Patterns of Microbiome Distributions Across Different Vendors

This week I had some discussion with several CEOs of various microbiome testing companies and the question came up:

Can we take the percentile threshold from the Kaltoft-Møldrup(KM) Range computation and apply it to other tests?

If this is likely true, then we reduce the impact of the Blue “Whale in the Room”

Fortunately, I have the data to reasonably answer that (for the common good) and show charts from some of the 60+ providers that have had samples uploaded. Most people in this area are very siloed into one lab, one way and cannot see the forest, only the leaf that they are on.

Lactobacillus

Biomesight

Ubiome

Ombre

PrecisionBiome

Vitract

Thorne

Bifidobacterium Longum

Biomesight

Ubiome

Ombre

Not sufficient data (3 samples had it)

PrecisionBiome

Vitract

Not sufficient data (3 samples had it)

Thorne

Faecalibacterium prausnitzii

Biomesight

Ubiome

Ombre

PrecisionBiome

Vitract

Thorne

Bottom Line

The first item of note: Two labs will typically (99% odds!!) report no Bifidobacterium Longum! In both cases, they do report it, but rarely detect any. Some medical practitioners (not knowing better about the test) will advocate this strongly as a probiotic with no safe evidence support that. This returns us to Scott’s quotation cited above, the blue whale!

While conceptually, the ability to transfer percentile ranges between labs is very appealing, it appears to be unsafe. Looking at the lower bounds for Faecalibacterium prausnitzii we see the following suggested (eye balling – make your own estimates):

Biomesight: 18%ile
uBiome: 30%ile
Ombre: 12%ile
PrecisionBiome: 30%ile
Vitract: 12%ile
Thorne: 20%ile

To me, this settles the issues. The KM percentile estimates for ranges cannot be transfered across labs. They are lab specific (and unlike the naive mean and standard deviation approach that ignores the high skews) require significant sample size.

The hidden Minefield in Microbiome Data and AI

Most contemporary AI models has a quiet unspoken assumption: data is a near normal distribution or Bayesian. This translate into assuming the data distribution has a statistical SKEWNESS of near zero(0). Often these models improve when the data is transformed to reduced skewness (often a log function is used). If a model improves with data normalization, it is skew sensitive.

A skew near zero is true for a very small percentage of taxa as shown by this table based on shotgun analysis of 1000 healthy individuals. This issue often has huge impacts for reference range computation.

