name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Homo sapiens	128919	S	1430725	0	1430725	0.75096
s__Escherichia coli_D	3231	S	156422	33922	190344	0.09991
s__Escherichia sp000208585	3232	S	40	1	41	0.00002
s__Escherichia albertii	3234	S	21	0	21	0.00001
s__Escherichia marmotae	3233	S	11	0	11	0.00001
s__Citrobacter freundii	3258	S	360	46	406	0.00021
s__Citrobacter youngae	3261	S	10	0	10	0.00001
s__Klebsiella pneumoniae	3228	S	242	105	347	0.00018
s__Klebsiella variicola	3229	S	43	6	49	0.00003
s__Salmonella enterica	3319	S	263	3	266	0.00014
s__Enterobacter hormaechei_A	3248	S	171	12	183	0.00010
s__Enterobacter ludwigii	3278	S	30	1	31	0.00002
s__Enterobacter cloacae	3240	S	12	0	12	0.00001
s__Enterobacter roggenkampii	3237	S	10	0	10	0.00001
s__Serratia marcescens_K	3289	S	146	0	146	0.00008
s__Pseudescherichia sp002298805	3344	S	105	0	105	0.00006
s__Pantoea septica	3283	S	69	0	69	0.00004
s__Morganella morganii_A	3255	S	13	0	13	0.00001
s__Raoultella ornithinolytica	3247	S	10	0	10	0.00001
s__Haemophilus_D parainfluenzae	3216	S	1173	1086	2259	0.00119
s__Haemophilus_D parainfluenzae_K	3213	S	185	158	343	0.00018
s__Haemophilus_D sp900755445	3217	S	144	84	228	0.00012
s__Haemophilus_D parainfluenzae_J	3225	S	20	3	23	0.00001
s__Unknown_1754	3218	S	15	26	41	0.00002
s__Haemophilus_D sp900756875	3214	S	14	9	23	0.00001
s__Haemophilus_D parainfluenzae_M	3223	S	11	4	15	0.00001
s__Aggregatibacter segnis	3311	S	13	0	13	0.00001
s__Parasutterella excrementihominis	2152	S	55	12	67	0.00004
s__Comamonas kerstersii	2190	S	11	0	11	0.00001
s__Sphingomonas yabuuchiae	6085	S	668	1	669	0.00035
s__51-20 sp001917175	4901	S	27	1	28	0.00001
s__Lachnospira rogosae_A	3539	S	3362	3252	6614	0.00347
s__Lachnospira sp000436535	3691	S	2966	1027	3993	0.00210
s__Lachnospira sp900316325	3510	S	1280	526	1806	0.00095
s__Lachnospira eligens_A	3513	S	1233	2046	3279	0.00172
s__Lachnospira sp000437735	3607	S	760	259	1019	0.00053
s__Lachnospira sp900551945	3828	S	60	5	65	0.00003
s__Lachnospira sp000436475	3547	S	53	18	71	0.00004
s__Lachnospira sp003537285	3514	S	17	29	46	0.00002
s__Roseburia inulinivorans	3591	S	7454	10108	17562	0.00922
s__Roseburia intestinalis	3681	S	1208	2261	3469	0.00182
s__Roseburia sp003470905	3680	S	230	190	420	0.00022
s__Roseburia hominis	3528	S	178	75	253	0.00013
s__Roseburia sp900542495	3592	S	90	45	135	0.00007
s__Agathobacter rectalis	3541	S	3870	2938	6808	0.00357
s__Agathobacter faecis	3574	S	1985	2704	4689	0.00246
s__Agathobacter sp900546625	3542	S	15	10	25	0.00001
s__CAG-81 sp900066535	3675	S	3245	2924	6169	0.00324
s__CAG-81 sp900541255	3838	S	111	1	112	0.00006
s__CAG-81 sp900066785	3676	S	65	26	91	0.00005
s__CAG-81 sp900066055	3677	S	10	6	16	0.00001
s__Clostridium_Q sp003024715	3569	S	3169	1778	4947	0.00260
s__Clostridium_Q sp000435655	3598	S	127	14	141	0.00007
s__Clostridium_Q symbiosum	3663	S	30	3	33	0.00002
