name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Streptococcus salivarius	1304	S	62	35	97	0.00059
Streptococcus sanguinis	1305	S	7	0	7	0.00005
Streptococcus suis	1307	S	22	18	40	0.00025
Anaerostipes hadrus	649756	S	2667	298	2965	0.01800
Turicibacter sp. H121	1712675	S	15	1	16	0.00010
Finegoldia magna	1260	S	6	0	6	0.00004
Streptococcus thermophilus	1308	S	47	11	58	0.00036
Cyclobacterium amurskyense	320787	S	8	3	11	0.00007
Heliobacterium modesticaldum	35701	S	8	0	8	0.00005
Arcanobacterium phocae	131112	S	8	0	8	0.00005
Bacteroides helcogenes	290053	S	205	3	208	0.00126
Mucilaginibacter mallensis	652787	S	8	0	8	0.00005
Methanobrevibacter smithii	2173	S	4024	21	4045	0.02455
Bacteroides thetaiotaomicron	818	S	7830	698	8528	0.05175
Acidaminococcus intestini	187327	S	7	5	12	0.00008
Parabacteroides sp. CT06	2025876	S	638	1636	2274	0.01380
Prevotella scopos	589437	S	114	246	360	0.00218
Prevotella fusca	589436	S	110	115	225	0.00137
Parvimonas micra	33033	S	6	0	6	0.00004
Bacteroides fragilis	817	S	432	88	520	0.00316
Chryseobacterium gallinarum	1324352	S	199	12	211	0.00128
Bacteroides caccae	47678	S	1894	55	1949	0.01183
Lachnoclostridium sp. YL32	1834196	S	73	10	83	0.00051
Streptococcus agalactiae	1311	S	11	1	12	0.00008
Streptococcus parasanguinis	1318	S	60	5	65	0.00040
Adlercreutzia equolifaciens	446660	S	7	3	10	0.00007
Clostridium botulinum	1491	S	12	23	35	0.00021
Bacteroides dorei	357276	S	15845	4439	20284	0.12308
Methanolacinia petrolearia	54120	S	5	0	5	0.00003
Clostridium cochlearium	1494	S	12	6	18	0.00011
Bacteroides caecimuris	1796613	S	1013	124	1137	0.00690
Ruminococcus albus	1264	S	15	3	18	0.00011
Akkermansia muciniphila	239935	S	15	0	15	0.00009
[Clostridium] bolteae	208479	S	682	113	795	0.00483
Pseudomonas salegens	1434072	S	10	3	13	0.00008
Riemerella anatipestifer	34085	S	11	2	13	0.00008
Methanosphaera stadtmanae	2317	S	119	0	119	0.00072
Herbinix luporum	1679721	S	9	0	9	0.00006
Clostridium aceticum	84022	S	6	1	7	0.00005
[Eubacterium] cellulosolvens	29322	S	55	0	55	0.00034
Mageeibacillus indolicus	884684	S	8	2	10	0.00006
Prevotella melaninogenica	28132	S	107	235	342	0.00208
Prevotella intermedia	28131	S	251	173	424	0.00258
Owenweeksia hongkongensis	253245	S	12	0	12	0.00007
Bacteroides vulgatus	821	S	18869	7378	26247	0.15926
Clostridium bornimense	1216932	S	10	1	11	0.00007
Clostridium saccharoperbutylacetonicum	36745	S	7	2	9	0.00006
Blautia hansenii	1322	S	317	80	397	0.00241
Tannerella sp. oral taxon HOT-286	712710	S	10	0	10	0.00006
Campylobacter coli	195	S	29	8	37	0.00022
Streptococcus anginosus	1328	S	15	2	17	0.00011
Roseburia hominis	301301	S	4071	517	4588	0.02784
Streptococcus infantarius	102684	S	11	45	56	0.00034
Clostridium acetobutylicum	1488	S	6	0	6	0.00004
Butyrivibrio hungatei	185008	S	10	5	15	0.00009
Methanobrevibacter sp. YE315	1609968	S	8	0	8	0.00005
Prevotella sp. oral taxon 299	652716	S	24	12	36	0.00022
[Clostridium] saccharolyticum	84030	S	224	5	229	0.00139
Prevotella ruminicola	839	S	300	6	306	0.00186
[Eubacterium] hallii	39488	S	2265	174	2439	0.01480
Clostridium beijerinckii	1520	S	9	4	13	0.00008
Prevotella denticola	28129	S	181	129	310	0.00189
Bacillus cereus	1396	S	9	15	24	0.00015
Faecalitalea cylindroides	39483	S	435	129	564	0.00343
Ruminococcus champanellensis	1161942	S	36	7	43	0.00027