NCBI Taxon	name	rank	skewness
291645	Bacteroides nordii	species	29.799
2759	Eukaryota	superkingdom	29.558
333367	Enterocloster asparagiformis	species	29.538
518636	[Clostridium] asparagiforme DSM 15981	strain	29.538
117743	Flavobacteriia	class	29.525
200644	Flavobacteriales	order	29.525
712633	Streptococcus sp. oral taxon 431	species	28.849
2759692	Streptococcus sp. Marseille-Q3533	species	28.405
712623	Streptococcus sp. oral taxon 061	species	28.334
2972784	Streptococcus sp. Marseille-Q6470	species	28.229
1386	Bacillus	genus	28.215
2005473	Muribaculaceae	family	28.206
68892	Streptococcus infantis	species	27.604
1736	Eubacterium limosum	species	27.486
2714358	Pusillibacter faecalis	species	27.285
2892397	Pusillibacter	genus	27.285
4751	Fungi	kingdom	26.227
347253	Streptococcus salivarius JIM8777	strain	26.222
2690837	Eggerthella guodeyinii	species	26.159
2762318	Weeksellaceae	family	25.877
1839799	Streptococcus sp. FDAARGOS_192	species	25.823
4890	Ascomycota	phylum	25.785
468	Moraxellaceae	family	25.736
2887326	Moraxellales	order	25.736
72274	Pseudomonadales	order	25.621
2682456	Veillonella nakazawae	species	25.587
135621	Pseudomonadaceae	family	25.569
469	Acinetobacter	genus	25.496
1547	Thomasclavelia ramosa	species	25.361
191303	Turicibacter	genus	25.108
2810281	Turicibacteraceae	family	25.108
387661	Parabacteroides johnsonii	species	25.06
2529408	Schaalia	genus	24.99
1918540	Muribaculum	genus	24.929
1683	Bifidobacterium angulatum	species	24.806
4892	Saccharomycetales	order	24.79
4891	Saccharomycetes	class	24.79
1852377	Actinomyces pacaensis	species	24.588
197614	Streptococcus pasteurianus	species	24.543
1297617	Intestinimonas butyriciproducens	species	24.533
1392389	Intestinimonas	genus	24.533
28127	Hoylesella buccalis	species	24.515
2610896	Streptococcus sp. LPB0220	species	24.27
1689	Bifidobacterium dentium	species	24.136
1871022	Parolsenella massiliensis	species	24.122
286	Pseudomonas	genus	23.772
2974257	Hoylesella	genus	23.703
2735723	Turicibacter bilis	species	23.682
1679	Bifidobacterium longum subsp. longum	subspecies	23.208
1944646	Phoenicibacter congonensis	species	23.137
1981050	Phoenicibacter	genus	23.137
1329	Streptococcus canis	species	22.882
1316408	Streptococcus sp. HSISM1	species	22.835
726	Haemophilus haemolyticus	species	22.752
1505	Paraclostridium sordellii	species	22.63
1849828	Paeniclostridium	genus	22.63
1981510	Monoglobus pectinilyticus	species	22.567
2039302	Monoglobus	genus	22.567
2834348	Caproicibacterium	genus	22.417
186804	Peptostreptococcaceae	family	22.213
49546	Flavobacteriaceae	family	22.14
186817	Bacillaceae	family	22.035
45634	Streptococcus cristatus	species	21.74
1712675	Turicibacter sp. H121	species	21.688
838	Prevotella	genus	21.625
86332	Mogibacterium pumilum	species	21.611
1903409	Erwiniaceae	family	21.56
2606626	Sodaliphilus pleomorphus	species	21.511
2815786	Sodaliphilus	genus	21.511
1903414	Morganellaceae	family	21.495
32067	Leptotrichia	genus	21.272
1129771	Leptotrichiaceae	family	21.258
135625	Pasteurellales	order	21.187
712	Pasteurellaceae	family	21.187
1433513	Streptococcus gwangjuense	species	21.148
1812935	Enterobacter roggenkampii	species	21.039
2842531	Solibaculum	genus	20.918
2780922	Solibaculum mannosilyticum	species	20.918
2944914	Allocoprobacillus halotolerans	species	20.909
3059504	Allocoprobacillus	genus	20.909
76860	Streptococcus constellatus	species	20.905
889201	Streptococcus cristatus ATCC 51100	strain	20.893
206351	Neisseriales	order	20.791
199	Campylobacter concisus	species	20.784
195	Campylobacter coli	species	20.759
724	Haemophilus	genus	20.749
481	Neisseriaceae	family	20.706
43675	Rothia mucilaginosa	species	20.655
482	Neisseria	genus	20.599
2598453	Streptococcus sp. 116-D4	species	20.541
548	Klebsiella aerogenes	species	20.51
39950	Dialister pneumosintes	species	20.383
59201	Salmonella enterica subsp. enterica	subspecies	20.349
133925	Olsenella	genus	20.343
729	Haemophilus parainfluenzae	species	20.246
518635	Bifidobacterium angulatum DSM 20098 = JCM 7096	strain	20.207
2948573	Peptoniphilus sp. SAHP1	species	20.133
1328	Streptococcus anginosus	species	20.096
2767842	Lactiplantibacillus	genus	20.094
1268	Micrococcaceae	family	19.951
32207	Rothia	genus	19.951
3018741	Cellulosilyticaceae	family	19.949
698776	Cellulosilyticum	genus	19.949
85006	Micrococcales	order	19.899
2530390	Muribaculum gordoncarteri	species	19.888
2049	Actinomycetaceae	family	19.868
2037	Actinomycetales	order	19.868
53335	Pantoea	genus	19.864
72294	Campylobacteraceae	family	19.835
194	Campylobacter	genus	19.835
84642	Aeromonadaceae	family	19.819
28037	Streptococcus mitis	species	19.786
642	Aeromonas	genus	19.782
862965	Haemophilus parainfluenzae T3T1	strain	19.769
158	Treponema denticola	species	19.679
162289	Peptoniphilus	genus	19.612
446660	Adlercreutzia equolifaciens	species	19.516
33958	Lactobacillaceae	family	19.511
28211	Alphaproteobacteria	class	19.479
204441	Rhodospirillales	order	19.456
165779	Anaerococcus	genus	19.293
433	Acetobacteraceae	family	19.269
543314	Eubacteriales Family XIII. Incertae Sedis	family	19.231
1434011	Komagataeibacter	genus	19.071
65958	Komagataeibacter oboediens	species	19.071
1485	Clostridium	genus	18.944
938288	Fenollaria massiliensis	species	18.89
1686313	Fenollaria	genus	18.89
154288	Turicibacter sanguinis	species	18.829
135614	Lysobacterales	order	18.784
1578	Lactobacillus	genus	18.769
29547	Campylobacterota	phylum	18.752
3031852	Epsilonproteobacteria	class	18.752
213849	Campylobacterales	order	18.749
1686	Bifidobacterium catenulatum	species	18.656
2942994	Buchavirus	genus	18.627
573	Klebsiella pneumoniae	species	18.592
1776384	Emergencia timonensis	species	18.586
1926556	Emergencia	genus	18.586
1639133	Citrobacter portucalensis	species	18.58
1648923	Bacillus paralicheniformis	species	18.559
136	Spirochaetales	order	18.546
2845253	Treponemataceae	family	18.545
157	Treponema	genus	18.545
506	Alcaligenaceae	family	18.54
674529	Bacteroides faecis	species	18.517
556259	Bacteroides sp. D2	species	18.427
31979	Clostridiaceae	family	18.413
365659	Streptococcus mitis B6	strain	18.407
1266	Sarcina	genus	18.393
2726954	Sarcina sp. JB2	species	18.393
1522	[Clostridium] innocuum	species	18.363
150055	Streptococcus lutetiensis	species	18.303
1352	Enterococcus faecium	species	18.288
556499	Propionibacterium acidifaciens	species	18.151
78448	Bifidobacterium pullorum	species	18.142
78344	Bifidobacterium pullorum subsp. gallinarum	subspecies	18.142
1903412	Hafniaceae	family	18.071
1796646	Muribaculum intestinale	species	18.017
2864143	Adlercreutzia equolifaciens subsp. equolifaciens	subspecies	17.965
1384484	Adlercreutzia equolifaciens DSM 19450	strain	17.965
292800	Flavonifractor plautii	species	17.91
946234	Flavonifractor	genus	17.91
32033	Lysobacteraceae	family	17.893
394340	Adlercreutzia equolifaciens subsp. celatus	subspecies	17.87
1649459	Hungatella	genus	17.797
154046	Hungatella hathewayi	species	17.79
2144175	Megasphaera stantonii	species	17.749
39778	Veillonella dispar	species	17.73
2682455	Veillonella sp. S12025-13	species	17.715
1502	Clostridium perfringens	species	17.684
544	Citrobacter	genus	17.656
735	Haemophilus parahaemolyticus	species	17.649
257758	Streptococcus pseudopneumoniae	species	17.644
208962	Escherichia albertii	species	17.64
1054460	Streptococcus pseudopneumoniae IS7493	strain	17.619
1903411	Yersiniaceae	family	17.596
680646	Rothia mucilaginosa DY-18	strain	17.513
546	Citrobacter freundii	species	17.495
2766537	Caproicibacterium amylolyticum	species	17.401
629	Yersinia	genus	17.393
1114965	Streptococcus parasanguinis FW213	strain	17.387
40323	Stenotrophomonas	genus	17.334
2819619	Streptococcus toyakuensis	species	17.312
1590	Lactiplantibacillus plantarum	species	17.249
1318	Streptococcus parasanguinis	species	17.246
1343	Streptococcus vestibularis	species	17.105
328812	Parabacteroides goldsteinii	species	17.067
204455	Rhodobacterales	order	17.018
1257	Peptostreptococcus	genus	16.978
1385942	Bifidobacterium breve 689b	strain	16.943
760570	Streptococcus parasanguinis ATCC 15912	strain	16.903
1463165	Klebsiella quasipneumoniae	species	16.89
747	Pasteurella multocida	species	16.833
203691	Spirochaetota	phylum	16.832
203692	Spirochaetia	class	16.832
2005386	Arabiibacter	genus	16.719
1870985	Arabiibacter massiliensis	species	16.719
28901	Salmonella enterica	species	16.716
105841	Anaerostipes caccae	species	16.663
61645	Enterobacter asburiae	species	16.658
1234680	Streptococcus rubneri	species	16.63
827	Campylobacter ureolyticus	species	16.573
85023	Microbacteriaceae	family	16.569
31989	Paracoccaceae	family	16.523
1260	Finegoldia magna	species	16.507
150022	Finegoldia	genus	16.507
54005	Peptoniphilus harei	species	16.453
1303	Streptococcus oralis	species	16.443
1918385	Acutalibacter	genus	16.383
1796620	Acutalibacter muris	species	16.383
2877527	Blautia parvula	species	16.379
1313	Streptococcus pneumoniae	species	16.378
487173	Dialister succinatiphilus	species	16.179
90964	Staphylococcaceae	family	16.134
1847725	Lawsonella	genus	16.112
1528099	Lawsonella clevelandensis	species	16.112
2805586	Lawsonellaceae	family	16.112
438033	Ruminococcus gauvreauii	species	16.111
1385	Bacillales	order	16.095
1314	Streptococcus pyogenes	species	16.081
590	Salmonella	genus	16.055
203490	Fusobacteriia	class	16.054
32066	Fusobacteriota	phylum	16.054
203491	Fusobacteriales	order	16.054
2743582	Peptacetobacter	genus	16.025
89152	Peptacetobacter hiranonis	species	16.025
447020	Adlercreutzia	genus	15.996
28126	Segatella buccae	species	15.942
583	Proteus	genus	15.938
137591	Weissella cibaria	species	15.924
1279	Staphylococcus	genus	15.923
1491	Clostridium botulinum	species	15.889
1357	Lactococcus	genus	15.888
135624	Aeromonadales	order	15.838
1358	Lactococcus lactis	species	15.828
739	Aggregatibacter segnis	species	15.766
862962	Bacteroides fragilis 638R	strain	15.764
2058152	Klebsiella grimontii	species	15.755
203492	Fusobacteriaceae	family	15.747
44008	Enterococcus cecorum	species	15.738
613	Serratia	genus	15.733
848	Fusobacterium	genus	15.669
221027	Treponema putidum	species	15.655
59732	Chryseobacterium	genus	15.65
626932	Alistipes indistinctus	species	15.619
564	Escherichia fergusonii	species	15.553
712122	Actinomyces sp. oral taxon 414	species	15.55
158787	Bifidobacterium scardovii	species	15.539
1150461	Bifidobacterium scardovii JCM 12489 = DSM 13734	strain	15.539
742737	Hungatella hathewayi WAL-18680	strain	15.511
766764	Debaryomycetaceae	family	15.464
839	Xylanibacter ruminicola	species	15.445
2806443	Turicibacter sp. TJ11	species	15.413
1762	Mycobacteriaceae	family	15.41
858619	Corynebacterium variabile DSM 44702	strain	15.399
1727	Corynebacterium variabile	species	15.399
727	Haemophilus influenzae	species	15.393
538949	uncultured Alistipes sp.	species	15.379
1902136	Streptococcus sp. NPS 308	species	15.327
1470540	Jeotgalibaca	genus	15.236
376805	Phocaeicola salanitronis	species	15.193
667015	Phocaeicola salanitronis DSM 18170	strain	15.193
544448	Mycoplasmatota	phylum	15.185
37734	Enterococcus casseliflavus	species	15.155
3025755	Thomasclavelia	genus	15.148
265	Paracoccus	genus	15.116
1737405	Tissierellales	order	15.088
33037	Anaerococcus vaginalis	species	15.071
1570339	Peptoniphilaceae	family	15.069
2763022	Bacteroides sp. M10	species	14.944
582	Morganella morganii	species	14.935
581	Morganella	genus	14.935
160674	Raoultella	genus	14.922
547	Enterobacter	genus	14.904
499174	Clostridioides difficile QCD-23m63	strain	14.886
2749267	Amedibacterium	genus	14.848
2583452	Amedibacterium intestinale	species	14.848
287	Pseudomonas aeruginosa	species	14.848
2585117	Alistipes onderdonkii subsp. vulgaris	subspecies	14.823
76859	Fusobacterium animalis	species	14.814
28038	Latilactobacillus curvatus	species	14.798
2816960	Lactococcus cremoris subsp. cremoris	subspecies	14.767
33959	Lactobacillus johnsonii	species	14.762
568	Hafnia	genus	14.713
46867	Clostridium chauvoei	species	14.685
837	Porphyromonas gingivalis	species	14.682
908937	Prevotella dentalis DSM 3688	strain	14.674
52227	Prevotella dentalis	species	14.674
1104322	Lactococcus cremoris subsp. cremoris A76	strain	14.606
2810280	Coprobacillaceae	family	14.602
571	Klebsiella oxytoca	species	14.567
1903410	Pectobacteriaceae	family	14.528
712150	Aggregatibacter sp. oral taxon 513	species	14.524
2497860	Cellulosilyticum sp. WCF-2	species	14.522
538	Eikenella	genus	14.517
2966552	Thermocaproicibacter melissae	species	14.504
3048127	Thermocaproicibacter	genus	14.504
579	Kluyvera	genus	14.489
76892	Caulobacteraceae	family	14.485
204458	Caulobacterales	order	14.485
85009	Propionibacteriales	order	14.472
31957	Propionibacteriaceae	family	14.471
1335	Streptococcus equinus	species	14.462
745	Pasteurella	genus	14.445
4893	Saccharomycetaceae	family	14.398
97138	Clostridium sp. MD294	species	14.388
1868794	Jeotgalibaca arthritidis	species	14.37
1504	Clostridium septicum	species	14.357
4930	Saccharomyces	genus	14.354
158847	Megamonas hypermegale	species	14.331
205913	Bifidobacterium longum DJO10A	strain	14.315
72407	Klebsiella pneumoniae subsp. pneumoniae	subspecies	14.283
423211	Streptococcus suis GZ1	strain	14.272
584	Proteus mirabilis	species	14.269
31969	Mollicutes	class	14.254
1499973	Escherichia marmotae	species	14.215
999416	Parabacteroides distasonis CL03T12C09	strain	14.203
84162	Cryptobacterium	genus	14.188
469378	Cryptobacterium curtum DSM 15641	strain	14.188
84163	Cryptobacterium curtum	species	14.188
95818	Candidatus Saccharibacteria	phylum	14.17
208479	Enterocloster bolteae	species	14.165
1229621	Anaerostipes rhamnosivorans	species	14.158
