name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Streptococcus salivarius	1304	S	83	47	130	0.00149
Bacteroidales bacterium CF	1400053	S	6	0	6	0.00007
Streptococcus suis	1307	S	16	20	36	0.00042
Anaerostipes hadrus	649756	S	975	87	1062	0.01214
Streptococcus gordonii	1302	S	6	0	6	0.00008
Erwinia gerundensis	1619313	S	5	0	5	0.00006
Chryseobacterium gallinarum	1324352	S	95	12	107	0.00123
Streptococcus thermophilus	1308	S	11	1	12	0.00014
Ruminococcus albus	1264	S	5	0	5	0.00006
Bacteroides helcogenes	290053	S	30	0	30	0.00035
Francisella sp. FSC1006	1547445	S	16	3	19	0.00022
Veillonella parvula	29466	S	122	6	128	0.00147
Turicibacter sp. H121	1712675	S	158	14	172	0.00197
Methanobrevibacter smithii	2173	S	636	1	637	0.00729
Veillonella rodentium	248315	S	5	0	5	0.00006
Bacteroides thetaiotaomicron	818	S	1956	543	2499	0.02858
Acidaminococcus intestini	187327	S	7	1	8	0.00009
Citrobacter freundii	546	S	6	1	7	0.00009
Parabacteroides sp. CT06	2025876	S	177	435	612	0.00701
Prevotella scopos	589437	S	175	407	582	0.00666
Prevotella fusca	589436	S	254	290	544	0.00622
Bacteroides fragilis	817	S	123	69	192	0.00220
Bacteroides caccae	47678	S	107	3	110	0.00127
Lachnoclostridium sp. YL32	1834196	S	82	7	89	0.00102
Streptococcus agalactiae	1311	S	10	1	11	0.00013
Haemophilus pittmaniae	249188	S	7	0	7	0.00009
Streptococcus parasanguinis	1318	S	60	4	64	0.00074
Nonlabens sediminis	319236	S	9	0	9	0.00011
Clostridium botulinum	1491	S	15	10	25	0.00029
Roseburia hominis	301301	S	1803	232	2035	0.02328
Methanolacinia petrolearia	54120	S	11	0	11	0.00013
Bacteroides caecimuris	1796613	S	303	71	374	0.00428
Mucilaginibacter mallensis	652787	S	10	0	10	0.00012
Akkermansia muciniphila	239935	S	16	0	16	0.00018
Capnocytophaga gingivalis	1017	S	10	2	12	0.00014
[Clostridium] bolteae	208479	S	107	10	117	0.00135
Methanosphaera stadtmanae	2317	S	261	1	262	0.00300
[Eubacterium] cellulosolvens	29322	S	326	3	329	0.00377
Mageeibacillus indolicus	884684	S	7	0	7	0.00009
Prevotella melaninogenica	28132	S	186	439	625	0.00715
Prevotella intermedia	28131	S	424	304	728	0.00833
Phoenicibacter massiliensis	1944646	S	9	0	9	0.00011
Bacteroides vulgatus	821	S	4988	2572	7560	0.08644
Parabacteroides distasonis	823	S	102	179	281	0.00322
Blautia hansenii	1322	S	154	26	180	0.00207
Campylobacter coli	195	S	7	0	7	0.00008
Streptococcus anginosus	1328	S	9	0	9	0.00011
Bacteroides coprosuis	151276	S	124	3	127	0.00145
Porphyromonas gingivalis	837	S	23	3	26	0.00030
Haemophilus influenzae	727	S	13	2	15	0.00018
[Clostridium] saccharolyticum	84030	S	58	1	59	0.00068
Prevotella ruminicola	839	S	446	13	459	0.00525
Leptotrichia sp. oral taxon 847	1785996	S	9	0	9	0.00010
[Eubacterium] hallii	39488	S	1076	72	1148	0.01313
Prevotella denticola	28129	S	78	60	138	0.00159
Faecalitalea cylindroides	39483	S	310	98	408	0.00467
