name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Streptococcus salivarius	1304	S	61	20	81	0.00035
Bacteroidales bacterium CF	1400053	S	7	0	7	0.00003
Streptococcus suis	1307	S	401	344	745	0.00320
Anaerostipes hadrus	649756	S	6610	881	7491	0.03217
Turicibacter sp. H121	1712675	S	10	1	11	0.00005
Chryseobacterium gallinarum	1324352	S	7	0	7	0.00003
Streptococcus thermophilus	1308	S	70	6	76	0.00033
Ruminococcus albus	1264	S	38	0	38	0.00017
Bacteroides helcogenes	290053	S	595	10	605	0.00260
Veillonella parvula	29466	S	16	2	18	0.00008
Methanobrevibacter smithii	2173	S	6127	28	6155	0.02643
Ethanoligenens harbinense	253239	S	7	1	8	0.00004
Bacteroides thetaiotaomicron	818	S	25221	2058	27279	0.11714
Parabacteroides sp. CT06	2025876	S	2136	4785	6921	0.02972
Prevotella scopos	589437	S	27	11	38	0.00016
Bacteroides fragilis	817	S	1127	318	1445	0.00621
Bacteroides caccae	47678	S	330	11	341	0.00147
Lachnoclostridium sp. YL32	1834196	S	110	13	123	0.00053
Streptococcus agalactiae	1311	S	48	4	52	0.00023
Bacteroides salanitronis	376805	S	382	15	397	0.00171
Adlercreutzia equolifaciens	446660	S	45	2	47	0.00020
Clostridium botulinum	1491	S	9	11	20	0.00009
Bacteroides dorei	357276	S	47867	17064	64931	0.27881
Blautia sp. YL58	1796616	S	7	599	606	0.00260
Clostridium cochlearium	1494	S	8	2	10	0.00005
Clostridioides difficile	1496	S	412	201	613	0.00263
Heliobacterium modesticaldum	35701	S	5	0	5	0.00002
Akkermansia muciniphila	239935	S	254	3	257	0.00111
[Clostridium] bolteae	208479	S	995	143	1138	0.00489
Gottschalkia acidurici	1556	S	6	0	6	0.00003
Desulfovibrio fairfieldensis	44742	S	343	16	359	0.00154
Bifidobacterium pseudocatenulatum	28026	S	9	0	9	0.00004
Herbinix luporum	1679721	S	8	0	8	0.00004
[Eubacterium] cellulosolvens	29322	S	29	0	29	0.00013
Mageeibacillus indolicus	884684	S	13	1	14	0.00006
Candidatus Izimaplasma sp. HR1	1541959	S	7	0	7	0.00003
Candidatus Methanomethylophilus alvus	1291540	S	6	9	15	0.00007
Phoenicibacter massiliensis	1944646	S	13	0	13	0.00006
Clostridium sp. SY8519	1042156	S	68	2	70	0.00030
Clostridium bornimense	1216932	S	5	0	5	0.00002
Parabacteroides distasonis	823	S	1658	3652	5310	0.02280
Blautia hansenii	1322	S	456	30	486	0.00209
Campylobacter coli	195	S	44	45	89	0.00038
Streptococcus anginosus	1328	S	22	3	25	0.00011
Staphylococcus argenteus	985002	S	6	1	7	0.00003
Bacteroides caecimuris	1796613	S	4171	593	4764	0.02046
Fibrobacter succinogenes	833	S	7	0	7	0.00003
Butyrivibrio hungatei	185008	S	16	2	18	0.00008
Methanobrevibacter sp. YE315	1609968	S	5	0	5	0.00002
Porphyromonas gingivalis	837	S	5	0	5	0.00002
[Clostridium] saccharolyticum	84030	S	175	6	181	0.00078
Prevotella ruminicola	839	S	6	0	6	0.00003
Gemella sp. oral taxon 928	1785995	S	7	1	8	0.00003
[Eubacterium] hallii	39488	S	3379	369	3748	0.01610
[Clostridium] cellulolyticum	1521	S	5	0	5	0.00002
Bacillus cereus	1396	S	11	16	27	0.00012
Faecalitalea cylindroides	39483	S	867	384	1251	0.00537
Ruminococcus champanellensis	1161942	S	82	3	85	0.00037
[Eubacterium] eligens	39485	S	2721	168	2889	0.01241
Desulfotomaculum gibsoniae	102134	S	11	2	13	0.00006
Streptococcus intermedius	1338	S	6	7	13	0.00006
Christensenella massiliensis	1805714	S	165	11	176	0.00076