1322	Blautia hansenii	species	14.125
537007	Blautia hansenii DSM 20583	strain	14.125
981540	Streptococcus pasteurianus ATCC 43144	strain	14.114
1805478	Olsenella timonensis	species	14.114
28128	Prevotella corporis	species	14.058
135623	Vibrionales	order	14.053
641	Vibrionaceae	family	14.053
475	Moraxella	genus	14.035
410072	Coprococcus comes	species	14.022
1805431	Enterococcus saigonensis	species	14.018
53442	Eubacterium callanderi	species	14.007
762982	Paraprevotella xylaniphila YIT 11841	strain	13.99
454155	Paraprevotella xylaniphila	species	13.99
411459	Blautia obeum ATCC 29174	strain	13.974
186827	Aerococcaceae	family	13.966
1508657	Ruminiclostridium	genus	13.926
122277	Pectobacterium	genus	13.907
2942991	Cohcovirus	genus	13.901
5475	Candida	genus	13.862
208224	Enterobacter kobei	species	13.837
171551	Porphyromonadaceae	family	13.802
2093857	Dysosmobacter welbionis	species	13.801
2591381	Dysosmobacter	genus	13.801
836	Porphyromonas	genus	13.794
76857	Fusobacterium polymorphum	species	13.755
1891914	Streptococcus oralis subsp. oralis	subspecies	13.751
1134687	Klebsiella michiganensis	species	13.734
237	Flavobacterium	genus	13.709
1912216	Cutibacterium	genus	13.686
1287640	Anaerococcus obesiensis	species	13.685
539	Eikenella corrodens	species	13.674
305719	Segatella baroniae	species	13.643
46255	Weissella	genus	13.628
34062	Moraxella osloensis	species	13.621
1776379	Leyella lascolaii	species	13.605
1122992	Hoylesella timonensis 4401737 = DSM 22865 = JCM 15640	strain	13.593
386414	Hoylesella timonensis	species	13.593
1582879	Ezakiella	genus	13.574
2715212	Bacteroides faecium	species	13.561
206389	Rhodocyclales	order	13.559
1529	Clostridium cadaveris	species	13.535
553973	[Clostridium] hylemonae DSM 15053	strain	13.532
1217282	Parabacteroides faecis	species	13.519
315405	Streptococcus gallolyticus	species	13.508
41275	Brevundimonas	genus	13.484
80865	Delftia	genus	13.454
39777	Veillonella atypica	species	13.436
2942965	Steigviridae	family	13.434
1282	Staphylococcus epidermidis	species	13.421
2942980	Kehishuvirus	genus	13.411
2719313	Enterocloster	genus	13.394
879243	Porphyromonas asaccharolytica DSM 20707	strain	13.371
28123	Porphyromonas asaccharolytica	species	13.371
2576376	Streptococcus sp. 1643	species	13.366
1305	Streptococcus sanguinis	species	13.345
2692118	Winkia	genus	13.338
33007	Winkia neuii	species	13.338
2650157	Bacteroides zhangwenhongii	species	13.304
28133	Prevotella nigrescens	species	13.268
46507	Ezakiella coagulans	species	13.26
2899133	Candidatus Nanosynbacter sp. HMT-352	species	13.255
1283	Staphylococcus haemolyticus	species	13.245
662	Vibrio	genus	13.232
4932	Saccharomyces cerevisiae	species	13.218
1490	Paraclostridium bifermentans	species	13.198
1849822	Paraclostridium	genus	13.198
1309	Streptococcus mutans	species	13.179
2026240	Klebsiella quasivariicola	species	13.176
51288	Kluyvera ascorbata	species	13.172
742725	Alistipes indistinctus YIT 12060	strain	13.169
1918454	Flintibacter	genus	13.156
2610895	Flintibacter sp. KGMB00164	species	13.156
5476	Candida albicans	species	13.141
3036302	Mobiluncus massiliensis	species	13.091
33043	Coprococcus eutactus	species	13.038
33208	Metazoa	kingdom	13.029
7711	Chordata	phylum	13.029
9443	Primates	order	13.029
9604	Hominidae	family	13.029
9605	Homo	genus	13.029
9606	Homo sapiens	species	13.029
40674	Mammalia	class	13.029
28025	Bifidobacterium animalis	species	13.025
561	Escherichia	genus	13.014
2584944	Sutterella faecalis	species	13.012
575	Raoultella planticola	species	12.997
2779518	Blautia liquoris	species	12.994
2050	Mobiluncus	genus	12.966
1385939	Bifidobacterium breve JCM 7017	strain	12.917
1330545	Lelliottia	genus	12.91
204457	Sphingomonadales	order	12.863
2093818	Candidatus Saccharimonadia	class	12.854
2093822	Candidatus Nanosynbacteraceae	family	12.853
2093823	Candidatus Nanosynbacter	genus	12.853
2093819	Candidatus Nanosynbacterales	order	12.853
526525	Erysipelotrichales	order	12.849
526524	Erysipelotrichia	class	12.849
1622	Ligilactobacillus murinus	species	12.847
1737404	Tissierellia	class	12.831
33945	Enterococcus avium	species	12.735
28130	Prevotella disiens	species	12.698
2763669	Qiania dongpingensis	species	12.681
2944195	Qiania	genus	12.681
89153	[Clostridium] hylemonae	species	12.679
400634	Lysinibacillus	genus	12.654
712310	Haemophilus sp. oral taxon 036	species	12.645
322095	Porphyromonas somerae	species	12.621
28449	Neisseria subflava	species	12.616
423477	Veillonella rogosae	species	12.607
158836	Enterobacter hormaechei	species	12.604
178339	Pauljensenia hongkongensis	species	12.598
2740557	Pauljensenia	genus	12.598
131110	Schaalia radingae	species	12.587
2772059	uncultured phage cr50_1	no rank	12.573
2955711	Cohcovirus hiberniae	species	12.573
29466	Veillonella parvula	species	12.556
1359	Lactococcus cremoris	species	12.521
824	Campylobacter gracilis	species	12.501
137838	Clostridium neonatale	species	12.417
1046629	Streptococcus salivarius 57.I	strain	12.394
565040	Bifidobacterium longum subsp. infantis 157F	strain	12.379
1647	Erysipelothrix	genus	12.37
43769	Corynebacterium propinquum	species	12.369
1016	Capnocytophaga	genus	12.337
238749	Diaphorobacter	genus	12.321
248744	Marvinbryantia	genus	12.311
168384	Marvinbryantia formatexigens	species	12.311
478749	Marvinbryantia formatexigens DSM 14469	strain	12.311
1747	Cutibacterium acnes	species	12.273
1531	Enterocloster clostridioformis	species	12.266
411490	Anaerostipes caccae L1-92	strain	12.256
615	Serratia marcescens	species	12.245
1492	Clostridium butyricum	species	12.244
905	Acidaminococcus fermentans	species	12.231
591001	Acidaminococcus fermentans DSM 20731	strain	12.231
2702	Gardnerella vaginalis	species	12.225
1200793	Streptococcus salivarius K12	strain	12.194
2701	Gardnerella	genus	12.194
2901164	Stutzerimonas	genus	12.188
1348	Streptococcus parauberis	species	12.187
1796635	Longicatena caecimuris	species	12.186
1918536	Longicatena	genus	12.186
61646	Lelliottia amnigena	species	12.182
137732	Granulicatella elegans	species	12.177
1769710	Sellimonas	genus	12.175
1653434	Sellimonas intestinalis	species	12.175
2948688	Delmidovirus	genus	12.147
3029088	Dethiosulfovibrionaceae	family	12.147
81852	Enterococcaceae	family	12.113
2093824	Candidatus Nanosynbacter lyticus	species	12.113
1350	Enterococcus	genus	12.107
40324	Stenotrophomonas maltophilia	species	12.079
40520	Blautia obeum	species	12.06
638847	Pyramidobacter	genus	12.04
638849	Pyramidobacter piscolens	species	12.04
1334	Streptococcus dysgalactiae	species	12.023
1316254	Veillonella parvula HSIVP1	strain	12.021
2905967	Candidatus Minimicrobia	genus	11.998
2841264	Candidatus Minimicrobia vallesae	species	11.998
1643824	Atopobiaceae	family	11.997
1912897	Blautia argi	species	11.99
82115	Rhizobiaceae	family	11.981
657309	Bacteroides xylanisolvens XB1A	strain	11.961
2942966	Suoliviridae	family	11.948
645	Aeromonas salmonicida	species	11.931
1750	Arachnia propionica	species	11.924
1871025	Ndongobacter massiliensis	species	11.9
1930845	Ndongobacter	genus	11.9
2734150	Toutatisvirus toutatis	species	11.891
2733138	Toutatisvirus	genus	11.891
2070187	Faecalibacterium phage FP_Toutatis	no rank	11.891
1351	Enterococcus faecalis	species	11.885
1598	Limosilactobacillus reuteri	species	11.871
1653	Corynebacteriaceae	family	11.858
1716	Corynebacterium	genus	11.858
713	Actinobacillus	genus	11.836
2027293	Escherichia coli O8:H8	serotype	11.82
1613	Limosilactobacillus fermentum	species	11.785
1035817	Bifidobacterium longum subsp. longum KACC 91563	strain	11.762
85025	Nocardiaceae	family	11.735
2650158	Bacteroides luhongzhouii	species	11.726
1308	Streptococcus thermophilus	species	11.694
2772085	crAssphage cr6_1	RUCEZ877	11.691
419005	Prevotella amnii	species	11.667
2742598	Limosilactobacillus	genus	11.652
1177574	Prevotella jejuni	species	11.643
388919	Streptococcus sanguinis SK36	strain	11.551
41297	Sphingomonadaceae	family	11.516
53345	Enterococcus durans	species	11.511
1077464	Streptococcus oralis subsp. tigurinus	subspecies	11.495
850	Fusobacterium mortiferum	species	11.478
469616	Fusobacterium mortiferum ATCC 9817	strain	11.478
626940	Phascolarctobacterium succinatutens	species	11.459
657308	Gordonibacter pamelaeae 7-10-1-b	strain	11.445
471189	Gordonibacter pamelaeae	species	11.445
84566	Sphingobacteriaceae	family	11.41
200666	Sphingobacteriales	order	11.41
117747	Sphingobacteriia	class	11.41
416916	Aggregatibacter	genus	11.408
428126	Thomasclavelia spiroformis DSM 1552	strain	11.407
29348	Thomasclavelia spiroformis	species	11.407
3047432	Maliibacteriaceae	family	11.388
3047433	Maliibacterium	genus	11.388
2086585	Maliibacterium massiliense	species	11.388
99822	Streptococcus dysgalactiae subsp. dysgalactiae	subspecies	11.363
47678	Bacteroides caccae	species	11.339
2767893	Lentilactobacillus	genus	11.314
1396	Bacillus cereus	species	11.311
1155388	Clostridium sp. C1	species	11.281
12916	Acidovorax	genus	11.279
2847299	Bacteroides sp. DH3716P	species	11.274
1364	Lactococcus piscium	species	11.272
28135	Segatella oris	species	11.258
1292	Staphylococcus warneri	species	11.248
1827	Rhodococcus	genus	11.244
2767885	Latilactobacillus	genus	11.24
186818	Planococcaceae	family	11.231
630	Yersinia enterocolitica	species	11.224
1624	Ligilactobacillus salivarius	species	11.219
48736	Ralstonia	genus	11.206
2692113	Gleimia	genus	11.191
883062	Bifidobacterium bifidum S17	strain	11.176
186532	Ceduovirus	genus	11.163
28453	Sphingobacterium	genus	11.159
222	Achromobacter	genus	11.156
927666	Streptococcus oralis Uo5	strain	11.111
1433288	Streptococcus thermophilus MTH17CL396	strain	11.106
32257	Kingella	genus	11.101
1074494	Streptococcus salivarius M18	strain	11.053
876	Desulfovibrio desulfuricans	species	11.052
1363	Lactococcus garvieae	species	11.044
85007	Mycobacteriales	order	11.021
830	Butyrivibrio	genus	11.009
118882	Brucellaceae	family	11.004
66228	Gleimia europaea	species	11.003
45851	Butyrivibrio crossotus	species	10.992
1501662	Streptococcus parasuis	species	10.988
570	Klebsiella	genus	10.959
2801844	Arachnia	genus	10.94
990721	Christensenella	genus	10.924
990719	Christensenellaceae	family	10.924
626937	Christensenella minuta	species	10.924
544580	Actinomyces oris	species	10.885
1156431	Streptococcus ilei	species	10.879
712362	Leptotrichia sp. oral taxon 221	species	10.863
1643822	Eggerthellales	order	10.854
1643826	Eggerthellaceae	family	10.854
2763062	Roseburia rectibacter	species	10.835
1161942	Ruminococcus champanellensis	species	10.82
234	Brucella	genus	10.812
1623	Ligilactobacillus ruminis	species	10.81
1259973	Klebsiella electrica	species	10.807
2709390	Bacteroides sp. ZJ-18	species	10.755
712411	Olsenella sp. oral taxon 807	species	10.754
190721	Ralstonia insidiosa	species	10.752
1353	Enterococcus gallinarum	species	10.719
82135	Fannyhessea vaginae	species	10.717
2767327	Fannyhessea	genus	10.717
29430	Acinetobacter haemolyticus	species	10.716
413496	Cronobacter	genus	10.703
2047	Rothia dentocariosa	species	10.7
1599	Latilactobacillus sakei	species	10.697
1654	Actinomyces	genus	10.683
697329	Ruminococcus albus 7 = DSM 20455	strain	10.675
1264	Ruminococcus albus	species	10.675
732	Aggregatibacter aphrophilus	species	10.667
29491	Aeromonas salmonicida subsp. salmonicida	subspecies	10.665
182773	Clostridium isatidis	species	10.633
1348911	Coprobacter	genus	10.63
2092	Mycoplasmataceae	family	10.607
2085	Mycoplasmatales	order	10.607
2005519	Barnesiellaceae	family	10.606
1099853	Coprobacter fastidiosus	species	10.603
407	Methylobacterium	genus	10.597
1379	Gemella haemolysans	species	10.597
33034	Anaerococcus prevotii	species	10.573
525919	Anaerococcus prevotii DSM 20548	strain	10.573
29465	Veillonella	genus	10.559
2820817	Aggregatibacter sp. 2125159857	species	10.549
5794	Apicomplexa	phylum	10.54
1301	Streptococcus	genus	10.522
2767886	Levilactobacillus	genus	10.5
1675036	Megasphaera hexanoica	species	10.495
2893057	Shouchella	genus	10.479
54291	Raoultella ornithinolytica	species	10.475
1796652	Turicimonas muris	species	10.474
1918598	Turicimonas	genus	10.474
862970	Streptococcus anginosus C1051	strain	10.473
1032069	Campylobacter ureolyticus RIGS 9880	strain	10.462
1300	Streptococcaceae	family	10.457
2848145	Escherichia coli O170:H18	no rank	10.428
577	Raoultella terrigena	species	10.426
1280412	Conoidasida	class	10.425
75739	Eucoccidiorida	order	10.425
861906	Escherichia coli O44:H18	serotype	10.423
216592	Escherichia coli 042	strain	10.423
114527	Mogibacterium diversum	species	10.421
360104	Campylobacter concisus 13826	strain	10.418
5809	Sarcocystidae	family	10.407
255248	Leuconostoc garlicum	species	10.401
29389	Streptococcus alactolyticus	species	10.398
1580	Levilactobacillus brevis	species	10.396
244366	Klebsiella variicola	species	10.395
5811	Toxoplasma gondii	species	10.388
5810	Toxoplasma	genus	10.388
1633	Limosilactobacillus vaginalis	species	10.373
2942990	Canhaevirus	genus	10.354
2488810	Ruminiclostridium herbifermentans	species	10.349
1506577	Tyzzerella	genus	10.34
36835	[Clostridium] colinum	species	10.34
704125	Clostridium gelidum	species	10.339
502	Kingella denitrificans	species	10.328
1637	Listeria	genus	10.318
28216	Betaproteobacteria	class	10.312
80840	Burkholderiales	order	10.305
2603836	Escherichia coli O10:H32	serotype	10.3
702459	Bifidobacterium bifidum PRL2010	strain	10.286
58231	Treponema medium	species	10.286
2866570	Aggregatibacter sp. Marseille-P9115	species	10.278
1252	Leuconostoc carnosum	species	10.273
1243	Leuconostoc	genus	10.267
28129	Prevotella denticola	species	10.241
2382163	Streptococcus koreensis	species	10.22
2572088	Candidatus Nanosynbacter featherlites	species	10.208
