name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Streptococcus salivarius	1304	S	153	122	275	0.00317
Bacteroidales bacterium CF	1400053	S	5	0	5	0.00006
Streptococcus suis	1307	S	10	9	19	0.00023
Anaerostipes hadrus	649756	S	821	70	891	0.01026
Turicibacter sp. H121	1712675	S	619	47	666	0.00766
Erwinia gerundensis	1619313	S	5	0	5	0.00006
Chryseobacterium gallinarum	1324352	S	116	10	126	0.00145
Streptococcus thermophilus	1308	S	27	4	31	0.00037
Ruminococcus albus	1264	S	6	0	6	0.00007
Bacteroides helcogenes	290053	S	57	1	58	0.00067
Francisella sp. FSC1006	1547445	S	15	0	15	0.00017
Veillonella parvula	29466	S	29	1	30	0.00035
Streptococcus gordonii	1302	S	7	1	8	0.00009
Methanobrevibacter smithii	2173	S	311	1	312	0.00359
Bacteroides thetaiotaomicron	818	S	2195	503	2698	0.03105
Acidaminococcus intestini	187327	S	6	0	6	0.00008
Citrobacter freundii	546	S	38	11	49	0.00057
Parabacteroides sp. CT06	2025876	S	330	775	1105	0.01271
Prevotella scopos	589437	S	160	368	528	0.00608
Prevotella fusca	589436	S	256	288	544	0.00626
Bacteroides fragilis	817	S	126	49	175	0.00201
Bacteroides caccae	47678	S	444	15	459	0.00529
Lachnoclostridium sp. YL32	1834196	S	63	9	72	0.00084
Streptococcus agalactiae	1311	S	8	0	8	0.00010
Streptococcus parasanguinis	1318	S	54	5	59	0.00068
Nonlabens sediminis	319236	S	8	0	8	0.00010
Clostridium botulinum	1491	S	42	68	110	0.00127
Bacteroides dorei	357276	S	603	207	810	0.00932
Methanolacinia petrolearia	54120	S	6	0	6	0.00007
Bacteroides caecimuris	1796613	S	459	88	547	0.00630
Mucilaginibacter mallensis	652787	S	10	0	10	0.00012
Akkermansia muciniphila	239935	S	9	0	9	0.00010
Capnocytophaga gingivalis	1017	S	9	1	10	0.00012
[Clostridium] bolteae	208479	S	125	22	147	0.00170
Bifidobacterium pseudocatenulatum	28026	S	7	1	8	0.00010
Clostridium sp. DL-VIII	641107	S	12	2	14	0.00016
Herbinix luporum	1679721	S	8	0	8	0.00010
[Eubacterium] cellulosolvens	29322	S	166	1	167	0.00193
Mageeibacillus indolicus	884684	S	8	0	8	0.00010
Prevotella melaninogenica	28132	S	214	500	714	0.00822
Prevotella intermedia	28131	S	350	241	591	0.00681
Phoenicibacter massiliensis	1944646	S	13	0	13	0.00016
Methanosphaera stadtmanae	2317	S	137	0	137	0.00158
Bacteroides vulgatus	821	S	8996	4329	13325	0.15330
Clostridium bornimense	1216932	S	7	0	7	0.00009
Clostridium saccharoperbutylacetonicum	36745	S	7	1	8	0.00009
Blautia hansenii	1322	S	189	40	229	0.00264
Streptococcus anginosus	1328	S	7	0	7	0.00009
Bacteroides coprosuis	151276	S	95	1	96	0.00111
Prevotella sp. oral taxon 299	652716	S	444	250	694	0.00799
[Clostridium] saccharolyticum	84030	S	59	1	60	0.00070
Prevotella ruminicola	839	S	413	10	423	0.00487
[Eubacterium] hallii	39488	S	1088	69	1157	0.01332
Clostridium beijerinckii	1520	S	26	5	31	0.00036
Prevotella denticola	28129	S	77	59	136	0.00157
Faecalitalea cylindroides	39483	S	298	73	371	0.00427
Ruminococcus champanellensis	1161942	S	24	0	24	0.00028
[Eubacterium] eligens	39485	S	20428	795	21223	0.24415
Paenibacillus polymyxa	1406	S	5	4	9	0.00010
Streptococcus intermedius	1338	S	13	9	22	0.00026
Prevotella enoeca	76123	S	156	130	286	0.00330
