name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Streptococcus salivarius	1304	S	63	17	80	0.00028
Bacteroidales bacterium CF	1400053	S	6	0	6	0.00002
Streptococcus suis	1307	S	496	381	877	0.00311
Anaerostipes hadrus	649756	S	3875	493	4368	0.01546
Streptococcus gordonii	1302	S	8	0	8	0.00003
Chryseobacterium gallinarum	1324352	S	6	1	7	0.00003
Streptococcus thermophilus	1308	S	208	19	227	0.00081
Ruminococcus albus	1264	S	26	0	26	0.00009
Bacteroides helcogenes	290053	S	531	8	539	0.00191
Rickettsia helvetica	35789	S	6	19	25	0.00009
Rothia mucilaginosa	43675	S	7	0	7	0.00003
Veillonella parvula	29466	S	12	3	15	0.00006
Hymenobacter sedentarius	1411621	S	5	2	7	0.00002
Methanobrevibacter smithii	2173	S	10278	73	10351	0.03664
Ethanoligenens harbinense	253239	S	18	5	23	0.00008
Bacteroides thetaiotaomicron	818	S	19886	1553	21439	0.07588
Parabacteroides sp. CT06	2025876	S	2159	4695	6854	0.02426
Prevotella scopos	589437	S	11	5	16	0.00006
Bacteroides fragilis	817	S	1410	333	1743	0.00617
Bacteroides caccae	47678	S	441	15	456	0.00161
Streptococcus pneumoniae	1313	S	11	19	30	0.00011
Lachnoclostridium sp. YL32	1834196	S	96	10	106	0.00038
Streptococcus agalactiae	1311	S	44	4	48	0.00017
Bacteroides salanitronis	376805	S	604	21	625	0.00221
Adlercreutzia equolifaciens	446660	S	49	2	51	0.00018
Clostridium botulinum	1491	S	10	18	28	0.00010
Bacteroides dorei	357276	S	57042	19200	76242	0.26985
Clostridium cochlearium	1494	S	14	2	16	0.00006
Clostridioides difficile	1496	S	358	165	523	0.00185
Heliobacterium modesticaldum	35701	S	10	1	11	0.00004
[Clostridium] bolteae	208479	S	1498	186	1684	0.00596
Bifidobacterium pseudocatenulatum	28026	S	6	0	6	0.00002
Desulfovibrio fairfieldensis	44742	S	531	42	573	0.00203
[Eubacterium] cellulosolvens	29322	S	20	0	20	0.00007
Mageeibacillus indolicus	884684	S	10	1	11	0.00004
Candidatus Izimaplasma sp. HR1	1541959	S	5	0	5	0.00002
Candidatus Methanomethylophilus alvus	1291540	S	5	3	8	0.00003
Phoenicibacter massiliensis	1944646	S	6	0	6	0.00002
Sebaldella termitidis	826	S	6	0	6	0.00002
Clostridium sp. SY8519	1042156	S	65	2	67	0.00024
Parabacteroides distasonis	823	S	1826	3964	5790	0.02049
Blautia hansenii	1322	S	364	100	464	0.00164
Coriobacteriaceae bacterium 68-1-3	1531429	S	5	0	5	0.00002
Campylobacter coli	195	S	68	45	113	0.00040
Streptococcus anginosus	1328	S	33	3	36	0.00013
Dehalococcoides mccartyi	61435	S	7	0	7	0.00002
Turicibacter sp. H121	1712675	S	22	2	24	0.00009
Bacteroides caecimuris	1796613	S	6396	840	7236	0.02561
Fibrobacter succinogenes	833	S	5	0	5	0.00002
Butyrivibrio hungatei	185008	S	14	4	18	0.00006
Methanobrevibacter sp. YE315	1609968	S	11	0	11	0.00004
Porphyromonas gingivalis	837	S	5	0	5	0.00002
[Clostridium] saccharolyticum	84030	S	198	7	205	0.00073
[Eubacterium] hallii	39488	S	2647	269	2916	0.01032
Akkermansia muciniphila	239935	S	236	3	239	0.00085
Bacillus cereus	1396	S	11	12	23	0.00008
Faecalitalea cylindroides	39483	S	712	310	1022	0.00362
Ruminococcus champanellensis	1161942	S	68	2	70	0.00025
[Eubacterium] eligens	39485	S	1069	62	1131	0.00401
Propionimicrobium sp. Marseille-P3275	1871034	S	5	0	5	0.00002
Streptococcus intermedius	1338	S	11	8	19	0.00007
Christensenella massiliensis	1805714	S	229	15	244	0.00086
Desulfotomaculum gibsoniae	102134	S	11	0	11	0.00004