[Eubacterium] eligens	39485	S	9715	390	10105	0.06132
Paenibacillus polymyxa	1406	S	12	6	18	0.00011
Streptococcus intermedius	1338	S	20	19	39	0.00024
Prevotella enoeca	76123	S	144	111	255	0.00155
Christensenella massiliensis	1805714	S	37	2	39	0.00024
Fermentimonas caenicola	1562970	S	18	0	18	0.00011
Gramella flava	1486245	S	16	0	16	0.00010
Megasphaera elsdenii	907	S	6	1	7	0.00005
Clostridium sp. SY8519	1042156	S	164	5	169	0.00103
Clostridium kluyveri	1534	S	8	0	8	0.00005
Parabacteroides distasonis	823	S	435	792	1227	0.00745
[Eubacterium] rectale	39491	S	53421	3582	57003	0.34589
Paludibacter propionicigenes	185300	S	11	0	11	0.00007
Klebsiella pneumoniae	573	S	7	26	33	0.00020
Flavonifractor plautii	292800	S	57	4	61	0.00037
Lachnoclostridium phocaeense	1871021	S	159	10	169	0.00103
Streptococcus pasteurianus	197614	S	17	12	29	0.00018
Acholeplasma palmae	38986	S	6	2	8	0.00005
Murdochiella vaginalis	1852373	S	9	2	11	0.00007
Barnesiella viscericola	397865	S	125	10	135	0.00082
Ornithobacterium rhinotracheale	28251	S	12	41	53	0.00032
Fusobacterium nucleatum	851	S	9	3	12	0.00007
Sphaerobacter thermophilus	2057	S	7	0	7	0.00004
Peptoclostridium acidaminophilum	1731	S	15	0	15	0.00009
Listeria monocytogenes	1639	S	5	1	6	0.00004
Cellulophaga lytica	979	S	9	0	9	0.00006
Eubacterium limosum	1736	S	19	0	19	0.00012
Clostridium perfringens	1502	S	10	2	12	0.00008
Campylobacter pinnipediorum	1965231	S	6	0	6	0.00004
Eggerthella sp. YY7918	502558	S	5	2	7	0.00004
Alistipes finegoldii	214856	S	292	39	331	0.00201
Campylobacter jejuni	197	S	15	9	24	0.00015
Lactococcus lactis	1358	S	23	12	35	0.00021
Enterococcus faecium	1352	S	127	30	157	0.00096
Escherichia coli	562	S	16	22	38	0.00023
Clostridium carboxidivorans	217159	S	8	12	20	0.00012
Clostridioides difficile	1496	S	210	85	295	0.00180
Lactobacillus ruminis	1623	S	53	7	60	0.00037
Oscillibacter valericigenes	351091	S	30	0	30	0.00018
Butyrivibrio proteoclasticus	43305	S	17	6	23	0.00015
Bacillus sp. 1NLA3E	666686	S	5	0	5	0.00003
Ruminococcus bicirculans	1160721	S	62	37	99	0.00060
Bacteroides cellulosilyticus	246787	S	226	8	234	0.00142
Streptococcus sp. FDAARGOS_192	1839799	S	6	9	15	0.00010
Clostridium saccharobutylicum	169679	S	7	2	9	0.00006
Haemophilus parainfluenzae	729	S	15	3	18	0.00011
Intestinimonas butyriciproducens	1297617	S	160	16	176	0.00107
uncultured crAssphage	1211417	S	290	0	290	0.00176
Treponema denticola	158	S	61	137	198	0.00121
Streptococcus pyogenes	1314	S	5	23	28	0.00017
Oceanisphaera profunda	1416627	S	9	1	10	0.00006
Faecalibaculum rodentium	1702221	S	8	1	9	0.00006
Clostridium sp. BNL1100	755731	S	5	0	5	0.00003
Alistipes shahii	328814	S	141	24	165	0.00100
Lachnoclostridium phytofermentans	66219	S	11	0	11	0.00007
Prevotella dentalis	52227	S	63	14	77	0.00047
Clostridium baratii	1561	S	17	4	21	0.00013
Petrimonas mucosa	1642646	S	11	0	11	0.00007
Bacteroides coprosuis	151276	S	160	1	161	0.00098
Bifidobacterium longum	216816	S	34	35	69	0.00042
Bacteroides salanitronis	376805	S	183	7	190	0.00116
Arcobacter butzleri	28197	S	5	1	6	0.00004
Clostridium butyricum	1492	S	14	2	16	0.00010
Bifidobacterium bifidum	1681	S	7	1	8	0.00005
Bacteroides ovatus	28116	S	9085	560	9645	0.05853
Bifidobacterium breve	1685	S	7	3	10	0.00007
Tannerella forsythia	28112	S	6	4	10	0.00006
Odoribacter splanchnicus	28118	S	2196	125	2321	0.01409