160453	Enterococcus gilvus	species	10.204
635	Edwardsiella	genus	10.185
1759399	Streptococcus sp. A12	species	10.178
2848144	Escherichia coli O158:H23	no rank	10.177
133448	Citrobacter youngae	species	10.175
2082587	Parolsenella	genus	10.175
617123	Lachnoanaerobaculum umeaense	species	10.152
119045	Methylobacteriaceae	family	10.152
76517	Campylobacter hominis	species	10.142
684066	Streptococcus lactarius	species	10.132
2778655	Escherichia coli O167:H26	serotype	10.108
831	Butyrivibrio fibrisolvens	species	10.099
2929492	Faecalibacterium sp. I3-3-33	species	10.095
702439	Prevotella nigrescens F0103	strain	10.082
1520	Clostridium beijerinckii	species	10.078
995019	Sutterellaceae	family	10.075
1563222	Citrobacter pasteurii	species	10.071
1433289	Streptococcus thermophilus M17PTZA496	strain	10.059
1632	Limosilactobacillus oris	species	10.049
47770	Lactobacillus crispatus	species	10.036
2020965	Bifidobacterium imperatoris	species	10.034
569	Hafnia alvei	species	10.024
906	Megasphaera	genus	10.023
33039	[Ruminococcus] torques	species	10.02
657313	[Ruminococcus] torques L2-14	strain	10.02
1304	Streptococcus salivarius	species	10.01
1667327	Klebsiella quasipneumoniae subsp. quasipneumoniae	subspecies	10.001
869209	Treponema succinifaciens DSM 2489	strain	9.9992
167	Treponema succinifaciens	species	9.9992
1253	Pediococcus	genus	9.9913
1246	Leuconostoc lactis	species	9.9872
299766	Enterobacter hormaechei subsp. steigerwaltii	subspecies	9.984
1415775	Clostridium baratii str. Sullivan	strain	9.9732
2133944	Pseudoprevotella muciniphila	species	9.9676
2884814	Pseudoprevotella	genus	9.9676
201	Campylobacter lari	species	9.9633
1354	Enterococcus hirae	species	9.9626
100886	Catenibacterium mitsuokai	species	9.9443
507	Alcaligenes	genus	9.9429
45972	Staphylococcus pasteuri	species	9.9336
1280	Staphylococcus aureus	species	9.915
1453988	Campylobacter lari RM16712	strain	9.9141
35703	Citrobacter amalonaticus	species	9.9078
1340	Streptococcus porcinus	species	9.9071
40544	Sutterella	genus	9.8886
244127	Anaerotruncus	genus	9.8579
169435	Anaerotruncus colihominis	species	9.8579
985008	Aggregatibacter aphrophilus ATCC 33389	strain	9.849
297352	Lactococcus piscium MKFS47	strain	9.8328
80864	Comamonadaceae	family	9.8266
2585119	Alistipes dispar	species	9.8242
86331	Mogibacterium	genus	9.8192
713030	Selenomonas sp. oral taxon 136	species	9.812
483	Neisseria cinerea	species	9.7938
604330	Parafannyhessea umbonata	species	9.7778
2847312	Parafannyhessea	genus	9.7778
2929493	Faecalibacterium sp. I3-3-89	species	9.7764
585397	Escherichia coli ED1a	strain	9.7746
40545	Sutterella wadsworthensis	species	9.774
1244	Leuconostoc gelidum	species	9.763
29375	Lacrimispora xylanolytica	species	9.7548
2005520	Dysgonomonadaceae	family	9.7493
2767890	Paucilactobacillus	genus	9.7489
1587	Lactobacillus helveticus	species	9.7475
33035	Blautia producta	species	9.7472
2955579	Canhaevirus hiberniae	species	9.7076
2772066	uncultured phage cr10_1	no rank	9.7076
649776	Synergistales	order	9.6987
649775	Synergistia	class	9.6987
508458	Synergistota	phylum	9.6987
2107999	Lactobacillus paragasseri	species	9.6854
1458253	Streptococcus oralis subsp. dentisani	subspecies	9.6652
470	Acinetobacter baumannii	species	9.6416
644652	Gordonibacter	genus	9.6373
2546350	Citrobacter arsenatis	species	9.6244
28132	Prevotella melaninogenica	species	9.6058
1870884	Clostridioides	genus	9.5655
539813	Enterobacter mori	species	9.5614
1446746	Escherichia coli O6:H16	serotype	9.5527
1903434	Atlantibacter	genus	9.5526
131111	Schaalia turicensis	species	9.5432
631220	Desulfovibrio sp. G11	species	9.5416
2027919	Enterobacter cloacae complex sp.	species	9.5295
2772067	uncultured phage cr11_1	no rank	9.5276
2955741	Delmidovirus splanchnicus	species	9.5276
3022127	Lancefieldella sp. Marseille-Q7238	species	9.5229
546367	Hafnia paralvei	species	9.5145
2767887	Ligilactobacillus	genus	9.5127
970	Selenomonas	genus	9.4953
1069494	Trueperella	genus	9.4832
155493	Gallibacterium	genus	9.4761
32008	Burkholderia	genus	9.476
1290	Staphylococcus hominis	species	9.467
1685	Bifidobacterium breve	species	9.4339
1326	Streptococcus acidominimus	species	9.4198
1300227	Bifidobacterium longum subsp. longum GT15	strain	9.4145
2003188	Parolsenella catena	species	9.4127
907	Megasphaera elsdenii	species	9.3998
505341	Gallibacterium salpingitidis	species	9.398
565	Atlantibacter hermannii	species	9.3863
1305849	Enterococcus faecium Aus0085	strain	9.3746
1232659	Haemophilus influenzae 2019	strain	9.3629
331111	Escherichia coli O139:H28 str. E24377A	strain	9.357
1603259	Escherichia coli O139:H28	serotype	9.357
1871021	Lachnoclostridium phocaeense	species	9.3261
1661	Trueperella pyogenes	species	9.2778
2109686	Butyricicoccus sp. GAM44	species	9.2646
580596	Butyricicoccus	genus	9.2646
67827	Citrobacter werkmanii	species	9.2591
525282	Finegoldia magna ATCC 53516	strain	9.2375
2598457	Streptococcus sp. KS 6	species	9.2263
1335613	Gordonibacter urolithinfaciens	species	9.2162
301301	Roseburia hominis	species	9.2112
249188	Haemophilus pittmaniae	species	9.2072
712538	Selenomonas sp. oral taxon 478	species	9.1851
2841037	Eubacterium sp. c-25	species	9.1726
547043	Bifidobacterium pseudocatenulatum DSM 20438 = JCM 1200 = LMG 10505	strain	9.161
2811390	Sporofaciens	genus	9.1239
2681861	Sporofaciens musculi	species	9.1239
32003	Nitrosomonadales	order	9.1194
1310	Streptococcus sobrinus	species	9.1181
1302	Streptococcus gordonii	species	9.0986
71452	Enterococcus raffinosus	species	9.0831
1743	Propionibacterium	genus	9.0806
13687	Sphingomonas	genus	9.0761
1245	Leuconostoc mesenteroides	species	9.0668
2051	Mobiluncus curtisii	species	9.0624
28144	Salmonella enterica subsp. enterica serovar Derby	no rank	9.0361
1655	Actinomyces naeslundii	species	9.0272
83655	Leclercia adecarboxylata	species	9.0215
447792	Phytobacter	genus	9.0141
1375	Aerococcus	genus	9.0125
69218	Enterobacter cancerogenus	species	9.0021
33905	Bifidobacterium thermophilum	species	9.0007
2937909	Desulfitobacteriaceae	family	8.9984
47714	Lacticaseibacillus paracasei subsp. paracasei	subspecies	8.9954
1682	Bifidobacterium longum subsp. infantis	subspecies	8.975
162	Treponema phagedenis	species	8.9692
85011	Kitasatosporales	order	8.9615
2062	Streptomycetaceae	family	8.9615
1338	Streptococcus intermedius	species	8.9432
190146	Actinotignum urinale	species	8.9392
2490633	Streptococcus periodonticum	species	8.9175
1311	Streptococcus agalactiae	species	8.9139
28119	Bacteroides zoogleoformans	species	8.8714
1470347	Alistipes ihumii	species	8.8466
1211813	Alistipes ihumii AP11	strain	8.8466
866777	Bifidobacterium breve ACS-071-V-Sch8b	strain	8.8371
67824	Citrobacter farmeri	species	8.8369
1642646	Petrimonas mucosa	species	8.8241
307628	Petrimonas	genus	8.8241
47670	Lautropia	genus	8.823
47671	Lautropia mirabilis	species	8.823
2041044	Eubacterium maltosivorans	species	8.8028
2913614	Prevotella communis	species	8.8008
1589	Lactiplantibacillus pentosus	species	8.7922
248315	Veillonella rodentium	species	8.7846
33033	Parvimonas micra	species	8.7761
543311	Parvimonas	genus	8.7761
115778	Leuconostoc gasicomitatum	species	8.7657
488	Neisseria mucosa	species	8.7539
1883	Streptomyces	genus	8.7351
2919589	Vaginimicrobium	genus	8.7251
1871034	Vaginimicrobium propionicum	species	8.7251
1561	Clostridium baratii	species	8.7189
1583	Weissella confusa	species	8.7086
2479767	Blautia sp. SC05B48	species	8.6993
87541	Aerococcus christensenii	species	8.6984
328813	Alistipes onderdonkii	species	8.6973
1547448	Arachnia rubra	species	8.6843
2663009	Fusobacterium pseudoperiodonticum	species	8.6832
38304	Corynebacterium tuberculostearicum	species	8.6822
1852381	Duodenibacillus massiliensis	species	8.671
1980697	Duodenibacillus	genus	8.671
2787628	Treponema peruense	species	8.6617
1296540	Paucilactobacillus nenjiangensis	species	8.6465
890402	Bifidobacterium longum subsp. longum BBMN68	strain	8.6424
181487	Schaalia cardiffensis	species	8.6333
888050	Schaalia cardiffensis F0333	strain	8.6333
1970189	Marinilabiliales	order	8.605
2714353	Vescimonas fastidiosa	species	8.585
1496	Clostridioides difficile	species	8.5787
2742601	Limosilactobacillus portuensis	species	8.5672
1597	Lacticaseibacillus paracasei	species	8.5651
1330547	Kosakonia	genus	8.5484
363265	Leyella stercorea	species	8.543
1122981	Prevotella corporis DSM 18810 = JCM 8529	strain	8.5289
214856	Alistipes finegoldii	species	8.5266
1255	Pediococcus pentosaceus	species	8.5236
470146	Coprococcus comes ATCC 27758	strain	8.508
2974265	Leyella	genus	8.5057
868129	Prevotella bivia DSM 20514	strain	8.4966
186820	Listeriaceae	family	8.4905
90371	Salmonella enterica subsp. enterica serovar Typhimurium	no rank	8.4744
679935	Alistipes finegoldii DSM 17242	strain	8.4679
2086584	Massilistercora timonensis	species	8.4675
2717089	Massilistercora	genus	8.4675
2773707	Escherichia coli O19:H7	no rank	8.4458
2763104	Escherichia coli O150:H6	serotype	8.4447
2803850	Mammaliicoccus	genus	8.4413
873513	Segatella buccae ATCC 33574	strain	8.4355
186826	Lactobacillales	order	8.4177
490	Neisseria sicca	species	8.4171
1048332	Streptococcus salivarius CCHSS3	strain	8.4076
1288121	Alistipes senegalensis	species	8.3998
196081	Scardovia	genus	8.3914
78259	Scardovia inopinata	species	8.3914
1150468	Scardovia inopinata JCM 12537	strain	8.3914
1796616	Blautia pseudococcoides	species	8.3643
730	[Haemophilus] ducreyi	species	8.3473
706438	Actinomyces sp. oral taxon 171	species	8.3329
706439	Actinomyces sp. oral taxon 171 str. F0337	strain	8.3329
69965	Macrococcus	genus	8.309
85020	Dermabacteraceae	family	8.2955
91061	Bacilli	class	8.2911
37637	Corynebacterium pseudodiphtheriticum	species	8.2794
147802	Lactobacillus iners	species	8.2667
632	Yersinia pestis	species	8.2177
2714355	Vescimonas coprocola	species	8.2067
2494234	Sutterella megalosphaeroides	species	8.1807
113107	Streptococcus australis	species	8.1803
411903	Collinsella aerofaciens ATCC 25986	strain	8.1347
722911	Bifidobacterium longum subsp. longum F8	strain	8.1118
57493	Kocuria	genus	8.1073
1436725	Streptococcus thermophilus TH1477	strain	8.101
1926677	Raoultibacter	genus	8.1003
1907662	Raoultibacter timonensis	species	8.1003
379	Rhizobium	genus	8.095
203275	Tannerella forsythia 92A2	strain	8.0864
28134	Hoylesella oralis	species	8.0598
1643686	Brachyspirales	order	8.0537
29521	Brachyspira	genus	8.0537
143786	Brachyspiraceae	family	8.0537
1336	Streptococcus equi	species	8.0488
1843490	Sporomusaceae	family	8.0442
997873	Bacteroides caccae CL03T12C61	strain	8.0427
693979	Bacteroides helcogenes P 36-108	strain	8.0376
290053	Bacteroides helcogenes	species	8.0376
1155385	Proteiniclasticum	genus	8.0255
3036945	Proteiniclasticum sp. QWL-01	species	8.0255
33040	Streptococcus milleri	species	8.0219
2815775	Berryella	genus	7.9936
823	Parabacteroides distasonis	species	7.9932
2478954	Catenibacterium sp. co_0103	species	7.9864
157687	Leptotrichia wadei	species	7.9769
119060	Burkholderiaceae	family	7.973
29391	Gemella morbillorum	species	7.9635
2060094	Aminipila	genus	7.9504
34105	Streptobacillus moniliformis	species	7.9161
34104	Streptobacillus	genus	7.9161
1046624	Lactococcus lactis subsp. lactis IO-1	strain	7.8953
2169621	Limdunavirus	genus	7.8846
2870563	Methanobrevibacter sp. TLL-48-HuF1	species	7.8845
861	Fusobacterium ulcerans	species	7.88
1931217	Bifidobacterium longum subsp. suillum	subspecies	7.8691
83231	Xylanibacter brevis	species	7.8565
299767	Enterobacter ludwigii	species	7.847
135858	Catenibacterium	genus	7.83
856	Fusobacterium varium	species	7.798
40041	Streptococcus equi subsp. zooepidemicus	subspecies	7.7883
1623305	Skunavirus	genus	7.7779
74426	Collinsella aerofaciens	species	7.7776
356	Hyphomicrobiales	order	7.7774
1584	Lactobacillus delbrueckii	species	7.7761
102106	Collinsella	genus	7.7633
84107	Coriobacteriaceae	family	7.7624
2666138	Caproicibacterium lactatifermentans	species	7.7593
2815358	Leclercia pneumoniae	species	7.7471
1905344	Ruthenibacterium	genus	7.746
1550024	Ruthenibacterium lactatiformans	species	7.746
33011	Cutibacterium granulosum	species	7.744
94869	Clostridium gasigenes	species	7.7341
1330546	Pluralibacter	genus	7.7283
283	Comamonas	genus	7.7169
2785531	Bacteroides sp. HF-162	species	7.7131
84999	Coriobacteriales	order	7.7122
941322	Escherichia coli O25b:H4-ST131	no rank	7.7036
1504576	Pseudocitrobacter	genus	7.7031
2891570	Pseudocitrobacter corydidari	species	7.7031
61592	Corynebacterium durum	species	7.7013
338	Xanthomonas	genus	7.6781
186814	Thermoanaerobacteraceae	family	7.6745
762210	Bifidobacterium saguini	species	7.6737
1360	Lactococcus lactis subsp. lactis	subspecies	7.6651
515620	[Eubacterium] eligens ATCC 27750	strain	7.6619
1623304	Moineauvirus	genus	7.6609
671267	Phocaeicola sartorii	species	7.6568
1150460	Bifidobacterium catenulatum subsp. kashiwanohense JCM 15439 = DSM 21854	strain	7.6556
106589	Cupriavidus	genus	7.6486
2696063	Anaerocolumna sedimenticola	species	7.646
881260	Enterobacter bugandensis	species	7.6448
375288	Parabacteroides	genus	7.6353
2005525	Tannerellaceae	family	7.6349
204	Campylobacter showae	species	7.6239
1531429	Berryella intestinalis	species	7.6229
2731643	Autographiviridae	family	7.5822
1681	Bifidobacterium bifidum	species	7.5668
195950	Tannerella	genus	7.561
253239	Ethanoligenens harbinense	species	7.5595
253238	Ethanoligenens	genus	7.5595
186828	Carnobacteriaceae	family	7.5478
445974	Thomasclavelia ramosa DSM 1402	strain	7.5476
28026	Bifidobacterium pseudocatenulatum	species	7.5419
930406	Escherichia coli O157:H16	strain	7.5377
2854732	Escherichia coli O78:H4	serotype	7.5209