Fermentimonas caenicola	1562970	S	6	0	6	0.00002
Cloacibacillus porcorum	1197717	S	185	2	187	0.00066
Bacillus xiamenensis	1178537	S	5	1	6	0.00002
Thermoplasmatales archaeon BRNA1	1054217	S	12	10	22	0.00008
Desulfovibrio piger	901	S	9	1	10	0.00004
Bacteroides vulgatus	821	S	13400	6648	20048	0.07096
Mucinivorans hirudinis	1433126	S	5	0	5	0.00002
Finegoldia magna	1260	S	5	0	5	0.00002
Clostridium kluyveri	1534	S	7	0	7	0.00003
[Eubacterium] rectale	39491	S	30667	2965	33632	0.11904
Klebsiella pneumoniae	573	S	6	65	71	0.00025
Flavonifractor plautii	292800	S	430	28	458	0.00162
Lachnoclostridium phocaeense	1871021	S	333	26	359	0.00127
Streptococcus pasteurianus	197614	S	24	8	32	0.00011
Carnobacterium inhibens	147709	S	6	0	6	0.00002
Candidatus Methanoplasma termitum	1577791	S	8	0	8	0.00003
Thioflavicoccus mobilis	80679	S	6	0	6	0.00002
Murdochiella vaginalis	1852373	S	18	4	22	0.00008
Clostridium perfringens	1502	S	27	4	31	0.00011
Ornithobacterium rhinotracheale	28251	S	21	39	60	0.00021
Dialister pneumosintes	39950	S	12	8	20	0.00007
Eggerthella lenta	84112	S	14	1	15	0.00006
Eubacterium limosum	1736	S	52	0	52	0.00019
Barnesiella viscericola	397865	S	210	15	225	0.00080
Eggerthella sp. YY7918	502558	S	25	0	25	0.00009
Alistipes finegoldii	214856	S	362	87	449	0.00159
Campylobacter jejuni	197	S	36	53	89	0.00032
Lactococcus lactis	1358	S	7	0	7	0.00003
Enterococcus faecium	1352	S	306	329	635	0.00225
Escherichia coli	562	S	18	34	52	0.00019
Lactobacillus gasseri	1596	S	6	1	7	0.00003
Treponema succinifaciens	167	S	6	21	27	0.00010
Lactobacillus ruminis	1623	S	5	0	5	0.00002
Anaerolineaceae bacterium oral taxon 439	1889813	S	6	0	6	0.00002
Oscillibacter valericigenes	351091	S	87	0	87	0.00031
Butyrivibrio proteoclasticus	43305	S	10	2	12	0.00004
Ruminococcus bicirculans	1160721	S	2769	312	3081	0.01091
Bacteroides cellulosilyticus	246787	S	5577	196	5773	0.02043
[Clostridium] stercorarium	1510	S	6	0	6	0.00002
Haemophilus parainfluenzae	729	S	21	12	33	0.00012
Intestinimonas butyriciproducens	1297617	S	440	41	481	0.00170
Filifactor alocis	143361	S	12	1	13	0.00005
Streptococcus pyogenes	1314	S	8	23	31	0.00011
Anaerotignum propionicum	28446	S	7	0	7	0.00003
Streptomyces antibioticus	1890	S	5	3	8	0.00003
Microbacterium sp. No. 7	1714373	S	9	1	10	0.00004
Faecalibaculum rodentium	1702221	S	5	1	6	0.00002
methanogenic archaeon ISO4-H5	1495144	S	9	5	14	0.00005
Alistipes shahii	328814	S	227	60	287	0.00102
Lachnoclostridium phytofermentans	66219	S	15	0	15	0.00005
Prevotella dentalis	52227	S	9	0	9	0.00003
Yersinia rohdei	29485	S	6	0	6	0.00002
Clostridium baratii	1561	S	5	1	6	0.00002
Ruminococcaceae bacterium CPB6	1572656	S	7	3	10	0.00004
Bifidobacterium longum	216816	S	4061	703	4764	0.01686
Streptococcus parasanguinis	1318	S	32	1	33	0.00012
[Clostridium] cellulosi	29343	S	6	1	7	0.00003
Thermoanaerobacterium sp. RBIITD	1550240	S	6	0	6	0.00002
Streptococcus mitis	28037	S	17	3	20	0.00007
Lactobacillus agilis	1601	S	7	0	7	0.00003
Roseburia hominis	301301	S	9446	1495	10941	0.03873
Bifidobacterium bifidum	1681	S	8	1	9	0.00003
Bacteroides ovatus	28116	S	49436	3682	53118	0.18801
Bifidobacterium breve	1685	S	35	33	68	0.00024
Tannerella forsythia	28112	S	11	0	11	0.00004
Streptococcus sp. A12	1759399	S	8	0	8	0.00003
Odoribacter splanchnicus	28118	S	249	7	256	0.00091