This is a literal dumping of the results of processing all viable symptoms from the donated, self-annotated Biomesight samples. The methodology of getting the data is described in New Standards for Microbiome Analysis?. I am de-cluttering the tables using:

• Only Genus and Species results
• Only the top 20 items in each group.
• Only items with at least P < 0.01 are shown

It is just the data with suggestions on how to use the data at the bottom.

Averages and Medians

I prefer medians over averages. Medians are the values where half of the people have less and half has more. If the data was a bell-curve, then the values will almost be the same… with bacteria that happens rarely.

If symptom median is higher than reference median, it means there is more of this bacteria.If lower, then less. This ignores how often the bacteria is seen.

tax_name	Rank	Symptom Avarage	Reference Average	Symptom Median	Reference Median
Bacteroides	genus	27.956	25.653	26.986	23.764
Phocaeicola vulgatus	species	6.281	5.721	4.107	3.333
Bacteroides uniformis	species	3.014	2.676	1.917	1.498
Coprococcus	genus	1.356	1.449	0.614	0.744
Pedobacter	genus	1.09	0.994	0.62	0.549
Bifidobacterium	genus	0.727	0.974	0.071	0.139
Bacteroides thetaiotaomicron	species	1.11	1.056	0.513	0.453
Bacteroides rodentium	species	0.428	0.383	0.222	0.177
Bilophila wadsworthia	species	0.359	0.336	0.232	0.196
Bilophila	genus	0.368	0.344	0.24	0.206
Bacteroides cellulosilyticus	species	0.894	0.835	0.107	0.073
Insolitispirillum	genus	0.879	0.872	0.126	0.098
Insolitispirillum peregrinum	species	0.879	0.872	0.126	0.098
Novispirillum	genus	0.879	0.872	0.123	0.097
Ruminococcus bromii	species	0.791	0.782	0.189	0.164
Hathewaya histolytica	species	0.294	0.275	0.172	0.154
Hathewaya	genus	0.294	0.275	0.172	0.154
Bifidobacterium longum	species	0.258	0.337	0.035	0.051
Bacteroides stercoris	species	1.716	1.541	0.022	0.038
Sutterella wadsworthensis	species	0.687	0.67	0.045	0.061

Bacteria Incidence – How often is it reported

The common sense belief is that if a bacteria is reported more often, then the amount should be higher. This is often not true. The microbiome is a complex thing. Look at Methanobrevibacter below, it is seen almost half as often with this condition. Bacteria like Desulfomonile are items to reduce, it is occurring too often.

tax_name	Rank	Incidence Odds Ratio	Chi2	Symptoms %	Reference %
Shewanella upenei	species	1.46	13	35.8	24.4
Methanobrevibacter	genus	0.61	10.4	13.8	22.4
Methanobrevibacter smithii	species	0.62	10.1	13.5	21.9
Slackia isoflavoniconvertens	species	0.62	9	12.7	20.4
Prosthecobacter	genus	1.68	12.9	17	10.1
Bifidobacterium cuniculi	species	0.66	7.1	12.7	19.4
Desulfomonile tiedjei	species	1.45	7.8	20.2	13.9
Desulfomonile	genus	1.44	7.6	20.2	14

More or Less often based on Symptom Median All Incidence

This is a little more complex to understand. If we compute the mid point for people with the symptom, then if the bacteria was not involved then half of the reference should be above this value and half below this value. If not, it means that the symptom tends to over or under growth. Look at Isoalcanivorax below, almost 80% of the reference set has less than the median (and the symptom only has 50%); this implies that Isoalcanivorax is prone to overgrowth (“bumper harvest”) with the symptom.

Note: Many of these are rarely reported bacteria, but they are reported sufficiently to compute significance. Below, we restrict to common bacteria only.

tax_name	Rank	Symptom Median	Odds Ratio	Chi2	Below	Above
Bilophila	genus	0.3095	0.55	30.3	2147	1184
Bilophila wadsworthia	species	0.2905	0.58	24.8	2096	1222
Bacteroides	genus	29.302	0.62	20.2	2318	1428
Ruminococcus callidus	species	0.003	1.63	19.1	817	1331
Bifidobacterium	genus	0.055	1.57	17.3	1433	2245
Caloramator uzoniensis	species	0.005	0.63	16.8	1224	772
Oribacterium	genus	0.049	1.56	16.6	1315	2045
Phocaeicola	genus	11.3735	0.65	15.9	2268	1476
Peptoniphilus methioninivorax	species	0.005	0.65	15.8	1590	1027
Bacteroides fluxus	species	0.015	0.65	15.7	1875	1218
Acidaminococcus	genus	0.029	0.65	15.1	1703	1112
Limnobacter	genus	0.02	0.65	15.1	1678	1096
Turicibacter	genus	0.005	1.54	15.1	961	1476
Limnobacter litoralis	species	0.02	0.65	15	1676	1096
Oribacterium sinus	species	0.049	1.52	14.9	1328	2018
Acidaminococcus fermentans	species	0.028	0.67	13.2	1499	1004
Luteibacter anthropi	species	0.0075	1.5	13.1	820	1230
Candidatus Amoebophilus asiaticus	species	0.013	0.68	12.8	2064	1402
Candidatus Amoebophilus	genus	0.013	0.68	12.8	2064	1402
Shewanella	genus	0.007	0.67	12.7	1421	957

More or Less often based on Reference Median All Incidence

This is like the above, but with a different line in the sand. Instead of the median of those with the condition, we use the median of the reference set.

