This is a follow up to Technical Note: Identifying Key Bacteria to Address, part of this series Technical Notes on Microbiome Analysis. I am working with a new EU based start-up Precision Biome and in refining their algorithms they asked me to identify the key genus that should be considered (and other information).

The table below shows the top results that may be of interest in a clinical setting.

• Occurrences is the number of times it was detected as statistically significant.
• We averaged Chi² to provide more generic detection.
• [Shift] indicates if Chi² is for the low range test or the high range test.
  • Low with High Count indicates that the absence of cells is more severe in the low range than than the abundance of cells in the top range.
  • Often there is a shift to upper, resulting in over population of the top range and almost complete disappearance of the low range.
• Majority of the results were from 16s processing (with the inherent risk of misidentification)
• Contrary to common belief, low levels seems to be rarely the apparent cause, they may be a consequence of multiple highs.
• The data below can be replicated from data at https://citizenscience.microbiomeprescription.com/ (Open data) with the processes referred to above.

taxon	Tax Name	Shift	Occurrences	Average Chi2	Density
84567	Pedobacter	Low	355	127.9	High Count
114627	Alkaliphilus	Low	356	127.7	High Count
33951	Acetobacterium	Low	358	126.6	High Count
190972	Sedimentibacter	Low	353	126.4	High Count
1769729	Hathewaya	Low	362	126.4	High Count
100883	Coprobacillus	Low	360	125.4	High Count
28453	Sphingobacterium	Low	350	123	High Count
970	Selenomonas	Low	353	120.1	High Count
44000	Caldicellulosiruptor	Low	352	120	High Count
1378	Gemella	Low	353	119.3	High Count
82373	Anaerovibrio	Low	350	117.6	High Count
281119	Candidatus Amoebophilus	Low	352	117.2	High Count
29548	Rhodothermus	Low	348	115.2	High Count
69894	Tindallia	Low	347	110.1	High Count
864	Pectinatus	Low	351	108.1	High Count
33926	Candidatus Phytoplasma	Low	340	107.1	High Count
256319	Chlorobaculum	Low	348	106.4	High Count
89958	Natronincola	Low	332	105.1	High Count
2304693	Pseudoclostridium	Low	346	104.9	High Count
561	Escherichia	Low	345	103.6	High Count
1647	Erysipelothrix	Low	354	103.6	High Count
2093	Mycoplasma	Low	345	103.5	High Count
46205	Pseudobutyrivibrio	Low	587	103.4	High Count
94008	Thermicanus	Low	338	103.2	High Count
156973	Dysgonomonas	Low	345	102.1	High Count
119852	Oscillospira	Low	569	101.6	High Count
1263	Ruminococcus	Low	669	100.8	High Count
2316020	Mediterraneibacter	Low	670	100.7	High Count
33042	Coprococcus	Low	670	100.5	High Count
42447	Anaerobranca	Low	328	99.7	High Count
1350	Enterococcus	Low	264	99.3	High Count
35829	Acetivibrio	Low	664	97.6	High Count
1730	Eubacterium	Low	667	96.6	High Count
44260	Moorella	Low	254	96.3	High Count
376469	Olivibacter	Low	198	96.1	High Count
2740	Peptococcus	Low	543	95.2	High Count
131079	Limnobacter	Low	151	95.2	High Count
52784	Anaerofilum	Low	526	94.4	High Count
44258	Caloramator	Low	629	93.8	High Count
572511	Blautia	Low	897	93.3	High Count
816	Bacteroides	Low	897	93.2	High Count
841	Roseburia	Low	897	93	High Count
1485	Clostridium	Low	896	92.8	High Count
43994	Johnsonella	Low	618	92.8	High Count
265975	Oribacterium	Low	661	92.7	High Count
216851	Faecalibacterium	Low	897	92.7	High Count
909656	Phocaeicola	Low	895	92.6	High Count