2748	Carnobacterium divergens	species	7.5192
79603	Denitrobacterium	genus	7.5137
79604	Denitrobacterium detoxificans	species	7.5137
83654	Leclercia	genus	7.5007
2994078	Caproicibacterium sp. BJN0003	species	7.4953
57706	Citrobacter braakii	species	7.4818
72293	Helicobacteraceae	family	7.4558
1505652	Terrisporobacter	genus	7.449
2813371	Terrisporobacter hibernicus	species	7.449
209	Helicobacter	genus	7.4295
1408428	Bilophila wadsworthia ATCC 49260	strain	7.4156
1385940	Bifidobacterium breve JCM 7019	strain	7.4014
371601	Bacteroides xylanisolvens	species	7.3943
546269	Filifactor alocis ATCC 35896	strain	7.3853
143361	Filifactor alocis	species	7.3853
44259	Filifactor	genus	7.3853
43768	Corynebacterium matruchotii	species	7.3703
1296	Mammaliicoccus sciuri	species	7.3674
225991	Comamonas aquatica	species	7.3652
2304687	Petroclostridium	genus	7.3651
2068655	Novisyntrophococcus fermenticellae	species	7.3633
2888809	Novisyntrophococcus	genus	7.3633
28131	Prevotella intermedia	species	7.3572
1118202	Cruoricaptor ignavus	species	7.3522
1433995	Cruoricaptor	genus	7.3522
649777	Synergistaceae	family	7.352
1197717	Cloacibacillus porcorum	species	7.3467
508459	Cloacibacillus	genus	7.3467
33968	Leuconostoc pseudomesenteroides	species	7.3374
904	Acidaminococcus	genus	7.3273
5204	Basidiomycota	phylum	7.3243
47715	Lacticaseibacillus rhamnosus	species	7.324
329854	Bacteroides intestinalis	species	7.318
2507160	Aminipila luticellarii	species	7.3171
28111	Bacteroides eggerthii	species	7.3138
2044467	Escherichia sp. E4742	species	7.3061
2747	Carnobacterium	genus	7.3044
1296536	Enterobacter hormaechei subsp. xiangfangensis	subspecies	7.3022
165695	Sphingobium	genus	7.2626
246787	Bacteroides cellulosilyticus	species	7.251
46124	Granulicatella adiacens	species	7.2148
244320	Escherichia coli O55:H7	no rank	7.2102
186807	Peptococcaceae	family	7.1915
3016343	Peptoniphilus equinus	species	7.1807
1852374	Ezakiella massiliensis	species	7.1398
33010	Cutibacterium avidum	species	7.1351
871541	Actinomyces oris K20	strain	7.1305
563008	Segatella oris C735	strain	7.1223
1269	Micrococcus	genus	7.1209
2942964	Intestiviridae	family	7.1129
28112	Tannerella forsythia	species	7.104
864564	Parascardovia denticolens DSM 10105 = JCM 12538	strain	7.0854
196082	Parascardovia	genus	7.0854
78258	Parascardovia denticolens	species	7.0854
909929	Selenomonadales	order	7.0844
129337	Geobacillus	genus	7.0763
545	Citrobacter koseri	species	7.0745
1680	Bifidobacterium adolescentis	species	7.0698
1579	Lactobacillus acidophilus	species	7.0498
712116	Actinomyces sp. oral taxon 169	species	7.0411
1843491	Selenomonadaceae	family	7.0396
501783	Cloacibacterium	genus	7.0337
1298	Deinococcus	genus	7.0322
118964	Deinococcales	order	7.0322
183710	Deinococcaceae	family	7.0322
502558	Eggerthella sp. YY7918	species	7.0314
1281486	Lactococcus formosensis	species	7.0247
1069534	Ligilactobacillus ruminis ATCC 27782	strain	7.0092
1659	Actinomyces israelii	species	7.0028
33682	Euglenozoa	phylum	6.9992
2704949	Trypanosomatida	order	6.9992
5654	Trypanosomatidae	family	6.9992
5653	Kinetoplastea	class	6.9992
435591	Parabacteroides distasonis ATCC 8503	strain	6.98
68933	Thermales	order	6.964
188786	Thermaceae	family	6.964
521095	Lancefieldella parvula DSM 20469	strain	6.9621
1382	Lancefieldella parvula	species	6.9621
172042	Rothia aeria	species	6.9552
5658	Leishmania	genus	6.9546
1596	Lactobacillus gasseri	species	6.9527
1501	Clostridium pasteurianum	species	6.9374
29385	Staphylococcus saprophyticus	species	6.925
718252	Faecalibacterium prausnitzii L2-6	strain	6.9208
1064535	Megasphaera elsdenii DSM 20460	strain	6.9198
2772089	uncultured phage cr115_1	no rank	6.9105
2955498	Birpovirus hiberniae	species	6.9105
84998	Coriobacteriia	class	6.9096
151276	Bacteroides coprosuis	species	6.905
679937	Bacteroides coprosuis DSM 18011	strain	6.905
61647	Pluralibacter gergoviae	species	6.9039
633147	Olsenella uli DSM 7084	strain	6.8991
133926	Olsenella uli	species	6.8991
2778656	Escherichia coli O20:H12	no rank	6.8893
622	Shigella dysenteriae	species	6.8791
712710	Tannerella serpentiformis	species	6.873
147206	Collinsella stercoris	species	6.8677
28035	Staphylococcus lugdunensis	species	6.8665
2751	Carnobacterium maltaromaticum	species	6.865
97478	Limosilactobacillus mucosae	species	6.8606
2848143	Escherichia coli O85:H1	no rank	6.8604
2823317	Phascolarctobacterium sp. Marseille-Q4147	species	6.8584
34037	Rahnella	genus	6.8453
1297793	Lacrimispora sphenoides JCM 1415	strain	6.845
29370	Lacrimispora sphenoides	species	6.845
2507162	Caproiciproducens sp. NJN-50	species	6.8446
1738645	Caproiciproducens	genus	6.8446
634176	Aggregatibacter aphrophilus NJ8700	strain	6.8286
69710	Treponema vincentii	species	6.8193
1380	Atopobium	genus	6.8137
712157	Atopobium sp. oral taxon 416	species	6.8137
496	Neisseria macacae	species	6.7759
84112	Eggerthella lenta	species	6.7669
2678885	Faecalibacillus	genus	6.7549
1982626	Faecalibacillus intestinalis	species	6.7549
2564099	Ruminococcus bovis	species	6.7505
69966	Macrococcoides caseolyticum	species	6.7491
33038	Mediterraneibacter gnavus	species	6.7395
2759736	Lacticaseibacillus	genus	6.7368
1307	Streptococcus suis	species	6.7281
31977	Veillonellaceae	family	6.7226
1843489	Veillonellales	order	6.7226
102684	Streptococcus infantarius	species	6.7157
46123	Abiotrophia	genus	6.7149
46125	Abiotrophia defectiva	species	6.7149
10239	Viruses	superkingdom	6.7143
2731360	Heunggongvirae	kingdom	6.7048
2731618	Uroviricota	phylum	6.7048
2731619	Caudoviricetes	class	6.7048
84111	Eggerthella	genus	6.7039
1866885	Mycolicibacterium	genus	6.7014
2789425	Actinomyces sp. HMT 175	species	6.6931
1297	Deinococcota	phylum	6.6774
188787	Deinococci	class	6.6774
187327	Acidaminococcus intestini	species	6.6718
2569097	Anaerobutyricum	genus	6.6708
39488	Anaerobutyricum hallii	species	6.6708
712624	Streptococcus sp. oral taxon 064	species	6.6649
2767353	Lancefieldella	genus	6.6614
649757	Anaerostipes hadrus ATCC 29173 = JCM 17467	strain	6.6558
2767881	Fructilactobacillus	genus	6.6508
1978007	Crassvirales	order	6.6435
75984	Mannheimia	genus	6.643
1694	Bifidobacterium pseudolongum	species	6.6391
1161918	Brachyspira pilosicoli WesB	strain	6.6058
2070	Pseudonocardiaceae	family	6.6023
85010	Pseudonocardiales	order	6.6023
586	Providencia	genus	6.574
577309	Paraprevotella	genus	6.5725
28113	Bacteroides heparinolyticus	species	6.5688
2955997	Jahgtovirus intestinihominis	species	6.5634
2772061	uncultured phage cr107_1	no rank	6.5634
1447716	Bifidobacterium catenulatum PV20-2	strain	6.5632
28125	Prevotella bivia	species	6.5578
117563	Granulicatella	genus	6.5547
2364787	Alistipes megaguti	species	6.5427
357	Agrobacterium	genus	6.5327
409322	Treponema pedis	species	6.5216
550	Enterobacter cloacae	species	6.5156
69823	Selenomonas sputigena	species	6.5146
479437	Eggerthella lenta DSM 2243	strain	6.5079
29388	Staphylococcus capitis	species	6.4974
225992	Comamonas kerstersii	species	6.4867
1002367	Leyella stercorea DSM 18206	strain	6.4853
76123	Hoylesella enoeca	species	6.4814
295405	Bacteroides fragilis YCH46	strain	6.4692
2995122	Leptogranulimonas	genus	6.469
2894156	Leptogranulimonas caecicola	species	6.469
2608867	Escherichia ruysiae	species	6.4602
282402	Prevotella multiformis	species	6.4572
454154	Paraprevotella clara	species	6.4555
387090	Phocaeicola coprophilus	species	6.4459
1232428	Megasphaera massiliensis	species	6.4433
2948767	Jahgtovirus	genus	6.4375
862967	Streptococcus intermedius B196	strain	6.4322
679191	Prevotella amnii CRIS 21A-A	strain	6.4208
28141	Cronobacter sakazakii	species	6.4014
77635	Bifidobacterium subtile	species	6.3808
2035811	Pseudodesulfovibrio	genus	6.3616
200795	Chloroflexota	phylum	6.3564
29347	[Clostridium] scindens	species	6.3545
166486	Roseburia intestinalis	species	6.3404
361101	Streptococcus pseudoporcinus	species	6.3338
2707299	Adlercreutzia hattorii	species	6.3315
39948	Dialister	genus	6.3261
536231	Roseburia intestinalis L1-82	strain	6.3257
2691580	Prevotella sp. Rep29	species	6.3242
52584	Brachyspira pilosicoli	species	6.2966
2946830	Birpovirus	genus	6.276
186822	Paenibacillaceae	family	6.2575
1216932	Clostridium bornimense	species	6.249
83334	Escherichia coli O157:H7	serotype	6.2455
44249	Paenibacillus	genus	6.2446
33964	Leuconostoc citreum	species	6.2316
1458465	Megasphaera elsdenii 14-14	strain	6.2267
384636	Lacrimispora xylanisolvens	species	6.2198
1051631	Streptococcus phage YMC-2011	species	6.2196
270	Thermus	genus	6.1948
2093856	Butyricimonas faecalis	species	6.1941
2679910	Intestinibaculum	genus	6.1884
2487118	Intestinibaculum porci	species	6.1884
84135	Gemella sanguinis	species	6.1868
85019	Brevibacteriaceae	family	6.1839
1696	Brevibacterium	genus	6.1839
2718	Cardiobacterium hominis	species	6.1641
1231072	Clostridium tetani 12124569	strain	6.1618
2892396	Vescimonas	genus	6.1578
52773	Schaalia meyeri	species	6.1559
2081702	Actinomyces sp. oral taxon 897	species	6.1547
818	Bacteroides thetaiotaomicron	species	6.1537
1625	Fructilactobacillus sanfranciscensis	species	6.1495
420247	Methanobrevibacter smithii ATCC 35061	strain	6.1307
2929491	Faecalibacterium sp. HTF-F	species	6.1091
68295	Thermoanaerobacterales	order	6.1008
291644	Bacteroides salyersiae	species	6.0944
1507512	Romboutsia hominis	species	6.0655
515622	Butyrivibrio proteoclasticus B316	strain	6.0578
43305	Butyrivibrio proteoclasticus	species	6.0578
69277	Phyllobacteriaceae	family	6.0402
2767879	Companilactobacillus	genus	6.0245
161879	Corynebacterium kroppenstedtii	species	6.0242
1042156	Clostridium sp. SY8519	species	6.0184
2841528	Eubacterium sp. MSJ-33	species	6.0089
1506553	Lachnoclostridium	genus	6.0082
1660	Schaalia odontolytica	species	6.0077
216816	Bifidobacterium longum	species	6.0001
1573534	Faecalitalea	genus	5.9918
717960	Faecalitalea cylindroides T2-87	strain	5.9918
39483	Faecalitalea cylindroides	species	5.9918
59310	Streptococcus macedonicus	species	5.9885
33967	Leuconostoc mesenteroides subsp. mesenteroides	subspecies	5.9866
5042	Eurotiales	order	5.977
147545	Eurotiomycetes	class	5.977
714	Aggregatibacter actinomycetemcomitans	species	5.9456
301297	Dehalococcoidia	class	5.9432
1378	Gemella	genus	5.9309
243164	Dehalococcoides mccartyi 195	strain	5.9267
61434	Dehalococcoides	genus	5.9031
1202464	Dehalococcoidaceae	family	5.9031
1202465	Dehalococcoidales	order	5.9031
61435	Dehalococcoides mccartyi	species	5.881
31983	Helcococcus	genus	5.8788
40091	Helcococcus kunzii	species	5.8788
3029087	Aminobacteriaceae	family	5.855
651822	Fretibacterium fastidiosum	species	5.855
1434006	Fretibacterium	genus	5.855
2316020	Mediterraneibacter	genus	5.8469
1366	Lactococcus raffinolactis	species	5.8243
762948	Rothia dentocariosa ATCC 17931	strain	5.8122
470565	Prevotella histicola	species	5.8068
2737	Vagococcus	genus	5.8051
2733199	Oengusvirus	genus	5.8011
2734262	Oengusvirus oengus	species	5.8011
2070188	Faecalibacterium phage FP_oengus	no rank	5.8011
128827	Erysipelotrichaceae	family	5.7976
862966	Streptococcus intermedius C270	strain	5.7869
119602	Streptococcus dysgalactiae subsp. equisimilis	subspecies	5.7807
84108	Slackia	genus	5.7723
84110	Slackia heliotrinireducens	species	5.7723
469617	Fusobacterium ulcerans ATCC 49185	strain	5.7705
624	Shigella sonnei	species	5.7682
1501226	Romboutsia	genus	5.7627
1449093	Lactococcus cremoris subsp. cremoris IBB477	strain	5.7419
158846	Megamonas	genus	5.7268
44742	Desulfovibrio fairfieldensis	species	5.7252
768503	Cytophagia	class	5.7247
768507	Cytophagales	order	5.7247
997879	Bacteroides fragilis CL03T12C07	strain	5.7183
2489014	Klebsiella variicola subsp. tropica	subspecies	5.6997
187101	Sneathia vaginalis	species	5.6958
168808	Sneathia	genus	5.6958
2724150	Romboutsia sp. CE17	species	5.6846
197	Campylobacter jejuni	species	5.6711
551	Erwinia	genus	5.6707
437897	Megamonas funiformis	species	5.6624
2806552	Bulleidia sp. zg-1006	species	5.6621
118747	Bulleidia	genus	5.6621
1744	Propionibacterium freudenreichii	species	5.6534
1601	Ligilactobacillus agilis	species	5.6514
2764325	[Eubacterium] hominis	species	5.6479
89966	Hymenobacter	genus	5.6449
1131492	Aspergillaceae	family	5.6363
1852373	Murdochiella vaginalis	species	5.6353
1161127	Murdochiella	genus	5.6353
186329	Acholeplasmatales	order	5.6347
2146	Acholeplasmataceae	family	5.6347
868	Cardiobacteriaceae	family	5.6326
135615	Cardiobacteriales	order	5.6316
589437	Prevotella scopos	species	5.6177
1236518	Prevotella scopos JCM 17725	strain	5.6177
77095	Segatella bryantii	species	5.5925
2717	Cardiobacterium	genus	5.5818
1160721	Ruminococcus bicirculans (ex Wegman et al. 2014)	species	5.5818
859	Fusobacterium necrophorum	species	5.575
2025876	Parabacteroides sp. CT06	species	5.5687
1585	Lactobacillus delbrueckii subsp. bulgaricus	subspecies	5.5675
40214	Acinetobacter johnsonii	species	5.5605
1115758	Romboutsia ilealis	species	5.5565
751585	Coprococcus sp. ART55/1	species	5.5551
2709410	Chordicoccus furentiruminis	species	5.5376
3031933	Chordicoccus	genus	5.5376
495	Neisseria elongata	species	5.5305
623	Shigella flexneri	species	5.5099
851	Fusobacterium nucleatum	species	5.5022
1853232	Hymenobacteraceae	family	5.4842
433286	Anaerocolumna cellulosilytica	species	5.4546
549	Pantoea agglomerans	species	5.4521
971	Selenomonas ruminantium	species	5.4355
114197	Selenomonas ruminantium subsp. lactilytica	subspecies	5.4355
927704	Selenomonas ruminantium subsp. lactilytica TAM6421	strain	5.4355
46503	Parabacteroides merdae	species	5.4332
2763670	Wujia chipingensis	species	5.4314
2944152	Wujia	genus	5.4314
2490855	Lachnoanaerobaculum gingivalis	species	5.3855
2528203	Bacteroides sp. A1C1	species	5.3817
