	96	92	10

genus	Thryve	BiomeSight	Thorne
Acetivibrio	66	86	14
Acetobacterium	98	85	13
Acholeplasma	77	48	6
Actinobaculum	38	83	3
Actinomyces	74	79	53
Actinotignum	51	71	62
Akkermansia	82	85	69
Alloscardovia	93	93	1
Anaerococcus	94	96	81
Anaerostipes	90	73	41
Arcanobacterium	97	97	5
Bacillus	21	93	96
Bacteroides	26	16	71
Bifidobacterium	19	18	44
Bilophila	59	61	2
Blautia	84	94	4
Brevibacillus	41	85	87
Butyricimonas	73	56	82
Butyrivibrio	94	87	74
Caloramator	65	60	7
Campylobacter	67	67	96
Clostridium	78	87	16
Coprobacillus	87	49	1
Coprococcus	27	4	22
Corynebacterium	90	92	95
Desulfotomaculum	82	75	60
Desulfovibrio	69	84	87
Dialister	97	93	45
Dorea	90	69	1
Dysgonomonas	60	4	40
Eggerthella	75	78	86
Enterococcus	26	67	88
Erysipelothrix	76	67	17
Escherichia	72	32	52
Ethanoligenens	99	37	47
Eubacterium	92	54	38
Faecalibacterium	33	32	21
Filifactor	78	97	50
Finegoldia	90	84	75
Gemella	65	97	18
Hathewaya	88	77	1
Helcococcus	99	87	6
Lachnospira	5	93	88
Lactobacillus	89	60	64
Ligilactobacillus	58	15	81
Limosilactobacillus	24	23	49
Mediterraneibacter	86	81	46
Megasphaera	91	97	41
Mobiluncus	18	16	3
Mogibacterium	98	96	31
Mycoplasma	88	86	47
Mycoplasmopsis	35	94	0
Negativicoccus	75	92	24
Odoribacter	98	98	58
Paenibacillus	95	99	96
Parabacteroides	29	20	76
Pectinatus	23	19	2
Peptococcus	82	90	1
Peptoniphilus	95	99	69
Phocaeicola	3	25	55
Porphyromonas	94	95	97
Prevotella	67	64	58
Pseudobutyrivibrio	40	43	28
Roseburia	69	60	63
Ruminiclostridium	76	46	5
Ruminococcus	91	84	8
Schaalia	36	10	26
Slackia	37	81	10
Streptococcus	56	70	75
Sutterella	46	14	16
Syntrophomonas	97	20	2
Thermoclostridium	60	38	34
Turicibacter	26	27	22
Varibaculum	86	86	2
Veillonella	60	84	20
Weissella	87	13	31

Pass #2: Percentage

phylum	Thryve	BiomeSight	Thorne
Acidobacteria	0.011	0.002	0.005
Actinobacteria	0.652	0.364	2.117
Bacteroidetes	12.526	12.633	60.723
Chloroflexi	0.183	0.02	0.02
Cyanobacteria	0.123	0.374	0.024
Firmicutes	82.61	82.717	27.458
Fusobacteria	0.002	0.002	0.02
Proteobacteria	1.163	1.502	1.894
Synergistetes	0.004	0.002	0.005
Tenericutes	0.049	0.048	0.015
Verrucomicrobia	1.994	1.954	0.627

class	Thryve	BiomeSight	Thorne
Actinomycetia	0.641	0.351	1.093
Alphaproteobacteria	0.013	0.085	0.171
Anaerolineae	0.002	0.011	0.003
Bacilli	2.931	0.729	0.765
Bacteroidia	12.522	10.238	60.036
Betaproteobacteria	0.266	0.263	0.175
Caldilineae	0.182	0.009	0.001
Clostridia	73.508	81.689	25.405
Coriobacteriia	0.665	0.527	0.989
Cytophagia	0.004	0.036	0.047
Deltaproteobacteria	0.723	0.735	0.875
Epsilonproteobacteria	0.011	0.009	0.275
Erysipelotrichia	0.281	0.191	0.336
Fusobacteriia	0.002	0.002	0.02
Gammaproteobacteria	0.152	0.198	0.359
Mollicutes	0.049	0.048	0.013
Negativicutes	3.839	3.4	0.069
Opitutae	0.004	0.008	0.004
Synergistia	0.004	0.002	0.005
Tissierellia	1.468	3.352	0.386
Verrucomicrobiae	1.993	1.946	0.621