1301	Streptococcus	Low	894	92.4	High Count
189330	Dorea	Low	897	92.4	High Count
28050	Lachnospira	Low	884	92.3	High Count
35832	Bilophila	Low	558	91.5	High Count
375288	Parabacteroides	Low	887	91.5	High Count
906	Megasphaera	Low	559	90.5	High Count
140625	Lachnobacterium	Low	634	88.6	High Count
1678	Bifidobacterium	Low	869	88	High Count
244127	Anaerotruncus	Low	867	87.3	High Count
207244	Anaerostipes	Low	893	86.4	High Count
838	Prevotella	Low	859	85.9	High Count
40544	Sutterella	Low	839	85.2	High Count
84108	Slackia	Low	508	83.8	High Count
29465	Veillonella	Low	842	83.6	High Count
1578	Lactobacillus	Low	870	82.2	High Count
162289	Peptoniphilus	Low	852	81.8	High Count
283168	Odoribacter	Low	857	80.6	High Count
61170	Holdemania	Low	860	79.5	High Count
102106	Collinsella	Low	853	79.3	High Count
33024	Phascolarctobacterium	Low	853	77.6	High Count
447020	Adlercreutzia	Low	473	76.5	High Count
1508657	Ruminiclostridium	Low	436	75.5	High Count
724	Haemophilus	Low	451	74.5	High Count
239934	Akkermansia	Low	824	74.3	High Count
86331	Mogibacterium	Low	841	73.5	High Count
872	Desulfovibrio	Low	806	72.6	High Count
836	Porphyromonas	Low	813	70.3	High Count
84111	Eggerthella	Low	767	69.6	High Count
574697	Butyricimonas	Low	779	69	High Count
1266	Sarcina	Low	228	68.8	High Count
1407607	Fusicatenibacter	Low	535	68.2	High Count
1506553	Lachnoclostridium	Low	314	68.1	High Count
292632	Subdoligranulum	Low	537	68	High Count
1505663	Erysipelatoclostridium	Low	540	67.7	High Count
1506577	Tyzzerella	Low	314	67.5	High Count
577309	Paraprevotella	Low	412	67.4	High Count
946234	Flavonifractor	Low	540	67.3	High Count
239759	Alistipes	Low	540	66.9	High Count
1654	Actinomyces	Low	718	66.9	High Count
43996	Catonella	Low	312	66.5	High Count
459786	Oscillibacter	Low	537	66.3	High Count
1769729	Hathewaya	High	270	66.2	High Count
1392389	Intestinimonas	Low	531	65.7	High Count
84567	Pedobacter	High	267	65.7	High Count
1649459	Hungatella	Low	311	65.5	High Count
33951	Acetobacterium	High	270	65.5	High Count
114627	Alkaliphilus	High	272	65.3	High Count
1164882	Lachnoanaerobaculum	Low	313	65.3	High Count
2048137	Agathobaculum	Low	312	65.3	High Count
698776	Cellulosilyticum	Low	308	64.8	High Count
2039240	Anaerotignum	Low	311	64.6	High Count
100883	Coprobacillus	High	277	64.4	High Count
190972	Sedimentibacter	High	268	64.1	High Count
52784	Anaerofilum	High	291	64	High Count
2569097	Anaerobutyricum	Low	309	63.6	High Count
1774128	Murimonas	Low	303	63.5	High Count
2740	Peptococcus	High	282	63.4	High Count
2719313	Enterocloster	Low	309	63.3	High Count
28453	Sphingobacterium	High	267	63.1	High Count
970	Selenomonas	High	259	62.7	High Count
1427378	Acetatifactor	Low	304	62.5	High Count
44000	Caldicellulosiruptor	High	256	61.7	High Count
1378	Gemella	High	269	61.4	High Count
204475	Gemmiger	Low	300	61.2	High Count
119852	Oscillospira	High	333	61.1	High Count
29548	Rhodothermus	High	258	60.8	High Count
281119	Candidatus Amoebophilus	High	253	60.5	High Count
82373	Anaerovibrio	High	257	59.8	High Count
1505657	Intestinibacter	Low	488	59.7	High Count
248744	Marvinbryantia	Low	502	59.4	High Count
253238	Ethanoligenens	Low	303	59.1	High Count
46205	Pseudobutyrivibrio	High	371	58.9	High Count
241189	Hespellia	Low	519	58.3	High Count
69894	Tindallia	High	252	57.7	High Count
864	Pectinatus	High	259	57.5	High Count
89958	Natronincola	High	253	57.4	High Count
43994	Johnsonella	High	346	57.4	High Count
131079	Limnobacter	High	140	57.3	High Count