s__UBA9502 sp003478505	3825	S	1313	522	1835	0.00096
s__UBA9502 sp003506385	3883	S	1235	395	1630	0.00086
s__UBA9502 sp003480315	3826	S	62	18	80	0.00004
s__UBA9502 sp003481825	3882	S	27	7	34	0.00002
s__UBA9502 sp900538475	3780	S	13	2	15	0.00001
s__Enterocloster sp900541315	3544	S	1302	487	1789	0.00094
s__Enterocloster sp900543885	3545	S	655	121	776	0.00041
s__Enterocloster sp001517625	3576	S	175	80	255	0.00013
s__Enterocloster aldenensis	3803	S	92	12	104	0.00005
s__Enterocloster sp000431375	3543	S	79	59	138	0.00007
s__Enterocloster bolteae	3643	S	64	15	79	0.00004
s__Enterocloster citroniae	3872	S	44	2	46	0.00002
s__Enterocloster lavalensis	3878	S	29	0	29	0.00002
s__Eisenbergiella sp900066775	3520	S	2510	964	3474	0.00182
s__Acetatifactor sp900066565	3553	S	1511	2258	3769	0.00198
s__Acetatifactor sp900066365	3552	S	69	93	162	0.00009
s__Acetatifactor sp003447295	3554	S	12	7	19	0.00001
s__CAG-882 sp003486385	3617	S	1974	310	2284	0.00120
s__Anaerostipes hadrus	3523	S	1189	719	1908	0.00100
s__UBA7182 sp003480725	3874	S	1105	221	1326	0.00070
s__UBA7182 sp003481535	3864	S	12	3	15	0.00001
s__TF01-11 sp001414325	3674	S	761	130	891	0.00047
s__TF01-11 sp003529475	3614	S	87	16	103	0.00005
s__TF01-11 sp000436755	3672	S	19	1	20	0.00001
s__Blautia_A wexlerae_A	3683	S	280	634	914	0.00048
s__Blautia_A obeum	3697	S	155	129	284	0.00015
s__Blautia_A faecis	3705	S	148	88	236	0.00012
s__Blautia_A sp000436615	3715	S	57	25	82	0.00004
s__Blautia_A sp003471165	3684	S	43	32	75	0.00004
s__Blautia_A massiliensis	3629	S	21	13	34	0.00002
s__Blautia_A sp900066145	3788	S	13	2	15	0.00001
s__Eubacterium_F sp003491505	3568	S	531	100	631	0.00033
s__Eubacterium_F sp900539115	3775	S	22	2	24	0.00001
s__Mediterraneibacter faecis	3698	S	415	269	684	0.00036
s__Mediterraneibacter lactaris	3597	S	53	38	91	0.00005
s__Mediterraneibacter torques	3521	S	26	25	51	0.00003
s__Fusicatenibacter saccharivorans	3517	S	406	559	965	0.00051
s__Dorea_A longicatena_B	3692	S	284	266	550	0.00029
s__Dorea_A longicatena	3693	S	20	22	42	0.00002
s__Blautia stercoris	3546	S	362	37	399	0.00021
s__Blautia hansenii	3717	S	20	5	25	0.00001
s__Dorea formicigenerans	3873	S	218	91	309	0.00016
s__Coprococcus eutactus	3619	S	110	60	170	0.00009
s__Coprococcus eutactus_A	3618	S	26	14	40	0.00002
s__Coprococcus sp900066115	3609	S	18	9	27	0.00001
s__KLE1615 sp900066985	3532	S	160	29	189	0.00010
s__Anaerobutyricum soehngenii	3734	S	128	54	182	0.00010
s__Anaerobutyricum hallii	3548	S	15	8	23	0.00001
s__UMGS1375 sp900066615	3529	S	119	53	172	0.00009
s__CAG-510 sp000434615	3724	S	102	5	107	0.00006
s__RUG115 sp900066395	3624	S	101	21	122	0.00006
s__Eubacterium_G sp000435815	3565	S	55	9	64	0.00003
s__Eubacterium_G ventriosum	3566	S	27	8	35	0.00002
s__Eubacterium_I ramulus_A	3603	S	87	19	106	0.00006
s__Frisingicoccus caecimuris	3810	S	89	1	90	0.00005
s__Bariatricus comes	3690	S	80	64	144	0.00008
s__Ruminococcus_B gnavus	3719	S	63	61	124	0.00007