2582419	Dialister hominis	species	5.3716
2662363	Alistipes sp. dk3624	species	5.3691
1703250	Citrobacter sp. CRE-46	species	5.3544
302911	Bifidobacterium animalis subsp. lactis	subspecies	5.3507
41294	Nitrobacteraceae	family	5.3501
1871109	Neisseria sp. RH3002v2g	species	5.3386
66219	Lachnoclostridium phytofermentans	species	5.3383
357809	Lachnoclostridium phytofermentans ISDg	strain	5.3383
40215	Acinetobacter junii	species	5.3372
2161821	Dialister massiliensis	species	5.3275
46205	Pseudobutyrivibrio	genus	5.3271
185007	Pseudobutyrivibrio xylanivorans	species	5.3271
1183380	Campylobacter coli RM5611	strain	5.3228
1249	Weissella paramesenteroides	species	5.3221
484	Neisseria flavescens	species	5.3157
2585118	Alistipes communis	species	5.2944
649756	Anaerostipes hadrus	species	5.2889
1649	Kurthia	genus	5.2799
2732414	Petitvirales	order	5.2753
2732412	Phixviricota	phylum	5.2753
2732091	Sangervirae	kingdom	5.2753
2732413	Malgrandaviricetes	class	5.2753
10841	Microviridae	family	5.2753
841	Roseburia	genus	5.2685
1843210	Anaerocolumna	genus	5.2599
817	Bacteroides fragilis	species	5.2242
294702	Proteiniphilum	genus	5.2238
847	Oxalobacter formigenes	species	5.2219
479831	Clostridioides difficile QCD-63q42	strain	5.1847
29393	Dolosigranulum	genus	5.1813
29394	Dolosigranulum pigrum	species	5.1813
1513	Clostridium tetani	species	5.1794
79880	Shouchella clausii	species	5.1644
143387	Fusobacterium necrophorum subsp. funduliforme	subspecies	5.1549
872	Desulfovibrio	genus	5.1511
135622	Alteromonadales	order	5.1463
2733190	Lughvirus	genus	5.1334
2734248	Lughvirus lugh	species	5.1334
2070184	Faecalibacterium phage FP_Lugh	no rank	5.1334
207244	Anaerostipes	genus	5.1222
374	Bradyrhizobium	genus	5.044
2942993	Blohavirus	genus	5.0409
901	Desulfovibrio piger	species	5.0326
712361	Leptotrichia sp. oral taxon 218	species	5.0265
2708053	Romboutsia sp. 13368	species	5.0245
1263	Ruminococcus	genus	5.0125
2956053	Kehishuvirus primarius	species	5.0117
2301731	Bacteroides phage crAss001	no rank	5.0117
884684	Mageeibacillus indolicus	species	4.9975
699246	Mageeibacillus indolicus UPII9-5	strain	4.9975
1637257	Mageeibacillus	genus	4.9975
1647988	Akkermansiaceae	family	4.9733
239934	Akkermansia	genus	4.9733
48461	Verrucomicrobiales	order	4.9731
203494	Verrucomicrobiia	class	4.9731
74201	Verrucomicrobiota	phylum	4.973
2709317	Bacteroides phage crAss002	no rank	4.9597
2955998	Jahgtovirus secundus	species	4.9597
2913621	Prevotella sp. E9-3	species	4.9552
941323	Escherichia coli VR50	strain	4.9255
562	Escherichia coli	species	4.923
568816	Acidaminococcus intestini RyC-MR95	strain	4.9002
411470	Mediterraneibacter gnavus ATCC 29149	strain	4.8944
28890	Euryarchaeota	phylum	4.8866
2734096	Brigitvirus brigit	species	4.8861
2070181	Faecalibacterium phage FP_Brigit	no rank	4.8861
2733097	Brigitvirus	genus	4.8861
1653174	Actinotignum	genus	4.8813
239935	Akkermansia muciniphila	species	4.8803
2157	Archaea	superkingdom	4.8576
1583098	Fusobacterium hwasookii	species	4.8541
2789424	Actinomyces sp. HMT897	species	4.8316
38284	Corynebacterium accolens	species	4.8257
85015	Nocardioidaceae	family	4.8191
1796613	Bacteroides caecimuris	species	4.8184
2576755	Caproicibacter	genus	4.8161
2576756	Caproicibacter fermentans	species	4.8161
630129	Bifidobacterium catenulatum subsp. kashiwanohense	subspecies	4.8136
589436	Prevotella fusca	species	4.8083
1236517	Prevotella fusca JCM 17724	strain	4.8083
936351	Bifidobacterium breve S27	strain	4.8057
2845437	Skunavirus P656	species	4.7933
2662298	Lactococcus phage P656	no rank	4.7933
2874051	Escherichia coli O99:H6	serotype	4.7887
208223	Kosakonia cowanii	species	4.7698
204037	Dickeya	genus	4.7678
2792859	Bacteroides humanifaecis	species	4.7329
84030	Lacrimispora saccharolytica	species	4.7099
2719231	Lacrimispora	genus	4.6978
1655645	Parabacteroides phage YZ-2015b	species	4.6918
657314	Blautia obeum A2-162	strain	4.6831
1117	Cyanobacteriota	phylum	4.68
1051074	Streptococcus thermophilus JIM 8232	strain	4.6739
2773705	Escherichia coli O18ac:H14	no rank	4.6698
2751153	Coprobacter secundus subsp. similis	subspecies	4.6668
1501392	Coprobacter secundus	species	4.6668
3031451	Desulfobulbia	class	4.6547
3024411	Desulfobulbales	order	4.6547
33882	Microbacterium	genus	4.6498
459786	Oscillibacter	genus	4.5986
2763056	Oscillibacter hominis	species	4.5986
411486	Clostridium sp. M62/1	species	4.5983
185008	Butyrivibrio hungatei	species	4.5971
997877	Phocaeicola dorei CL03T12C01	strain	4.5875
33042	Coprococcus	genus	4.5745
1727145	Anaerocolumna chitinilytica	species	4.5703
3028117	Cyanophyceae	class	4.5658
28116	Bacteroides ovatus	species	4.5602
1122979	Prevotella amnii DSM 23384 = JCM 14753	strain	4.5417
203682	Planctomycetota	phylum	4.5364
411474	Coprococcus eutactus ATCC 27759	strain	4.5352
2944198	Wansuia	genus	4.5336
2763667	Wansuia hejianensis	species	4.5336
28137	Prevotella veroralis	species	4.53
267890	Shewanellaceae	family	4.5142
42817	Corynebacterium argentoratense	species	4.5132
1348662	Corynebacterium argentoratense DSM 44202	strain	4.5132
2173	Methanobrevibacter smithii	species	4.5082
2159	Methanobacteriaceae	family	4.5036
183925	Methanobacteria	class	4.5035
2158	Methanobacteriales	order	4.5035
22	Shewanella	genus	4.4975
75682	Oxalobacteraceae	family	4.4902
2944193	Simiaoa	genus	4.4833
2763672	Simiaoa sunii	species	4.4833
718255	Roseburia intestinalis XB6B4	strain	4.4785
2837504	Heyndrickxia	genus	4.4783
61648	Kluyvera intermedia	species	4.4707
239759	Alistipes	genus	4.4593
171550	Rikenellaceae	family	4.4593
909932	Negativicutes	class	4.4521
213121	Desulfobulbaceae	family	4.4201
226186	Bacteroides thetaiotaomicron VPI-5482	strain	4.4156
2172	Methanobrevibacter	genus	4.415
2779519	Thermophilibacter immobilis	species	4.3952
2847307	Thermophilibacter	genus	4.3952
1822464	Paraburkholderia	genus	4.3847
236753	Fastidiosipila sanguinis	species	4.3749
236752	Fastidiosipila	genus	4.3749
1656	Actinomyces viscosus	species	4.3346
846	Oxalobacter	genus	4.3282
46228	[Ruminococcus] lactaris	species	4.3105
471875	[Ruminococcus] lactaris ATCC 29176	strain	4.3105
2070186	Faecalibacterium phage FP_Taranis	no rank	4.3072
2733134	Taranisvirus	genus	4.3072
2734146	Taranisvirus taranis	species	4.3072
1729679	Faecalibaculum	genus	4.274
1702221	Faecalibaculum rodentium	species	4.274
46506	Bacteroides stercoris	species	4.2581
620	Shigella	genus	4.2577
39486	Dorea formicigenerans	species	4.2514
2583584	Streptococcus sp. NCTC 11567	species	4.248
2316	Methanosphaera	genus	4.2035
657315	Roseburia intestinalis M50/1	strain	4.2022
2108523	Lawsonibacter asaccharolyticus	species	4.1622
2172004	Lawsonibacter	genus	4.1622
1385938	Bifidobacterium breve 12L	strain	4.1593
310298	Phocaeicola coprocola	species	4.142
470145	Phocaeicola coprocola DSM 17136	strain	4.142
328814	Alistipes shahii	species	4.1124
717959	Alistipes shahii WAL 8301	strain	4.1124
2070182	Faecalibacterium phage FP_Epona	no rank	4.1016
2734105	Eponavirus epona	species	4.1016
2733103	Eponavirus	genus	4.1016
397864	Barnesiella	genus	4.0951
397865	Barnesiella viscericola	species	4.0951
880074	Barnesiella viscericola DSM 18177	strain	4.0951
2317	Methanosphaera stadtmanae	species	4.091
39496	Eubacterium ventriosum	species	4.0826
2899121	Tannockella kyphosi	species	4.0805
2943184	Tannockella	genus	4.0805
1398	Heyndrickxia coagulans	species	4.0793
2866573	Cardiobacterium sp. Marseille-Q4385	species	4.0783
196	Campylobacter fetus	species	4.07
997890	Bacteroides uniformis CL03T12C37	strain	4.0546
116085	Coprococcus catus	species	4.032
2929490	Faecalibacterium sp. I2-3-92	species	4.02
39485	Lachnospira eligens	species	4.0161
28050	Lachnospira	genus	4.0161
393921	Porphyromonas crevioricanis	species	4.0144
37923	Rothia kristinae	species	4.0086
572511	Blautia	genus	3.9996
155615	Fusobacterium vincentii	species	3.979
32020	Campylobacter fetus subsp. venerealis	subspecies	3.9746
418240	Blautia wexlerae	species	3.9542
1121115	Blautia wexlerae DSM 19850	strain	3.9542
2948680	Diorhovirus	genus	3.9512
2929494	Faecalibacterium sp. I4-1-79	species	3.918
138851	Treponema parvum	species	3.8965
2929488	Faecalibacterium sp. IP-1-18	species	3.8962
657322	Faecalibacterium prausnitzii SL3/3	strain	3.8736
1164882	Lachnoanaerobaculum	genus	3.8719
88431	Dorea longicatena	species	3.8655
2489010	Klebsiella africana	species	3.8568
1870984	Anaerococcus mediterraneensis	species	3.856
853	Faecalibacterium prausnitzii	species	3.8524
449673	Bacteroides stercoris ATCC 43183	strain	3.8297
1643513	Treponema sp. OMZ 857	species	3.7909
2603322	Vallitaleaceae	family	3.764
357276	Phocaeicola dorei	species	3.7613
2946593	Oxalobacter aliiformigenes	species	3.7341
34084	Riemerella	genus	3.7314
2518495	Duncaniella	genus	3.7118
203	Campylobacter rectus	species	3.6624
2029659	Lactococcus phage 16802	no rank	3.6177
2845153	Skunavirus sv16802	species	3.6177
28124	Porphyromonas endodontalis	species	3.6127
2755405	Bacteroides sp. CACC 737	species	3.6041
2772080	uncultured phage cr53_1	no rank	3.6009
2955510	Blohavirus americanus	species	3.6009
44283	Pasteurella multocida subsp. multocida	subspecies	3.5988
543	Enterobacteriaceae	family	3.5941
1730	Eubacterium	genus	3.5859
186806	Eubacteriaceae	family	3.5857
91347	Enterobacterales	order	3.5611
85004	Bifidobacteriales	order	3.5348
31953	Bifidobacteriaceae	family	3.5348
1678	Bifidobacterium	genus	3.5344
189330	Dorea	genus	3.5324
1760	Actinomycetes	class	3.5314
1236	Gammaproteobacteria	class	3.4912
35832	Bilophila	genus	3.4836
35833	Bilophila wadsworthia	species	3.4836
1224	Pseudomonadota	phylum	3.4676
3024823	Anaeromicropila	genus	3.4646
2785025	Anaeromicropila herbilytica	species	3.4646
2845434	Skunavirus P4565	species	3.4294
2662297	Lactococcus phage P4565	no rank	3.4294
228603	Hoylesella shahii	species	3.4198
2981344	Xiamenia	genus	3.4192
2682776	Xiamenia xianingshaonis	species	3.4192
28256	Halomonadaceae	family	3.4033
575614	Prevotella sp. oral taxon 299 str. F0039	strain	3.3998
652716	Prevotella sp. oral taxon 299	species	3.3998
574697	Butyricimonas	genus	3.3966
420952	Paraburkholderia bryophila	species	3.358
28264	Arcanobacterium haemolyticum	species	3.3414
544645	Butyricimonas virosa	species	3.3361
2162637	Bacteroides sp. PHL 2737	species	3.3095
1534	Clostridium kluyveri	species	3.3081
2763068	Streptococcus sp. NSJ-72	species	3.2893
201174	Actinomycetota	phylum	3.2891
13076	Globicatella sanguinis	species	3.2685
13075	Globicatella	genus	3.2685
186823	Alicyclobacillaceae	family	3.2346
2518971	Duncaniella dubosii	species	3.2306
183963	Halobacteria	class	3.2226
1737424	Blautia massiliensis (ex Durand et al. 2017)	species	3.1839
717605	Thermobacillus composti KWC4	strain	3.1738
377615	Thermobacillus composti	species	3.1738
76632	Thermobacillus	genus	3.1738
292632	Subdoligranulum	genus	3.1698
214851	Subdoligranulum variabile	species	3.1698
33024	Phascolarctobacterium	genus	3.1137
135619	Oceanospirillales	order	3.0941
165179	Segatella copri	species	3.006
2974251	Segatella	genus	3.006
194924	Desulfovibrionaceae	family	3.0022
213115	Desulfovibrionales	order	3.0017
3031449	Desulfovibrionia	class	3.0017
200940	Thermodesulfobacteriota	phylum	2.999
28263	Arcanobacterium	genus	2.9903
2375	Sporomusa	genus	2.9612
411483	Faecalibacterium duncaniae	species	2.96
171552	Prevotellaceae	family	2.9365
394503	Ruminiclostridium cellulolyticum H10	strain	2.9305
1521	Ruminiclostridium cellulolyticum	species	2.9305
33926	Candidatus Phytoplasma	genus	2.9252
1843488	Acidaminococcales	order	2.9156
909930	Acidaminococcaceae	family	2.9156
1853229	Chitinophagales	order	2.9063
563835	Chitinophagaceae	family	2.9063
1853228	Chitinophagia	class	2.9063
3031651	Desulfuromonadia	class	2.9025
33025	Phascolarctobacterium faecium	species	2.8972
2377	Sporomusa termitida	species	2.8942
3039116	Anaerocolumna sp. AGMB13025	species	2.8324
3031668	Geobacterales	order	2.8267
213422	Geobacteraceae	family	2.8267
621	Shigella boydii	species	2.8033
537011	Segatella copri DSM 18205	strain	2.7553
1538075	Malasseziomycetes	class	2.7053
742845	Malasseziaceae	family	2.7053
55193	Malassezia	genus	2.7053
162474	Malasseziales	order	2.7053
2734634	Berryella wangjianweii	species	2.6998
76775	Malassezia restricta	species	2.6771
2929495	Faecalibacterium sp. I4-3-84	species	2.6632
109328	Leptotrichia trevisanii	species	2.6442
359110	Pseudomonas extremaustralis	species	2.6212
2929489	Faecalibacterium sp. IP-3-29	species	2.6134
213118	Desulfobacterales	order	2.566
3024418	Desulfobacteria	class	2.566
28118	Odoribacter splanchnicus	species	2.5061
283168	Odoribacter	genus	2.5061
820	Bacteroides uniformis	species	2.4089
709991	Odoribacter splanchnicus DSM 20712	strain	2.3887
2913616	Prevotella sp. E13-17	species	2.3359
28446	Anaerotignum propionicum	species	2.3254
2039240	Anaerotignum	genus	2.3254
991789	Anaerotignum propionicum DSM 1682	strain	2.3254
1853231	Odoribacteraceae	family	2.276
821	Phocaeicola vulgatus	species	2.1936
2725997	Escherichia sp. SCLE84	species	2.1911
611	Salmonella enterica subsp. enterica serovar Heidelberg	no rank	2.1785
2818505	Myxococcota	phylum	2.0115
1124936	Salmonella enterica subsp. enterica serovar Heidelberg str. 41578	strain	1.9976
216851	Faecalibacterium	genus	1.9532
909656	Phocaeicola	genus	1.7058
592316	Pantoea sp. At-9b	species	1.6002
216572	Oscillospiraceae	family	1.5468
186803	Lachnospiraceae	family	1.5367
1239	Bacillota	phylum	0.9549
816	Bacteroides	genus	0.9515
186801	Clostridia	class	0.9074
186802	Eubacteriales	order	0.9074
815	Bacteroidaceae	family	0.2148
171549	Bacteroidales	order	-0.482
200643	Bacteroidia	class	-0.482
976	Bacteroidota	phylum	-0.498