1843210	Anaerocolumna	Low	293	56.8	High Count
44249	Paenibacillus	Low	297	56.7	High Count
1481960	Peptoclostridium	Low	208	56.7	High Count
94008	Thermicanus	High	253	56.6	High Count
84108	Slackia	High	271	56.6	High Count
577310	Parasutterella	Low	501	56.5	High Count
830	Butyrivibrio	Low	499	56.4	High Count
906	Megasphaera	High	315	56.4	High Count
44258	Caloramator	High	355	56.2	High Count
256319	Chlorobaculum	High	247	56.1	High Count
437755	Moryella	Low	497	56.1	High Count
1647	Erysipelothrix	High	255	56	High Count
33926	Candidatus Phytoplasma	High	244	56	High Count
561	Escherichia	High	247	55.9	High Count
2304693	Pseudoclostridium	High	249	55.9	High Count
33042	Coprococcus	High	438	55.5	High Count
1505652	Terrisporobacter	Low	504	55.5	High Count
1569	Sporosarcina	Low	294	55.5	High Count
35829	Acetivibrio	High	410	55.3	High Count
2316020	Mediterraneibacter	High	441	55.2	High Count
376469	Olivibacter	High	181	55.1	High Count
2093	Mycoplasma	High	251	54.6	High Count
588605	Robinsoniella	Low	294	54.6	High Count
156973	Dysgonomonas	High	258	54.6	High Count
35832	Bilophila	High	319	54.5	High Count
1263	Ruminococcus	High	456	54.5	High Count
1562	Desulfotomaculum	Low	283	54.5	High Count
838	Prevotella	High	447	54.3	High Count
140625	Lachnobacterium	High	348	54.1	High Count
1350	Enterococcus	High	221	54.1	High Count
44748	Sporobacter	Low	493	54	High Count
42447	Anaerobranca	High	242	53.8	High Count
40544	Sutterella	High	444	53.3	High Count
162289	Peptoniphilus	High	428	53.1	High Count
1485	Clostridium	High	536	53	High Count
909656	Phocaeicola	High	541	52.9	High Count
572511	Blautia	High	545	52.8	High Count
816	Bacteroides	High	548	52.8	High Count
44260	Moorella	High	212	52.6	High Count
189330	Dorea	High	546	52.6	High Count
841	Roseburia	High	552	52.5	High Count
1017280	Pseudoflavonifractor	Low	490	52.4	High Count
39948	Dialister	Low	498	52.3	High Count
265975	Oribacterium	High	419	52.3	High Count
216851	Faecalibacterium	High	563	52.3	High Count
1678	Bifidobacterium	High	492	52.1	High Count
29465	Veillonella	High	450	52.1	High Count
66831	Facklamia	Low	275	52	High Count
244127	Anaerotruncus	High	480	52	High Count
1730	Eubacterium	High	462	51.9	High Count
375288	Parabacteroides	High	539	51.9	High Count
1301	Streptococcus	High	564	51.9	High Count
28050	Lachnospira	High	555	51.6	High Count
1501226	Romboutsia	Low	480	51.3	High Count
379899	Niabella	Low	292	51.3	High Count
1432051	Eisenbergiella	Low	485	50.5	High Count
579	Kluyvera	Low	208	50	High Count
1578	Lactobacillus	High	475	49.9	High Count
283168	Odoribacter	High	456	49.6	High Count
653683	Anaerosporobacter	Low	209	49.6	High Count
724	Haemophilus	High	266	49.4	High Count
207244	Anaerostipes	High	549	49.3	High Count
61170	Holdemania	High	446	49.3	High Count
404402	Howardella	Low	268	49.2	High Count
872	Desulfovibrio	High	395	48.7	High Count
1433991	Brassicibacter	Low	270	48.6	High Count
86331	Mogibacterium	High	396	48.6	High Count
836	Porphyromonas	High	390	48.4	High Count
33024	Phascolarctobacterium	High	439	48.2	High Count
1508657	Ruminiclostridium	High	285	48.1	High Count
2282743	Desulfohalotomaculum	Low	269	47.9	High Count
239934	Akkermansia	High	407	47.7	High Count
397864	Barnesiella	Low	476	47.6	High Count
447020	Adlercreutzia	High	247	47.3	High Count
150022	Finegoldia	Low	484	47.3	High Count
1470353	Candidatus Soleaferrea	Low	201	47.1	High Count
102106	Collinsella	High	478	46.7	High Count