order	Thryve	BiomeSight	Thorne
Acholeplasmatales	0.023	0.033	0.002
Acidaminococcales	0.008	0.007	0.007
Actinomycetales	0.092	0.321	0.021
Alteromonadales	0.002	0.065	0.021
Anaerolineales	0.002	0.002	0.003
Bacillales	0.231	0.147	0.233
Bacteroidales	12.567	10.238	60.01
Bifidobacteriales	0.164	0.03	0.123
Burkholderiales	0.267	0.259	0.127
Caldilineales	0.182	0.009	0.001
Campylobacterales	0.011	0.009	0.273
Chromatiales	0.004	0.03	0.013
Coriobacteriales	0.143	0.527	0.025
Corynebacteriales	0.196	0.202	0.81
Cytophagales	0.004	0.036	0.047
Desulfovibrionales	0.716	0.727	0.825
Eggerthellales	0.517	0.525	0.963
Enterobacterales	0.011	0.012	0.157
Erysipelotrichales	0.282	0.191	0.336
Eubacteriales	73.717	80.554	25.38
Fusobacteriales	0.002	0.002	0.02
Halanaerobiales	0.013	0.239	0.004
Hyphomicrobiales	0.002	0.008	0.07
Lactobacillales	2.71	0.388	0.525
Micrococcales	0.006	0.002	0.063
Micromonosporales	0.004	0.002	0.006
Mycoplasmatales	0.021	0.015	0.007
Nostocales	0.006	0.357	0.005
Oceanospirillales	0.008	0.002	0.02
Oscillatoriales	0.117	0.009	0.002
Puniceicoccales	0.004	0.002	0
Rhodospirillales	0.002	0.069	0.021
Rickettsiales	0.002	0.002	0.004
Selenomonadales	0.096	0.392	0.02
Streptosporangiales	0.004	0.008	0.007
Synergistales	0.004	0.002	0.005
Thermoanaerobacterales	0.002	0.007	0.019
Tissierellales	0.99	3.424	0.267
Veillonellales	3.749	3.4	0.041
Verrucomicrobiales	2	1.946	0.621

family	Thryve	BiomeSight	Thorne
Acholeplasmataceae	0.023	0.033	0.002
Acidaminococcaceae	0.008	0.007	0.007
Actinomycetaceae	0.096	0.086	0.021
Aerococcaceae	0.096	0.084	0.007
Akkermansiaceae	2.07	1.903	0.616
Anaerolineaceae	0.002	0.002	0.003
Atopobiaceae	0.141	0.002	0.018
Bacillaceae	0.014	0.07	0.085
Bacteroidaceae	8.206	7.869	30.336
Bifidobacteriaceae	0.17	0.03	0.123
Bradyrhizobiaceae	0.002	0.002	0.011
Caldilineaceae	0.189	0.009	0.001
Campylobacteraceae	0.012	0.009	0.267
Carnobacteriaceae	0.004	0.002	0.007
Clostridiaceae	2.456	11.827	0.304
Coprobacillaceae Verbarg et al. 2014	0.051	0.138	0
Coriobacteriaceae	0.006	0.527	0.007
Corynebacteriaceae	0.195	0.192	0.776
Desulfovibrionaceae	0.743	0.721	0.822
Dysgonomonadaceae	0.006	0.002	0.023
Eggerthellaceae	0.537	0.525	0.963
Enterobacteriaceae	0.012	0.012	0.117
Enterococcaceae	0.004	0.015	0.06
Erysipelotrichaceae	0.293	0.138	0.336
Eubacteriaceae	8.637	0.25	0.054
Eubacteriales Family XIII. Incertae Sedis	0.377	0.188	0.047
Lachnospiraceae	35.558	38.817	15.522
Lactobacillaceae	2.488	0.047	0.09
Micrococcaceae	0.002	0.002	0.027
Microcoleaceae	0.121	0.007	0.001
Micromonosporaceae	0.004	0.002	0.006
Mycoplasmataceae	0.022	0.015	0.006
Odoribacteraceae	1.028	0.955	0.588
Oscillospiraceae	1.604	21.973	5.153
Paenibacillaceae	0.105	0.007	0.085
Peptococcaceae	0.295	0.178	0.03
Peptoniphilaceae	1.028	3.413	0.261
Peptostreptococcaceae	0.162	0.047	0.81
Planococcaceae	0.006	0.006	0.015
Porphyromonadaceae	1.701	0.886	1.001
Prevotellaceae	0.654	0.507	0.285
Puniceicoccaceae	0.004	0.004	0
Rhodospirillaceae	0.002	0.065	0.012
Rickettsiaceae	0.002	0.002	0.002
Selenomonadaceae	0.078	0.388	0.016
Sporomusaceae	0.022	0.004	0.004
Streptococcaceae	0.18	0.165	0.344
Streptosporangiaceae	0.004	0.002	0.003
Sutterellaceae	0.277	0.255	0.028
Syntrophomonadaceae	0.016	0.034	0.001
Tannerellaceae	0.389	0.545	2.972
Thermoactinomycetaceae	0.01	0.015	0.004
Turicibacteraceae Verbarg et al. 2014	0.004	0.004	0.004
Veillonellaceae	3.892	3.4	0.041