As a FYI, my preferred transformation reduces skew to zero for everyone above. Life is good.

Vaccinations and the Microbiome

This post was triggered by the email below. They included a Biomesight microbiome test, Mosaic Organic Acid Test and a Gastric Tissue report. My expertise is solely the microbiome as a statistican so I will ignore all except the microbiome test.

Key Question: Is “vaccine injury” is a permanent condition?

Answer: No, the most probable cause of vaccine injury is a vaccine response triggering or worsening a microbiome dysbiosis. See the literature below.
- A microbiome dysbiosis may self-resolve for some people (i.e. people feel off for a few days or weeks after the shot) or become stable — requiring sophisticated intervention.
- There can be other speculated mechanism (autoimmunity induced, molecular mimicry or bystander activation) but they lack clear evidence, and are often based on ideological beliefs. I keep to Osler Principle and the simplest explanation supported by evidence.
- Followup from reader: H1N1 Influenza Pandemrix vaccine which caused narcolepsy (autoimmune disease) due molecular mimicry, which is my worst fear..
  - Correct: Narcolepsy Associated with Pandemrix Vaccine [2018]. This is one specific vaccine, not for all vaccines (my scope). The researchers who found this in the data would have reported all vaccines with similar side effects if there was data supporting it. [Studies] It seems to be associated to H1N1 vaccines.

I wanted to give you a rundown of what’s been going on with me. On January 6, 2023, I got the third dose of the nonavalent HPV vaccine, Gardasil 9. Immediately after the shot, I felt wiped out and weird, but my symptoms subsided only to come back with vengeance two weeks later.

The symptoms I experienced were all the classic ME/CFS ones, specifically POTS, tachycardia, panic attacks, brain fog, blurred vision, shortness of breath, trouble finding words, fatigue, PEM, fasciculations, neuropathy, pins and needles, Raynaud’s phenomenon, joint pain and joint cracking, food intolerances and food malabsorption, yellow mushy stools, and some more alarming sensations: like feeling that my body was heavy, like it was made of concrete, a sensation of electric shocks in my arms, and tingling in my feet that moved to my hands a couple of times.

Since then, some symptoms have disappeared, but others remain and new ones pop up. Right now, the symptoms I still have are joint pain and joint cracking, fasciculations, malabsorption and yellow stools, what I think is Raynaud’s phenomenon (my hands are red most of the time), and, at the moment I’m writing this message, heavy drowsiness and a general feeling of malaise, which is discouraging, since I felt better earlier this month and thought I was finally getting out of this nightmare.
A reader on CFS Remission

Overview

This is a two-sided discussion exploring the interaction between vaccinations and the microbiome from both perspectives:

How vaccinations may alter the microbiome
How the existing state of the microbiome may influence the effectiveness of a vaccination

To be transparent, I want to share that I personally experienced an adverse side effect following a series of vaccinations. The side effect involved severe gingival (gum) recession, causing the roots of my teeth to become fully exposed. Unfortunately, the condition progressed to the point where dentures became necessary due to the extent of gum loss.

At a high level, interactions in both directions are not only possible but expected. Vaccinations stimulate the immune system, similar to a natural infection — and any shift in immune function can, in turn, affect the microbiome. Conversely, the microbiome plays a key role in shaping immune responses, meaning it can directly influence how the body responds to vaccines.

It’s important to remember that the primary goal of any vaccination is to safely prompt the immune system to build protection against a specific infection. However, because the microbiome and immune system are deeply interconnected, this process can be more complex than it first appears.

Vaccination to Microbiome

A few studies of interest:

Growing evidence shows that the composition of the intestinal microbiota, which is known to play an important role in the development and regulation of immune responses⁷, influences responses to vaccination^8,9,10. Studies which have investigated this have shown that a higher relative abundance of the phylum Actinobacteria is consistently associated with higher vaccine responses and a higher relative abundance of Bacteroides with lower responses, while the association between the relative abundance of the phyla Firmicutes and Proteobacteria and vaccine responses varies for different genera and species^{11,12,13,14,15,16,17,18}.

The immunological interplay between vaccination and the intestinal microbiota [2023]

A recent study using metagenomic sequencing, reported that the intramuscular administration of an inactivated and an mRNA SARS-CoV-2 vaccine was associated with lower bacterial diversity, an increase in the relative abundance of Bacteroides caccae and a decrease in the relative abundance of Clostridiales (Coprococcus comes, Dorea longicatena and Ruminococcus obeum) in the intestinal microbiota one month after vaccination

… a total of 15 bacterial species in the baseline gut microbiome were identified, of which Bifidobacterium adolescentis was enriched in high-responders while Bacteroides vulgatus, Bacteroides thetaiotaomicron and Ruminococcus gnavus were more abundant in low-responders

Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events [2021]

Microbiome to Vaccination Effectiveness

Not only do pathogens exert immunomodulatory effects, but the microbes that populate a healthy human host, known as the microbiome, can also influence the immune response.^4,11

Influence of the microbiome on response to vaccination [2015]

When facing respiratory syncytial virus (RSV), mice supplemented with Lactobacillus showed an enhanced immune response

Lactobacillus johnsonii supplementation attenuates respiratory viral infection via metabolic reprogramming and immune cell modulation. [2017]

One of these factors seems to be the microbiome differences among individuals (101, 102). A growing number of studies suggest that the microbiome can modulate immune responses induced by vaccines (103, 104). Huda et al. (105) studied infants’ microbiomes to evaluate how their microbiome composition influenced the response to oral PV and hepatitis B virus vaccines. They found that Actinobacteria species prevalence may increase the vaccine response, while Enterobacteriales, Pseudomonadales, and Clostridiales were associated with lower response to the aforementioned vaccines. Hagan et al. (106) showed that differences in the microbiome can alter the responses of humans vaccinated against IAV.

The Interplay between the Host Microbiome and Pathogenic Viral Infections [2021]

Gut microbiota composition is associated with SARS-CoV-2 vaccine immunogenicity and adverse events

Analysis

My model is that ME/CFS is a microbiome dysbiosis. A vaccination is a microbiome disruptor — for most people, they recover. If you start with dysbiosis, then recovery may be a bit less likely.

Urban Legend in some ME/CFS groups is that people with ME/CFS do not catch things. There may some truth to it — virus friendly to the typical microbiome may find the dysbiosis of the ME/CFS patient very unfriendly. Secondly, (with a little tongue in check humor) how can they tell!!!

It turns out that virii often requires specific species to infect a person.

certain microbiome can be essential for a virus to infect its host. Jones et al. (82) showed that human norovirus needs Enterobacteria spp. to successfully infect B cells, as this bacterium aids in the attachment of the virus to the host cell. Norovirus infection in mice requires the microbiota to be persistent (83): mice with a depleted microbiome prevented persistent norovirus infection.

The Interplay between the Host Microbiome and Pathogenic Viral Infections

Going Forward

The phrase of “Vaccine Injury” is very misleading and implies that the body is somehow injured in potentially a permanent way. I believe that “Vaccine Dysbiosis” is a better and more accurate term.

We find a mountain of literature associating a vast array of different virii to ME/CFS. A few examples are:

Epstein-Barr Virus (EBV)
EBV, which causes infectious mononucleosis, is one of the most frequently implicated viruses in ME/CFS. Studies show that 8–15% of people who develop infectious mononucleosis go on to meet ME/CFS criteria, and a subgroup of ME/CFS patients show evidence of EBV reactivation or immune response abnormalities related to EBV⁵ ⁷.
Human Herpesvirus 6 (HHV-6)
Reactivation of HHV-6, another common herpesvirus, has been hypothesized to contribute to ME/CFS symptoms, particularly in combination with EBV reactivation⁷.
Enteroviruses
Historical and contemporary evidence links enteroviruses (a group that includes polioviruses, coxsackieviruses, and echoviruses) to ME/CFS. Outbreaks of ME/CFS have coincided with enteroviral epidemics, and some researchers consider enteroviruses a likely culprit, especially in cluster cases¹.
Influenza Viruses
Influenza infection has been associated with a more than two-fold increased risk of developing ME/CFS in the years following infection¹ ⁷.
SARS-CoV-2 (COVID-19)
Many individuals with long COVID meet criteria for ME/CFS, and SARS-CoV-2 is recognized as a trigger for ME/CFS in some cases⁶ ⁷.
Other Herpesviruses
Varicella zoster virus (which causes chickenpox and shingles) and other herpesviruses have also been reported as potential triggers⁷.
Ross River Virus
This mosquito-borne virus has been linked to ME/CFS onset, likely through immune system dysregulation³.
Retroviruses (e.g., XMRV)
Early studies suggested an association between the retrovirus XMRV and ME/CFS, but this link has been discredited by subsequent research and retraction of the original findings².

The goal of vaccines is to trigger enough of a response to set up the body to fight the target infection. Unfortunately, it also has a risk of triggering ME/CFS in some cases. If the person has ME/CFS, it may trigger cascades like reported above.

Going Forward

Forget about trying to “repair the injury”, the ‘injury’ is dysbiosis. You want to correct the dysbiosis. He did not have a prior to vaccination test to use for reference 🙁 .

Looking at the forecasted symptoms and the symptoms he marked we see a lot of matches at a high level (> 85%)

Looking at the bacteria that the above picked, we have one that is in the literature is associated with norovirus above.

Looking at the shifts reported for COVID, we see 64 matches to reported bacteria shifts from the literature.

Adlercreutzia – genus : Low ²¹
Adlercreutzia equolifaciens – species : Low ¹⁴
Aeromonadaceae – family : Low ²
Akkermansia – genus : Low ¹² ¹⁵ ¹⁶ ²² ²⁴
Akkermansia muciniphila – species : Low ¹⁰ ¹³
Anaerococcus – genus : Low ¹³
Bacillota – phylum : Low ¹⁴
Bacteroides – genus : High ¹ ⁴ ¹¹ ¹³ ¹⁴ ²⁴ ²⁵
Bacteroides stercoris – species : High ¹³ ¹⁴
Bacteroides uniformis – species : Low ¹³ ¹⁴
Bacteroidia – class : High ⁹
Bacteroidota – phylum : High ⁹ ¹⁴
Blautia – genus : Low ⁵ ⁶ ¹² ¹³ ¹⁶
Blautia obeum – species : Low ⁸ ¹³
Clostridia – class : Low ²³
Clostridiaceae – family : Low ¹⁴
Collinsella aerofaciens – species : High ⁷ ¹⁴
Coprococcus – genus : Low ¹² ¹³ ¹⁴
Coprococcus catus – species : Low ¹⁴a

Dorea formicigenerans – species : Low ⁸ ¹³
Enterobacterales – order : High ¹⁸
Enterobacteriaceae – family : High ² ¹³ ¹⁴ ¹⁶ ¹⁷ ¹⁹ ²⁰
Escherichia – genus : High ³ ¹⁴ ¹⁷
Escherichia coli – species : High ¹⁴
Eubacterium – genus : Low ¹¹ ¹³ ²¹
Faecalibacterium – genus : High ¹ ⁴ ¹²
Finegoldia – genus : Low ¹³
Flavobacteriaceae – family : High ¹⁴
Gammaproteobacteria – class : High ¹⁴
Haemophilus – genus : High ¹⁶
Lachnospiraceae – family : Low ³ ¹¹ ¹⁴ ²¹
Moraxellaceae – family : Low ²
Oscillospira – genus : Low ²⁴
Ruminococcus – genus : Low ⁶ ¹² ¹³ ¹⁶ ²⁴
Ruminococcus bromii – species : Low ¹³
Spirochaetia – class : Low ¹⁴
Spirochaetota – phylum : Low ¹⁴
Verrucomicrobiota – phylum : Low ²²

The top results are very typical for ME/CFS: specific antibiotics used with the Jadin Protocol for ME/CFS. I know that both getting specific antibiotics off-label and often human reluctance to do them(valid from many horror stories of them being arbitrarily selected by MDs and making people worse) — makes that a path rarely travelled.

Looking at the R² model for making probiotics do the work, the top ones (that are commercially available)

In Research — not for sale
- Anaerobutyricum hallii – rank: 998
- Christensenella minuta – rank: 888
- Roseburia intestinalis – rank: 882
- Blautia wexlerae – rank: 823
- Blautia hansenii – rank: 748
- Faecalibacterium prausnitzii – rank: 697
Top Recommendations
- Enterococcus faecium – rank: 687
- Lactococcus cremoris – rank: 558
- Akkermansia muciniphila – rank: 547
- Lactococcus lactis – rank: 331
- Leuconostoc mesenteroides – rank: 282
- Levilactobacillus brevis – rank: 236
Fall backs – very small impact.
- Segatella copri – rank: 189
- Bacteroides uniformis – rank: 137
- Parabacteroides goldsteinii – rank: 136
- Ligilactobacillus salivarius – rank: 127
- Latilactobacillus sakei – rank: 111
- Bacteroides thetaiotaomicron – rank: 106
- Streptococcus thermophilus – rank: 89
- Lactiplantibacillus plantarum – rank: 88
- Bifidobacterium adolescentis – rank: 67

All of the items listed in 2 above are available from one or more of my usual sources except for Akkermansia which does have several providers today:

The next item are other suggestions which are listed below and high in herbs. As a FYI, Enterococcus faecium is actually the top probiotic using PubMed literature (and not R² infererence) – I do like that type of convergence of different paths.