s__CAG-127 sp900319515	3533	S	52	29	81	0.00004
s__CAG-603 sp900066105	3751	S	56	0	56	0.00003
s__Ruminococcus_A faecicola	3615	S	21	2	23	0.00001
s__Ruminococcus_A sp003011855	3616	S	11	3	14	0.00001
s__GCA-900066135 sp900543575	3522	S	27	2	29	0.00002
s__1XD42-69 sp014287635	3913	S	26	3	29	0.00002
s__Lachnoclostridium_B phocaeensis	3926	S	21	0	21	0.00001
s__Hungatella effluvii	3799	S	18	1	19	0.00001
s__Unknown_2442	3582	S	19	0	19	0.00001
s__CAG-95 sp000438155	3740	S	11	1	12	0.00001
s__COE1 sp001916965	3738	S	11	2	13	0.00001
s__Schaedlerella sp900066545	3599	S	10	2	12	0.00001
s__UBA3402 sp003478355	3820	S	12	1	13	0.00001
s__Butyrivibrio_A crossotus	3742	S	10	1	11	0.00001
s__UBA11774 sp003507655	3509	S	12	1	13	0.00001
s__Sellimonas intestinalis	3650	S	10	0	10	0.00001
s__Anaerotignum sp001304995	3652	S	298	19	317	0.00017
s__UMGS1670 sp900553995	3891	S	218	4	222	0.00012
s__Unknown_2445	3952	S	27	0	27	0.00001
s__CAG-274 sp900545305	3570	S	15	9	24	0.00001
s__Faecalibacterium prausnitzii	4190	S	13006	15612	28618	0.01502
s__Faecalibacterium prausnitzii_E	4255	S	2473	776	3249	0.00171
s__Faecalibacterium prausnitzii_D	4326	S	1732	2749	4481	0.00235
s__Faecalibacterium prausnitzii_C	4177	S	1552	1017	2569	0.00135
s__Faecalibacterium prausnitzii_G	4303	S	1143	795	1938	0.00102
s__Faecalibacterium sp900539945	4362	S	919	846	1765	0.00093
s__Faecalibacterium prausnitzii_J	4191	S	130	222	352	0.00018
s__Faecalibacterium prausnitzii_I	4344	S	46	12	58	0.00003
s__Faecalibacterium sp900539885	4327	S	13	6	19	0.00001
s__Faecalibacterium prausnitzii_H	4357	S	11	2	13	0.00001
s__Faecalibacterium sp003449675	4202	S	11	5	16	0.00001
s__Faecalibacterium sp900765705	4203	S	10	2	12	0.00001
s__Gemmiger qucibialis	4176	S	1870	918	2788	0.00146
s__Gemmiger formicilis	4252	S	34	16	50	0.00003
s__Gemmiger sp900539695	4257	S	20	6	26	0.00001
s__Ruminococcus_C sp000980705	4223	S	144	49	193	0.00010
s__Ruminococcus_C sp000433635	4330	S	51	6	57	0.00003
s__Ruminococcus_C callidus	4259	S	10	2	12	0.00001
s__Ruminococcus_D bicirculans	4247	S	200	38	238	0.00012
s__Ruthenibacterium lactatiformans	4205	S	86	26	112	0.00006
s__Ruthenibacterium sp900546885	4379	S	16	0	16	0.00001
s__Negativibacillus sp000435195	4278	S	84	4	88	0.00005
s__UMGS966 sp900547185	4722	S	44	1	45	0.00002
s__QANG01 sp003150145	5959	S	12	4	16	0.00001
s__Unknown_4505	5951	S	11	5	16	0.00001
s__CAG-115 sp003531585	4329	S	18	6	24	0.00001
s__Ruminiclostridium_E siraeum	4182	S	15	1	16	0.00001
s__Anaerotruncus colihominis	4656	S	10	0	10	0.00001
s__Ruminococcus_E bromii_B	4211	S	964	814	1778	0.00093
s__Ruminococcus_E sp003526955	4209	S	14	10	24	0.00001
s__Eubacterium_R sp000436835	4258	S	1030	224	1254	0.00066
s__UMGS1071 sp900541905	4225	S	251	28	279	0.00015
s__CAG-180 sp000432435	4187	S	61	15	76	0.00004
s__CAG-177 sp003514385	4206	S	15	1	16	0.00001
s__Agathobaculum sp003481705	4245	S	1370	317	1687	0.00089