genus	Thryve	BiomeSight	Thorne
Acetivibrio	0.019	0.473	0.007
Acetobacterium	0.015	0.196	0.003
Acholeplasma	0.023	0.007	0.001
Actinobaculum	0.002	0.006	0
Actinomyces	0.015	0.014	0.009
Actinotignum	0.004	0.004	0.005
Akkermansia	1.995	1.903	0.616
Alloscardovia	0.009	0.009	0
Anaerococcus	0.414	0.407	0.073
Anaerostipes	4.839	0.144	0.173
Arcanobacterium	0.03	0.03	0.001
Bacillus	0.002	0.019	0.052
Bacteroides	7.908	7.869	30.336
Bifidobacterium	0.017	0.019	0.121
Bilophila	0.295	0.292	0.002
Blautia	13.004	18.727	1.315
Brevibacillus	0.002	0.004	0.004
Butyricimonas	0.147	0.142	0.374
Butyrivibrio	0.276	0.108	0.066
Caloramator	0.023	0.241	0.003
Campylobacter	0.011	0.009	0.263
Clostridium	1.006	3.204	0.188
Coprobacillus	0.051	0.138	0
Coprococcus	0.196	0.035	0.277
Corynebacterium	0.188	0.192	0.761
Desulfotomaculum	0.017	0.007	0.006
Desulfovibrio	0.414	0.429	0.813
Dialister	2.448	2.075	0.019
Dorea	1.94	0.535	0.001
Dysgonomonas	0.006	0.002	0.006
Eggerthella	0.077	0.046	0.139
Enterococcus	0.002	0.013	0.056
Erysipelothrix	0.008	0.019	0.003
Escherichia	0.011	0.01	0.03
Ethanoligenens	0.756	0.004	0.007
Eubacterium	8.214	0.039	0.051
Faecalibacterium	6.494	8.261	4.065
Filifactor	0.008	0.043	0.004
Finegoldia	0.154	0.054	0.041
Gemella	0.006	0.099	0.003
Hathewaya	0.013	0.349	0.001
Helcococcus	0.024	0.006	0.001
Lachnospira	0.004	7.122	4.473
Lactobacillus	2.397	0.017	0.043
Ligilactobacillus	0.006	0.002	0.029
Limosilactobacillus	0.002	0.002	0.003
Mediterraneibacter	5.661	0.813	0.456
Megasphaera	0.036	0.196	0.009
Mobiluncus	0.002	0.002	0.001
Mogibacterium	0.143	0.188	0.007
Mycoplasma	0.021	0.015	0.006
Mycoplasmopsis	0.002	0.015	0
Negativicoccus	0.008	0.06	0.002
Odoribacter	0.844	0.813	0.202
Paenibacillus	0.098	0.017	0.072
Parabacteroides	0.389	0.545	2.955
Pectinatus	0.002	0.004	0.001
Peptococcus	0.019	0.145	0.001
Peptoniphilus	0.395	2.946	0.09
Phocaeicola	0.002	3.922	10.611
Porphyromonas	0.352	0.335	1.001
Prevotella	0.63	0.507	0.158
Pseudobutyrivibrio	0.004	0.076	0.022
Roseburia	2.675	2.71	3.37
Ruminiclostridium	1.995	0.008	0.002
Ruminococcus	8.972	9.736	0.374
Schaalia	0.004	0.002	0.003
Slackia	0.008	0.107	0.003
Streptococcus	0.171	0.165	0.34
Sutterella	0.211	0.255	0.028
Syntrophomonas	0.015	0.002	0
Thermoclostridium	0.004	0.006	0.004
Turicibacter	0.004	0.004	0.004
Varibaculum	0.036	0.034	0.001
Veillonella	0.023	0.556	0.01
Weissella	0.017	0.002	0.003

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.