Suggested Methodology

Get the probiotics in 2 above.
- Start the first and keep taking for 4 weeks (then 2 week break)
- Every week, add in one more probiotic for 4 weeks followed by 2 week break
Do a lot of teas with different ones of the above herbs — if it is liquid, it should be a tea!
Wheat bread are all avoids, so do 100% Rye bread which is on the above list (not wheat-rye mixtures)

Go through the consensus list for more information. Do a retest about 2-3 months after starting the above. The retest will show the next course correction (often there are many).

Questions and Answers

The vaccine I got (HPV vaccine) is documented to cause ME/CFS and is one of the vaccines with higher number of reported adverse reactions compared to others. Why would you say is this?
- I tried to find this “documentation” and found this summary with studies
  - Extensive research, including large register-based studies from Norway and Denmark, has found no evidence of a causal link between HPV vaccination and an increased risk of developing ME/CFS. (9 studies)
  - Incidence rates of ME/CFS have not differed significantly between vaccinated and unvaccinated groups .
- Follow up from Reader: provided links to some studies
  - to chronic epipharyngitis induced by adjuvants, not ME/CFS. adjuvants
  - Possible Vaccine-Triggered Escalation of Undiagnosed Pre-Existing Mast Cell Disease – again not ME/CFS, and “possible” indicates speculation that is not supported by data.
  - Postural Orthostatic Tachycardia With Chronic Fatigue After HPV Vaccination as Part of the “Autoimmune/Auto-inflammatory Syndrome Induced by Adjuvants” Single person case report is not evidence. Also note that the suspect cause was not the vaccine but Adjuvants.
  - Postural tachycardia syndrome following human papillomavirus vaccination again not ME/CFS, but a condition shared by a few people with ME/CFS.
  - Note these (and other links provided) found no statistically significant link — Adjuvants appears the most likely cause of side effects. Studies based on casual US studies (versus studies based on whole population medical data – for example Iceland) tend to be low quality.
I see you highlight the family Enterobacteriacea but ignore others like Bacteroides
- I picked Enterobacteriacea for purpose of illustration of one virus-microbiome interaction, there is not sufficient literature on HPV vaccine. We have extremely sparse data in this area.
Microbiome Prescription also told me that I probably had lactic acid acidemia and biofilms but I didn’t understand it very well. Can you explain which implications have this and what bacteria may be causing it?
- Lactic Acid Acidosis means too much lactic acid. It is very common with ME/CFS and typically associated to brain fog. This is also associated with the following symptoms:
  - Nausea and vomiting.
  - Exhaustion and fatigue.
  - Fast, deep breathing (respiratory compensation).
  - Muscle cramps and body aches.
  - Increasing weakness and drowsiness.
  - Delirium and confusion.
  - Ataxia.
  - Oliguria (low urine output).
  - Low body temperature.
  - Low blood pressure.
  - Fever.
  - Jaundice (a yellow tint to the skin and whites of the eyes).
- Biofilms include dental plaque and often acts as “bullet proof vests” to bacteria that we want to change. See Wikipedia for more.
Regarding the antibiotics, I was terrorized when I saw Ciprofloxacin at the top of the recommendations as it’s infamous for injuring people and causing a ME/CFS like condition, even being sold with a black label warning in the US. It seemed ironic to me and I am frankly hesitant to try it.
- The system does not consider these risks — that is for your medical professional to evaluate.
- I strongly favor Cecile Jadin’s approach. One course (7-10 days) of one antibiotic, 3 weeks off, rotate to another appropriate one. the ones marked with [CFS] have been use with some success for ME/CFS. I believe the issue cited was for continuous use of this antibiotic for more than one course. See this video for her experience. She has never seen in 20+ years of using it, adverse interactions. This also details her process (to be reviewed by your medical professional).
The top two suggested probiotics, I haven’t heard of them in my life and haven’t seen them sold anywhere. Will they even still work?
- Enterococcus faecium – rank: 687 and Lactococcus cremoris – rank: 558 are likely not available at your local health food store. Enterococcus faecium Source, Lactococcus cremoris source
- They are computed to work — and my experience using the above sources for other probiotics is they work for me. One factor may be the freshness or the probiotics.
- Followup: I see Lactobacillus reuteri at the top of my probiotics suggestions list and don’t see Lactococcus cremoris at all. Are we look at the same screen?
  - We are — there are several places that probiotics are predicted based on different data sources. See this video: https://www.youtube.com/watch?v=KvxJLYEGrwU
I am coming out of a 14-day Rifaxamin cycle which I think caused my current neuropathy and I wonder if it altered my microbiome enough so the results of the Biomesight are no longer accurate. Is my suspicion of the neuropathy being caused by Rifaxamin accurate? It started on the very last days of the cycle and I also have neurological symptoms again after a long time without having them.
- Rifaximin are your current sample is listed as an avoid. Your neuropathy may have been contributed by it.
- I suspect that the suggestions will not be dramatically altered, so I would suggest implementing the top suggestions that you are comfortable with. Also, eliminate as many of the AVOIDS as is practical.
I am also still taking Saccharomyces Boulardii, Lactobacillus Plantarum, Lactobacillus Gasseri and will be adding Colostridium Butyricum, Bacillus Coagulans and the mix of Bifidobacterias “Seeking Health ProBiota Bifidobacterium.” All of them suggested by ChatGPT o3 model after feeding it my Biomesight, OAT, and a wide array of conventional medical tests.
- ChatGPT can be best described as a hearsay model with hallucinations being well known.
  - Most of the probiotics are fine — reservations on the Bifidobacterium mixture:
    bifidobacterium adolescentis and bifidobacterium bifidum are to be avoided
  - I advocate probiotic rotations and not continuous. Many probiotics produce natural antibiotics. Continuously taking them promote “antibiotic resistance”.
  - Also be aware of minimum effective dosages, Seeking Health ProBiota Bifidobacterium is 12 BCFU/capsule, it is not unusual to need at least 50 BCFU (of fresh probiotic) to have effect. See Probiotics — what is advertised may not be what you get for background.
I find some of the recommendations given by Microbiome Prescription weird, like whole milk and camel milk. Didn’t Biomesight said that my lactose processing was low? Or walnuts. What kind of walnuts they need to be? Can they be pecans or indian walnuts?
- Microbiome Prescription will differ from Biomesight see Why sites suggestions disagree on the same data. In short, MP uses over 7,431,437 facts to compute decisions as of today. I do not know the number BS uses, I suspect very few. All suggestions can be traced back to studies. The names of suggestions are based on the terms used in studies.
- I do not know how many studies they based “lactose processing was low”, I see lactose as a significant positive value in your results (400).
Also most of them are herbs like you said or non foods like spices and other odd things. Is this common for other microbiomes?
- I view every microbiome as different. The suggestions that I see are similar to others with ME/CFS, see other analysis here.

Followup: As I am not doing well economically and looking for ways to save, I feed ChatGPT o3 model the Microbiome Prescription suggestions table and told it to look for probiotic mixtures with the most amount of recommended strains and the least of strains to be avoided, Seeking Health ProBiota Bifidobacterium was the result.

I was aware of the wrong strains on the mixture and asked ChatGPT about the impact they would had. It told me that even then, it was still worth the risk as the strains to avoid had relatively low impact (Bifidobacterium bifidum -132.8) compared to the recommended strains on the mix (Bifidobacterium Longum 540.3).

You see this as an accurate analysis from ChatGPT or you would still recommend to avoid them?

In case that you say yes… Can I take all the probiotics I previously told at once or they antagonize each other? Is doing this risky?

ChatGPT and other Large Language Model are sophisticated Hearsay-Engines. The lack the expertise of a fuzzy logic expert system. If I was a judge, I would strike hearsay evidence from consideration. The issue of risk is a question for your medical professional. All that I can say is that it was decreased odds of helping and may have some risk of hurting.

5.- “I see lactose as a significant positive value in your results (400).”

A = I am talking about the lactose degrader shown as LOW (0.11%) under the food intolerances section on the Biomesight report.

There are some other findings here that disturb me, like butyrate producers LOW, colibactin producers HIGH, D-Lactate producers HIGH, gram negative bacteria HIGH and gram positive bacteria LOW.

Would you say that I fit on the classic ME/CFS profile? Anything else that stands out about my microbiome?

Thank you and I hope this format is easy to understand but if not, please let me know.

I avoid comment on any provider individual reports, i.e. Biomesight report, beyond what the US National Institute of Standards and Technology has stated. I will comment on methodologies, the usual comment is they “went cheap” and do not use sufficient data — MP consider 7,431,520 facts in computing suggestions.

Your sample have strong statistical associations to may symptoms of ME/CFS and Long COVID. “Fitting a profile” is question more suitable for a medical professional. I am a statistican.

Postscript – and Reminder

I am not a licensed medical professional and there are strict laws where I live about “appearing to practice medicine”. I am safe when it is “academic models” and I keep to the language of science, especially statistics. I am not safe when the explanations have possible overtones of advising a patient instead of presenting data to be evaluated by a medical professional before implementing.

I cannot tell people what they should take or not take. I can inform people items that have better odds of improving their microbiome as a results on numeric calculations. I am a trained experienced statistician with appropriate degrees and professional memberships. All suggestions should be reviewed by your medical professional before starting.

Also, I note that many people will make inferences (often based on influencers opinions) that are not supported by the evidence. Often people want absolute certainty and will deem things proven if they find a single case study supporting a hypothesis; this is not how science and statistics work… it is all odds.

The answers above describe my logic and thinking and is not intended to give advice to this person or any one. Always review with your knowledgeable medical professional.

Family Convergence of Microbiome

A reader wrote me saying:

I have 5 Biomesight samples uploaded to my MP.com account, of which 3 are mine and 2 are my kids.

When I choose a different sample from the dropdown list, the ‘Suggestions’ change as I would expect them to, however, the commercially available Probiotic recommendations do not change. So the Priobiotic ‘weighting’ is the same on all 5 samples, which I included a screenshot of.

Any idea why this is happening and how I can get accurate commercial Probiotic suggestions for each different sample?

Thanks much,

Step #1 Reproduce the issue

First item was checking that there was not duplicate uploads – there were not. I then got suggestions from each sample and list them below: I also included the top suggestion to verify that different suggestions were made.

There were duplicate suggestions between some samples:

Two the same (2024-12-17, 2024-03-10)
Three the same ( 2023-12-15, 2024-01-08, 2023-12-15)

One item was on all of the recommendation: L.Gasseri.

I also did Experimental Probiotics Suggestions using Taxa R2 Site. I find that I trust R2 suggestions more than the default suggestions. The differences are:

Default is based on available studies — most have not been duplicated and have small sample size. Small sample size means only things that really stand out are reported. Most are done with 16s testing which is much less accurate than shotgun. We have 4,625 data points.
R2 is based on 1000 shotgun samples and based on statistical associations ween between probiotic species and other species. There are no clinical studies showing that they work. We have 2,446,755 data points.

So the decision is trusting limited clinical studies, or trusting statistics with 529x more data points. My personal experience is that I have noticed more benefit from R2 suggestions than the default suggestions.

Sample 2025-06-29

Top amoxicillin [CFS] 1444

R2 Suggestions for Available:

Step #2 2024-12-17

Step #3 2024-03-10

Step #4 2023-12-15

Top Ferrum {Iron Supplements} 1013

R2 Suggestions for Available:

Step #5 2024-01-08

Top imipenemL 932

R2 Suggestions for Available:

Step #6 2023-12-15

Top Cichorium intybus {Chicory} 839

R2 Suggestions for Available:

Bifidobacterium longum 427
Bifidobacterium longum subsp. infantis 346
Bifidobacterium breve 328

Bottom Line

The reader did report correctly that the same suggestions were being made. The default probiotics were likely correct based on the sparse data from clinical studies available. I would suggest that this user try the top 3 probiotics suggested by the novel R2 algorithm; I suspect they will have a greater and more targeted impact.

I am not surprised that given the limited palette of probiotics from clinical studies that we have convergence because the microbiomes have convergenes.

Key findings from published studies include:

Overall Microbiome Similarity in Households: Multiple studies found that members of the same household, especially couples, have more similar gut, skin, and oral microbiota than individuals from different households. The effect is strongest for the skin microbiome, likely due to frequent direct contact and shared environment. The trend also extends to pets, with household dogs sharing microbiota with both adults and other dogs in the home.
- Cohabiting family members share microbiota with one another and with their dogs
- The person-to-person transmission landscape of the gut and oral microbiomes
Cohabitation and Person-to-Person Strain Sharing: A large-scale study using over 9,700 human metagenomes reported substantial strain sharing among cohabiting individuals. Cohabitants shared a median of 12% of gut microbiome strains and 32% of oral microbiome strains. Time spent living together correlated with increased microbiome similarity, and this sharing was driven more by social interactions and environment than by genetics.
- The person-to-person transmission landscape of the gut and oral microbiomes

Lactobacillus

Biomesight

Ubiome

Ombre

PrecisionBiome

Vitract

Thorne

Bifidobacterium Longum

Biomesight

Ubiome

Ombre

PrecisionBiome

Vitract

Thorne

Faecalibacterium prausnitzii

Biomesight

Ubiome

Ombre

PrecisionBiome

Vitract

Thorne

Bottom Line

Overview

Vaccination to Microbiome

Microbiome to Vaccination Effectiveness

Analysis

Going Forward

Going Forward

Suggested Methodology

Questions and Answers

Postscript – and Reminder

Step #1 Reproduce the issue

Sample 2025-06-29

Step #2 2024-12-17

Step #3 2024-03-10

Step #4 2023-12-15

Step #5 2024-01-08

Step #6 2023-12-15

Bottom Line

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