tax_name	Rank	Reference Median	Odds Ratio	Chi2	Below	Above
Deferribacter	genus	0.002	0.1	36.3	50	5
Deferribacter autotrophicus	species	0.002	0.1	35.4	49	5
Sutterella stercoricanis	species	0.005	0.41	33.3	143	59
Helicobacter	genus	0.002	0.35	32.4	108	38
Lentibacillus salinarum	species	0.002	0.19	32.4	59	11
Lentibacillus	genus	0.002	0.19	32.4	59	11
Helicobacter suncus	species	0.002	0.33	30.6	92	30
Isoalcanivorax	genus	0.002	0.14	27.6	43	6
Isoalcanivorax indicus	species	0.002	0.14	27.6	43	6
Bilophila	genus	0.203	1.89	27.4	108	204
Viridibacillus neidei	species	0.002	0.22	27.1	55	12
Alcanivorax	genus	0.002	0.16	26.5	44	7
Bilophila wadsworthia	species	0.1925	1.86	26.3	109	203
Devosia	genus	0.002	0.41	26.2	110	45
Niabella	genus	0.002	0.28	26.1	65	18
Bacteroides	genus	23.9055	1.78	25.6	129	229
Coraliomargarita akajimensis	species	0.002	0.32	25.6	75	24
Coraliomargarita	genus	0.002	0.32	25.6	75	24
Actinopolyspora	genus	0.002	0.24	25.5	55	13
Niabella aurantiaca	species	0.002	0.27	25	60	16

More or Less often based on Symptom Median High Incidence

Above we see that many of the top bacteria identified are sparse, that is not reported often. We then restrict them to those that occur above 50% or the time. For example, Bilophila is more often high than with the reference.

tax_name	Rank	Symptom Median Freq	Odds Ratio	Chi2	Below	Above
Bilophila	genus	0.3095	0.55	30.3	2147	1184
Bilophila wadsworthia	species	0.2905	0.58	24.8	2096	1222
Bacteroides	genus	29.302	0.62	20.2	2318	1428
Ruminococcus callidus	species	0.003	1.63	19.1	817	1331
Bifidobacterium	genus	0.055	1.57	17.3	1433	2245
Caloramator uzoniensis	species	0.005	0.63	16.8	1224	772
Oribacterium	genus	0.049	1.56	16.6	1315	2045
Phocaeicola	genus	11.3735	0.65	15.9	2268	1476
Peptoniphilus methioninivorax	species	0.005	0.65	15.8	1590	1027
Bacteroides fluxus	species	0.015	0.65	15.7	1875	1218
Acidaminococcus	genus	0.029	0.65	15.1	1703	1112
Limnobacter	genus	0.02	0.65	15.1	1678	1096
Turicibacter	genus	0.005	1.54	15.1	961	1476
Limnobacter litoralis	species	0.02	0.65	15	1676	1096
Oribacterium sinus	species	0.049	1.52	14.9	1328	2018
Acidaminococcus fermentans	species	0.028	0.67	13.2	1499	1004
Luteibacter anthropi	species	0.0075	1.5	13.1	820	1230
Candidatus Amoebophilus asiaticus	species	0.013	0.68	12.8	2064	1402
Candidatus Amoebophilus	genus	0.013	0.68	12.8	2064	1402
Shewanella	genus	0.007	0.67	12.7	1421	957

More or Less often based on Reference Median High Incidence

Above we see that many of the top bacteria identified are sparse, that is not reported often. We then restrict them to those that occur above 50% or the time.

tax_name	Rank	Reference Median Freq	Odds Ratio	Chi2	Below	Above
Sutterella stercoricanis	species	0.005	0.41	33.3	143	59
Bilophila	genus	0.203	1.89	27.4	108	204
Bilophila wadsworthia	species	0.1925	1.86	26.3	109	203
Bacteroides	genus	23.9055	1.78	25.6	129	229
Bacteroides rodentium	species	0.179	1.75	24.2	130	227
Tetragenococcus doogicus	species	0.003	0.53	18.9	135	71
Dethiosulfovibrio	genus	0.004	0.55	18.6	155	86
Ruminococcus callidus	species	0.008	0.52	18.4	127	66
Bifidobacterium	genus	0.132	0.62	17.2	216	135
Bacteroides uniformis	species	1.524	1.59	16.9	138	219
Candidatus Phytoplasma prunorum	species	0.006	0.59	16.9	171	101
Clostridium taeniosporum	species	0.003	0.55	16.6	137	76
Coprococcus	genus	0.747	0.63	16.4	219	139
Phocaeicola	genus	9.194	1.54	14.8	141	217
Clostridium akagii	species	0.003	0.57	14.5	127	72
Bacteroides gallinarum	species	0.003	0.57	14	122	69
Tetragenococcus	genus	0.003	0.59	13.2	132	78
Bifidobacterium adolescentis	species	0.013	0.63	12.7	163	103
Luteibacter anthropi	species	0.016	0.59	12.3	122	72
Coprococcus eutactus	species	0.01	0.62	12.2	149	93

Summary

Above, we have identified a ton of bacteria that have P < 0.01 shifts with this condition. The next issue is how to adjust them. A deep modification model such as that illustrated on the Microbiome Taxa R² Site may be used for probiotics. Once probiotics are suggested, then more conventional US National Library of Medicine based suggestion could be done base on the probiotics selected. Most of the bacteria above lack any literature on how to modify.

This is pending work because I must create a database using Biomesight samples. The above site used data shared from PrecisionBiome. We cannot safely mix data from different sample processing methods (see The taxonomy nightmare before Christmas… ). Once that database is built, I will add its probiotics suggestions below.