s__Agathobaculum butyriciproducens	4229	S	1099	194	1293	0.00068
s__Butyricicoccus pullicaecorum	4463	S	92	3	95	0.00005
s__Flavonifractor plautii	4250	S	622	312	934	0.00049
s__Lawsonibacter sp900066825	4231	S	242	118	360	0.00019
s__Lawsonibacter asaccharolyticus	4500	S	18	4	22	0.00001
s__Unknown_3154	4546	S	82	12	94	0.00005
s__Dysosmobacter welbionis	4178	S	66	52	118	0.00006
s__Unknown_2963	4541	S	12	0	12	0.00001
s__ER4 sp000765235	4272	S	79	46	125	0.00007
s__CAG-110 sp900544405	4503	S	30	0	30	0.00002
s__CAG-110 sp000434635	4306	S	28	7	35	0.00002
s__CAG-83 sp000435555	4348	S	11	3	14	0.00001
s__CAG-83 sp000431575	4230	S	10	2	12	0.00001
s__Evtepia sp900546255	4459	S	22	0	22	0.00001
s__CAG-448 sp003150135	4345	S	13	0	13	0.00001
s__CAG-245 sp000435175	5121	S	491	206	697	0.00037
s__CAG-269 sp003525075	5119	S	12	3	15	0.00001
s__CAG-273 sp000438355	5129	S	16	3	19	0.00001
s__Romboutsia timonensis	4830	S	160	35	195	0.00010
s__CAG-41 sp900066215	4109	S	94	41	135	0.00007
s__Fenollaria massiliensis	5258	S	32	1	33	0.00002
s__Fenollaria sp900539225	5252	S	12	0	12	0.00001
s__Clostridium sp900540255	2426	S	11	2	13	0.00001
s__UBA5394 sp003150565	2273	S	39	0	39	0.00002
s__UBA11524 sp000437595	2251	S	28	1	29	0.00002
s__Phocaeicola dorei	1673	S	19057	62519	81576	0.04282
s__Phocaeicola plebeius_A	1668	S	95	83	178	0.00009
s__Phocaeicola coprocola	1676	S	89	27	116	0.00006
s__Phocaeicola massiliensis	1853	S	32	19	51	0.00003
s__Phocaeicola plebeius	1669	S	23	14	37	0.00002
s__Phocaeicola coprophilus	1756	S	20	2	22	0.00001
s__Bacteroides ovatus	1679	S	5359	9364	14723	0.00773
s__Bacteroides fragilis	1776	S	3052	1216	4268	0.00224
s__Bacteroides uniformis	1658	S	2811	4339	7150	0.00375
s__Bacteroides xylanisolvens	1680	S	561	954	1515	0.00080
s__Bacteroides cellulosilyticus	1786	S	56	16	72	0.00004
s__Bacteroides stercoris	1651	S	40	16	56	0.00003
s__Bacteroides thetaiotaomicron	1794	S	33	18	51	0.00003
s__Bacteroides caccae	1799	S	27	18	45	0.00002
s__Bacteroides fragilis_A	1793	S	23	2	25	0.00001
s__Bacteroides sp900556215	1787	S	21	4	25	0.00001
s__Prevotella sp900557255	1732	S	191	75	266	0.00014
s__Prevotella sp900290275	1798	S	65	6	71	0.00004
s__Prevotella stercorea	1688	S	39	5	44	0.00002
s__Prevotella sp000436035	1855	S	36	4	40	0.00002
s__Prevotella copri_A	1770	S	33	10	43	0.00002
s__Unknown_0386	1697	S	29	1	30	0.00002
s__Prevotella sp002299635	1845	S	20	0	20	0.00001
s__Prevotella sp900543975	1784	S	20	0	20	0.00001
s__Prevotella sp003447235	1723	S	20	1	21	0.00001
s__Prevotella hominis	1852	S	19	3	22	0.00001
s__Prevotella lascolaii	1910	S	16	0	16	0.00001
s__Prevotella sp000436915	1838	S	15	1	16	0.00001
s__Prevotella timonensis	1913	S	11	0	11	0.00001
s__Prevotella sp900554695	1894	S	11	0	11	0.00001
s__Prevotella pectinovora	1764	S	11	0	11	0.00001
s__Paraprevotella clara	1654	S	34	5	39	0.00002
s__Paraprevotella sp003477995	2097	S	13	0	13	0.00001