577309	Paraprevotella	High	243	46.4	High Count
420345	Lactonifactor	Low	451	46.3	High Count
596767	Hydrogenoanaerobacterium	Low	441	45.8	High Count
2529408	Schaalia	Low	202	45.4	High Count
574697	Butyricimonas	High	381	45	High Count
1654	Actinomyces	High	361	45	High Count
84111	Eggerthella	High	394	44.3	High Count
177971	Shuttleworthia	Low	434	42.5	High Count
1870884	Clostridioides	Low	193	42.5	High Count
644652	Gordonibacter	Low	200	41.7	High Count
191303	Turicibacter	Low	190	41.6	High Count
292632	Subdoligranulum	High	258	40.2	High Count
1716	Corynebacterium	Low	202	40	High Count
1407607	Fusicatenibacter	High	260	39.9	High Count
946234	Flavonifractor	High	256	39.9	High Count
459786	Oscillibacter	High	251	39.8	High Count
1392389	Intestinimonas	High	247	39.3	High Count
1505663	Erysipelatoclostridium	High	279	39.1	High Count
1506577	Tyzzerella	High	161	39.1	High Count
44748	Sporobacter	High	163	38.5	High Count
239759	Alistipes	High	283	38.4	High Count
830	Butyrivibrio	High	181	38.2	High Count
1164882	Lachnoanaerobaculum	High	158	38.1	High Count
43996	Catonella	High	162	37.9	High Count
1649459	Hungatella	High	155	37.9	High Count
698776	Cellulosilyticum	High	154	37.8	High Count
241189	Hespellia	High	205	37.6	High Count
2048137	Agathobaculum	High	151	37.4	High Count
1774128	Murimonas	High	145	37.4	High Count
100175	Papillibacter	Low	194	37.3	High Count
2039240	Anaerotignum	High	148	37.3	High Count
2569097	Anaerobutyricum	High	142	37.2	High Count
1506553	Lachnoclostridium	High	191	37	High Count
2719313	Enterocloster	High	145	36.8	High Count
596767	Hydrogenoanaerobacterium	High	148	36.8	High Count
237	Flavobacterium	Low	168	36.3	High Count
1505657	Intestinibacter	High	210	36.3	High Count
437755	Moryella	High	174	36.2	High Count
1427378	Acetatifactor	High	147	36.1	High Count
577310	Parasutterella	High	191	35.9	High Count
253238	Ethanoligenens	High	132	35.8	High Count
165779	Anaerococcus	Low	194	35.7	High Count
248744	Marvinbryantia	High	204	35.4	High Count
204475	Gemmiger	High	145	34.9	High Count
39948	Dialister	High	161	34.9	High Count
397864	Barnesiella	High	124	34.6	High Count
420345	Lactonifactor	High	115	34.5	High Count
1017280	Pseudoflavonifractor	High	157	34.4	High Count
1505652	Terrisporobacter	High	190	34.2	High Count
177971	Shuttleworthia	High	120	34.2	High Count
588605	Robinsoniella	High	116	34	High Count
1432051	Eisenbergiella	High	167	34	High Count
1569	Sporosarcina	High	122	33.7	High Count
44249	Paenibacillus	High	126	33.7	High Count
1843210	Anaerocolumna	High	128	33.6	High Count
168934	Thalassospira	Low	176	33.6	High Count
1501226	Romboutsia	High	165	33	High Count
150022	Finegoldia	High	130	32.8	High Count
1562	Desulfotomaculum	High	109	32.6	High Count
66831	Facklamia	High	104	31.6	High Count
1348911	Coprobacter	Low	194	31.4	High Count
379899	Niabella	High	110	31.3	High Count
135858	Catenibacterium	Low	169	28.9	High Count
1472649	Dielma	Low	180	28	High Count
117563	Granulicatella	Low	162	26.3	High Count
172900	Victivallis	Low	157	26.3	High Count
194	Campylobacter	Low	181	26.1	High Count
109326	Anaerovorax	Low	155	25.7	High Count
184869	Varibaculum	Low	178	24.7	High Count
580024	Enterorhabdus	Low	167	24.5	High Count
963	Herbaspirillum	Low	159	24.4	High Count
1357	Lactococcus	Low	157	23.8	High Count
1161127	Murdochiella	Low	154	22.2	High Count
189326	Gelria	Low	149	20.7	High Count
1473205	Senegalimassilia	Low	135	20.4	High Count