Christensenella massiliensis	1805714	S	14	0	14	0.00017
Fermentimonas caenicola	1562970	S	7	0	7	0.00008
Gramella flava	1486245	S	43	1	44	0.00051
Desulfovibrio piger	901	S	23	1	24	0.00028
Clostridium butyricum	1492	S	35	2	37	0.00044
Megasphaera elsdenii	907	S	176	13	189	0.00218
Acidaminococcus fermentans	905	S	7	0	7	0.00009
Clostridium sp. SY8519	1042156	S	14	0	14	0.00017
Spirosoma aerolatum	1211326	S	6	0	6	0.00007
Clostridium kluyveri	1534	S	5	0	5	0.00006
Parabacteroides distasonis	823	S	281	537	818	0.00942
[Eubacterium] rectale	39491	S	18926	1293	20219	0.23260
Paludibacter propionicigenes	185300	S	6	0	6	0.00007
Klebsiella pneumoniae	573	S	17	62	79	0.00091
Flavonifractor plautii	292800	S	56	2	58	0.00068
Lachnoclostridium phocaeense	1871021	S	45	2	47	0.00055
Clostridium chauvoei	46867	S	71	5	76	0.00088
Barnesiella viscericola	397865	S	110	19	129	0.00149
Fibrella aestuarina	651143	S	26	0	26	0.00031
Eubacterium limosum	1736	S	15	0	15	0.00017
Clostridium perfringens	1502	S	359	28	387	0.00445
Clostridium pasteurianum	1501	S	12	0	12	0.00014
[Eubacterium] sulci	143393	S	6	0	6	0.00007
Alistipes finegoldii	214856	S	465	83	548	0.00631
Campylobacter jejuni	197	S	40	26	66	0.00076
Lactococcus lactis	1358	S	12	11	23	0.00028
Enterococcus faecium	1352	S	33	8	41	0.00048
Escherichia coli	562	S	216	421	637	0.00733
Clostridium carboxidivorans	217159	S	7	4	11	0.00013
Clostridium taeniosporum	394958	S	11	2	13	0.00016
Lactobacillus gasseri	1596	S	8	0	8	0.00010
Clostridioides difficile	1496	S	209	118	327	0.00377
Lactobacillus ruminis	1623	S	45	1	46	0.00053
Lactobacillus salivarius	1624	S	92	10	102	0.00117
Oscillibacter valericigenes	351091	S	13	0	13	0.00015
Butyrivibrio proteoclasticus	43305	S	7	3	10	0.00012
Sphingobacterium sp. 21	743722	S	5	0	5	0.00006
Ruminococcus bicirculans	1160721	S	4395	142	4537	0.05220
Bacteroides cellulosilyticus	246787	S	1407	96	1503	0.01729
Streptococcus sp. FDAARGOS_192	1839799	S	7	14	21	0.00024
Clostridium saccharobutylicum	169679	S	12	1	13	0.00016
Haemophilus parainfluenzae	729	S	45	9	54	0.00063
Intestinimonas butyriciproducens	1297617	S	82	5	87	0.00101
Corynebacterium argentoratense	42817	S	5	0	5	0.00006
Caldicellulosiruptor owensensis	55205	S	5	2	7	0.00008
Enterobacter cloacae	550	S	9	5	14	0.00017
Geobacter lovleyi	313985	S	6	0	6	0.00007
Alistipes shahii	328814	S	260	67	327	0.00376
Lachnoclostridium phytofermentans	66219	S	5	0	5	0.00006
Algoriphagus machipongonensis	388413	S	13	0	13	0.00015
Pseudoalteromonas rubra	43658	S	7	0	7	0.00008
Prevotella dentalis	52227	S	132	36	168	0.00194
Clostridium baratii	1561	S	29	3	32	0.00037
Petrimonas mucosa	1642646	S	44	3	47	0.00055
Bifidobacterium longum	216816	S	17	37	54	0.00063
Bacteroides salanitronis	376805	S	110	9	119	0.00138
Porphyromonas gingivalis	837	S	19	2	21	0.00024
Citrobacter braakii	57706	S	8	3	11	0.00013
Roseburia hominis	301301	S	2171	252	2423	0.02788
Bifidobacterium adolescentis	1680	S	35	1	36	0.00042
Bacteroides ovatus	28116	S	1287	149	1436	0.01653
Tannerella forsythia	28112	S	7	0	7	0.00008
Odoribacter splanchnicus	28118	S	1902	369	2271	0.02613