Ruminococcus champanellensis	1161942	S	27	0	27	0.00031
[Eubacterium] eligens	39485	S	40768	1564	42332	0.48403
Streptococcus intermedius	1338	S	12	7	19	0.00022
Prevotella enoeca	76123	S	170	145	315	0.00361
Christensenella massiliensis	1805714	S	9	0	9	0.00011
Fermentimonas caenicola	1562970	S	16	0	16	0.00019
Gramella flava	1486245	S	50	1	51	0.00059
Oxalobacter formigenes	847	S	8	3	11	0.00013
Desulfovibrio piger	901	S	16	3	19	0.00023
Megasphaera elsdenii	907	S	229	13	242	0.00277
Acidaminococcus fermentans	905	S	5	1	6	0.00007
Clostridium sp. SY8519	1042156	S	19	0	19	0.00022
Spirosoma aerolatum	1211326	S	8	0	8	0.00009
Marivirga tractuosa	1006	S	5	0	5	0.00006
[Eubacterium] rectale	39491	S	12019	861	12880	0.14728
Paludibacter propionicigenes	185300	S	6	0	6	0.00007
Flavonifractor plautii	292800	S	40	1	41	0.00048
Lachnoclostridium phocaeense	1871021	S	43	2	45	0.00052
Clostridium chauvoei	46867	S	7	0	7	0.00009
Barnesiella viscericola	397865	S	107	26	133	0.00152
Fibrella aestuarina	651143	S	28	0	28	0.00033
Eubacterium limosum	1736	S	20	0	20	0.00023
Clostridium perfringens	1502	S	50	4	54	0.00063
Streptococcus lutetiensis	150055	S	5	13	18	0.00022
Alistipes finegoldii	214856	S	395	64	459	0.00526
Campylobacter jejuni	197	S	9	13	22	0.00025
Lactococcus lactis	1358	S	8	4	12	0.00014
Enterococcus faecium	1352	S	27	7	34	0.00039
Escherichia coli	562	S	27	33	60	0.00069
Lactobacillus gasseri	1596	S	11	0	11	0.00014
Clostridioides difficile	1496	S	173	43	216	0.00248
Lactobacillus ruminis	1623	S	48	1	49	0.00056
Lactobacillus salivarius	1624	S	190	29	219	0.00251
Oscillibacter valericigenes	351091	S	16	0	16	0.00018
Butyrivibrio proteoclasticus	43305	S	10	2	12	0.00014
Sphingobacterium sp. 21	743722	S	11	0	11	0.00013
Ruminococcus bicirculans	1160721	S	2338	83	2421	0.02769
Bacteroides cellulosilyticus	246787	S	888	79	967	0.01106
Streptococcus sp. FDAARGOS_192	1839799	S	6	8	14	0.00016
Haemophilus parainfluenzae	729	S	88	18	106	0.00122
Intestinimonas butyriciproducens	1297617	S	65	4	69	0.00079
Streptococcus pyogenes	1314	S	6	31	37	0.00042
Faecalibaculum rodentium	1702221	S	5	1	6	0.00008
Geobacter lovleyi	313985	S	5	1	6	0.00007
Alistipes shahii	328814	S	157	42	199	0.00228
Algoriphagus machipongonensis	388413	S	17	0	17	0.00020
Pseudoalteromonas rubra	43658	S	5	0	5	0.00006
Prevotella dentalis	52227	S	130	38	168	0.00193
Petrimonas mucosa	1642646	S	41	4	45	0.00051
Bifidobacterium longum	216816	S	22	21	43	0.00050
Bacteroides salanitronis	376805	S	90	11	101	0.00116
Prevotella sp. oral taxon 299	652716	S	515	296	811	0.00928
Bacteroides dorei	357276	S	292	102	394	0.00451
Bifidobacterium adolescentis	1680	S	9	0	9	0.00011
Bacteroides ovatus	28116	S	798	51	849	0.00971
Bifidobacterium breve	1685	S	5	3	8	0.00009
Odoribacter splanchnicus	28118	S	1360	263	1623	0.01856