Streptococcus equi	1336	S	6	0	6	0.00003
Cloacibacillus porcorum	1197717	S	227	1	228	0.00098
Burkholderiales bacterium YL45	1834205	S	16	17	33	0.00014
Phycisphaerae bacterium L21-RPul-D3	1940790	S	6	1	7	0.00003
Desulfovibrio vulgaris	881	S	5	0	5	0.00002
Bacteroides vulgatus	821	S	4509	2939	7448	0.03198
Acholeplasma brassicae	61635	S	12	1	13	0.00006
Mogibacterium pumilum	86332	S	6	0	6	0.00003
Finegoldia magna	1260	S	5	0	5	0.00002
[Eubacterium] rectale	39491	S	23496	2442	25938	0.11138
Enterococcus cecorum	44008	S	5	0	5	0.00002
Klebsiella pneumoniae	573	S	8	66	74	0.00032
Flavonifractor plautii	292800	S	391	28	419	0.00180
Lachnoclostridium phocaeense	1871021	S	328	27	355	0.00153
Streptococcus pasteurianus	197614	S	43	17	60	0.00026
Candidatus Methanoplasma termitum	1577791	S	6	1	7	0.00003
Murdochiella vaginalis	1852373	S	21	6	27	0.00012
Clostridium perfringens	1502	S	35	3	38	0.00016
Ornithobacterium rhinotracheale	28251	S	18	35	53	0.00023
Dialister pneumosintes	39950	S	9	4	13	0.00006
Paenibacillus mucilaginosus	61624	S	9	2	11	0.00005
Eggerthella lenta	84112	S	10	1	11	0.00005
Eubacterium limosum	1736	S	61	2	63	0.00027
Barnesiella viscericola	397865	S	193	16	209	0.00090
Clostridium pasteurianum	1501	S	6	0	6	0.00003
Eggerthella sp. YY7918	502558	S	21	0	21	0.00009
Methylomicrobium alcaliphilum	271065	S	8	0	8	0.00003
Alistipes finegoldii	214856	S	296	84	380	0.00163
Campylobacter jejuni	197	S	52	80	132	0.00057
Lactococcus lactis	1358	S	14	2	16	0.00007
Enterococcus faecium	1352	S	272	284	556	0.00239
Escherichia coli	562	S	27	71	98	0.00042
Clostridium taeniosporum	394958	S	6	2	8	0.00003
Treponema succinifaciens	167	S	10	22	32	0.00014
Lactobacillus ruminis	1623	S	16	0	16	0.00007
Lactobacillus salivarius	1624	S	19	3	22	0.00010
Oscillibacter valericigenes	351091	S	60	0	60	0.00026
Butyrivibrio proteoclasticus	43305	S	9	1	10	0.00004
Ruminococcus bicirculans	1160721	S	3320	366	3686	0.01583
Bacteroides cellulosilyticus	246787	S	6754	266	7020	0.03015
Jeotgalicoccus saudimassiliensis	1461582	S	10	0	10	0.00004
Clostridium tetani	1513	S	6	2	8	0.00004
Intestinimonas butyriciproducens	1297617	S	322	32	354	0.00152
Filifactor alocis	143361	S	17	2	19	0.00009
Faecalibaculum rodentium	1702221	S	5	1	6	0.00003
methanogenic archaeon ISO4-H5	1495144	S	5	6	11	0.00005
Alistipes shahii	328814	S	166	52	218	0.00094
Lachnoclostridium phytofermentans	66219	S	14	0	14	0.00006
Prevotella dentalis	52227	S	7	0	7	0.00003
Halomonas huangheensis	1178482	S	6	0	6	0.00003
Petrimonas mucosa	1642646	S	6	1	7	0.00003
Ruminococcaceae bacterium CPB6	1572656	S	6	2	8	0.00004
Bifidobacterium longum	216816	S	2709	496	3205	0.01377
Streptococcus parasanguinis	1318	S	11	0	11	0.00005
[Clostridium] cellulosi	29343	S	5	0	5	0.00003
Thermoanaerobacterium sp. RBIITD	1550240	S	5	0	5	0.00002
Streptococcus mitis	28037	S	7	1	8	0.00004
Lactobacillus agilis	1601	S	24	3	27	0.00012
Roseburia hominis	301301	S	3970	690	4660	0.02001
Bifidobacterium angulatum	1683	S	5	0	5	0.00002
Bacteroides ovatus	28116	S	34981	2731	37712	0.16193
Bifidobacterium breve	1685	S	19	17	36	0.00016
Tannerella forsythia	28112	S	17	0	17	0.00007
Odoribacter splanchnicus	28118	S	240	8	248	0.00107