s__Prevotellamassilia timonensis	1720	S	13	0	13	0.00001
s__Prevotellamassilia sp900539625	1719	S	12	0	12	0.00001
s__Alistipes putredinis	1656	S	55	62	117	0.00006
s__Alistipes onderdonkii	1678	S	31	27	58	0.00003
s__Alistipes shahii	1644	S	13	16	29	0.00002
s__Alistipes sp900550925	1989	S	11	0	11	0.00001
s__Barnesiella intestinihominis	1653	S	114	11	125	0.00007
s__Parabacteroides distasonis	1652	S	65	10	75	0.00004
s__Parabacteroides merdae	1660	S	31	20	51	0.00003
s__CAG-279 sp900544305	1924	S	38	1	39	0.00002
s__Sodaliphilus sp004557565	1801	S	31	0	31	0.00002
s__Odoribacter splanchnicus	1675	S	40	12	52	0.00003
s__Porphyromonas sp900538385	1751	S	10	3	13	0.00001
s__RC9 sp000435075	1765	S	13	4	17	0.00001
s__Coprobacter fastidiosus	1735	S	12	0	12	0.00001
s__Streptococcus salivarius	3957	S	2143	3402	5545	0.00291
s__Streptococcus thermophilus	3958	S	406	1451	1857	0.00097
s__Latilactobacillus sakei	3978	S	23	10	33	0.00002
s__Staphylococcus haemolyticus	5105	S	1148	945	2093	0.00110
s__Staphylococcus epidermidis	5103	S	298	539	837	0.00044
s__Faecalibacillus intestinalis	3362	S	682	6363	7045	0.00370
s__Longibaculum muris	3395	S	13	2	15	0.00001
s__Amedibacterium intestinale	3376	S	115	80	195	0.00010
s__Holdemanella sp002299315	3356	S	32	69	101	0.00005
s__Ureaplasma parvum	4156	S	53	2	55	0.00003
s__Dialister invisus	5326	S	1024	116	1140	0.00060
s__Dialister hominis	5305	S	10	1	11	0.00001
s__Veillonella rogosae	5347	S	41	8	49	0.00003
s__Veillonella atypica	5361	S	32	3	35	0.00002
s__Veillonella tobetsuensis	5362	S	20	3	23	0.00001
s__Veillonella dispar_A	5346	S	16	16	32	0.00002
s__Veillonella parvula_A	5327	S	15	5	20	0.00001
s__F0422 sp001553345	5374	S	21	0	21	0.00001
s__Acidaminococcus sp000437815	1540	S	72	2	74	0.00004
s__Phascolarctobacterium_A succinatutens	1517	S	27	5	32	0.00002
s__Phascolarctobacterium_A sp900551335	1543	S	15	0	15	0.00001
s__Phascolarctobacterium sp000436095	1516	S	14	1	15	0.00001
s__Megamonas funiformis	5089	S	20	2	22	0.00001
s__Anaerovibrio sp900548165	5093	S	10	0	10	0.00001
s__Bifidobacterium adolescentis	1567	S	245	349	594	0.00031
s__Bifidobacterium animalis	1570	S	175	19	194	0.00010
s__Bifidobacterium pseudocatenulatum	1585	S	31	35	66	0.00003
s__Bifidobacterium infantis	1566	S	20	34	54	0.00003
s__Nigerium massiliense	6015	S	21	0	21	0.00001
s__Cutibacterium acnes	4876	S	11	1	12	0.00001
s__Adlercreutzia celatus_A	3097	S	24	1	25	0.00001
s__Eggerthella lenta	3086	S	12	0	12	0.00001
s__Unknown_0665	2243	S	12	1	13	0.00001
s__Campylobacter_B sp900539505	2242	S	10	1	11	0.00001
s__Campylobacter_D coli	2227	S	11	1	12	0.00001
s__HGM08974 sp900766555	5593	S	35	0	35	0.00002
s__Bilophila wadsworthia	3183	S	28	4	32	0.00002
s__UMGS1590 sp900552455	4802	S	32	0	32	0.00002
s__Brachyspira aalborgi	2124	S	27	0	27	0.00001
Chlorovirus conductrix	107550	S	59	0	59	0.00003
s__Methanobrevibacter_A smithii	4083	S	10	13	23	0.00001