name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Streptococcus salivarius	1304	S	50	14	64	0.00047
Streptococcus suis	1307	S	39	38	77	0.00056
Anaerostipes hadrus	649756	S	2278	462	2740	0.02000
Turicibacter sp. H121	1712675	S	72	13	85	0.00062
Chryseobacterium gallinarum	1324352	S	466	67	533	0.00390
Citrobacter amalonaticus	35703	S	5	0	5	0.00004
Ruminococcus albus	1264	S	12	1	13	0.00010
Bacteroides helcogenes	290053	S	279	5	284	0.00208
Veillonella parvula	29466	S	180	17	197	0.00144
Capnocytophaga canimorsus	28188	S	5	4	9	0.00007
Methanobrevibacter smithii	2173	S	8341	62	8403	0.06132
Ethanoligenens harbinense	253239	S	6	7	13	0.00010
Clostridium scatologenes	1548	S	6	2	8	0.00006
Akkermansia muciniphila	239935	S	3633	32	3665	0.02674
Bacteroides thetaiotaomicron	818	S	1145	120	1265	0.00923
Parabacteroides sp. CT06	2025876	S	956	2517	3473	0.02535
Prevotella scopos	589437	S	26	30	56	0.00041
Prevotella fusca	589436	S	7	3	10	0.00008
Bacteroides fragilis	817	S	620	325	945	0.00690
Solitalea canadensis	995	S	8	0	8	0.00006
Flavonifractor plautii	292800	S	73	4	77	0.00057
Lachnoclostridium sp. YL32	1834196	S	117	15	132	0.00097
Streptococcus agalactiae	1311	S	65	8	73	0.00054
Campylobacter hominis	76517	S	6	0	6	0.00004
Bacteroides salanitronis	376805	S	2020	144	2164	0.01579
Adlercreutzia equolifaciens	446660	S	10	0	10	0.00008
Clostridium botulinum	1491	S	25	37	62	0.00046
Clostridium butyricum	1492	S	52	3	55	0.00040
Paraphotobacterium marinum	1755811	S	6	0	6	0.00004
Clostridium cochlearium	1494	S	36	7	43	0.00032
Clostridioides difficile	1496	S	509	259	768	0.00561
Paenibacillus sp. LPB0068	1763538	S	7	10	17	0.00013
Olsenella sp. Marseille-P2300	1805478	S	5	1	6	0.00005
[Clostridium] bolteae	208479	S	626	97	723	0.00528
Riemerella anatipestifer	34085	S	7	0	7	0.00006
Bifidobacterium pseudocatenulatum	28026	S	18	1	19	0.00014
Herbinix luporum	1679721	S	21	3	24	0.00018
[Eubacterium] cellulosolvens	29322	S	22	0	22	0.00016
Mageeibacillus indolicus	884684	S	7	1	8	0.00006
Prevotella melaninogenica	28132	S	135	158	293	0.00214
Prevotella intermedia	28131	S	48	17	65	0.00048
Phoenicibacter massiliensis	1944646	S	15	0	15	0.00011
Clostridium sp. SY8519	1042156	S	143	7	150	0.00110
Clostridium bornimense	1216932	S	13	1	14	0.00011
Parabacteroides distasonis	823	S	1132	2466	3598	0.02626
Blautia hansenii	1322	S	751	124	875	0.00639
Bacillus clausii	79880	S	5	0	5	0.00004
Coriobacteriaceae bacterium 68-1-3	1531429	S	5	1	6	0.00004
Tannerella sp. oral taxon HOT-286	712710	S	10	0	10	0.00007
Campylobacter coli	195	S	48	61	109	0.00080
Streptococcus anginosus	1328	S	31	19	50	0.00037
Flavobacterium johnsoniae	986	S	9	1	10	0.00007
Proteus mirabilis	584	S	24	45	69	0.00051
Parabacteroides phage YZ-2015b	1655645	S	7	0	7	0.00005
Treponema brennaborense	81028	S	6	0	6	0.00004
Roseburia hominis	301301	S	11898	2648	14546	0.10615
Micavibrio aeruginosavorus	349221	S	5	3	8	0.00007
Bacteroides caecimuris	1796613	S	504	92	596	0.00435
Fibrobacter succinogenes	833	S	5	0	5	0.00004
Butyrivibrio hungatei	185008	S	11	3	14	0.00011
Prevotella sp. oral taxon 299	652716	S	14	4	18	0.00013
[Clostridium] saccharolyticum	84030	S	93	4	97	0.00071
Prevotella ruminicola	839	S	100	1	101	0.00074
Human endogenous retrovirus K	45617	S	6	0	6	0.00004
[Eubacterium] hallii	39488	S	1844	281	2125	0.01551
Clostridium beijerinckii	1520	S	9	1	10	0.00008
Prevotella denticola	28129	S	45	17	62	0.00046
Bacillus coagulans	1398	S	14	1	15	0.00012
Faecalitalea cylindroides	39483	S	901	656	1557	0.01136
Ruminococcus champanellensis	1161942	S	114	21	135	0.00099
[Eubacterium] eligens	39485	S	7692	649	8341	0.06086
Elizabethkingia genomosp. 4	1756150	S	10	5	15	0.00011
Streptococcus intermedius	1338	S	8	9	17	0.00013
Prevotella enoeca	76123	S	49	21	70	0.00051
Christensenella massiliensis	1805714	S	192	19	211	0.00155
Fermentimonas caenicola	1562970	S	7	1	8	0.00006
Burkholderiales bacterium YL45	1834205	S	6	18	24	0.00018
Desulfovibrio piger	901	S	8	4	12	0.00009
Acidaminococcus fermentans	905	S	7	5	12	0.00009
Bacteroides vulgatus	821	S	3502	2903	6405	0.04674
Bifidobacterium kashiwanohense	630129	S	9	1	10	0.00007
Clostridium kluyveri	1534	S	6	0	6	0.00005
Clostridium tetani	1513	S	5	0	5	0.00004
Bacillus thuringiensis	1428	S	10	17	27	0.00020
Treponema sp. OMZ 838	1539298	S	6	0	6	0.00004
[Eubacterium] rectale	39491	S	13493	1827	15320	0.11179
Paludibacter propionicigenes	185300	S	12	0	12	0.00009
Klebsiella pneumoniae	573	S	50	157	207	0.00151
Bacteroides caccae	47678	S	7233	264	7497	0.05471
Lachnoclostridium phocaeense	1871021	S	266	30	296	0.00217
Libanicoccus massiliensis	1871022	S	7	3	10	0.00008
Streptococcus pasteurianus	197614	S	6	2	8	0.00006
Streptococcus acidominimus	1326	S	24	1	25	0.00019
Clostridium chauvoei	46867	S	30	2	32	0.00024
Murdochiella vaginalis	1852373	S	52	22	74	0.00054
Clostridium perfringens	1502	S	233	18	251	0.00184
Ornithobacterium rhinotracheale	28251	S	65	339	404	0.00295
Weissella ceti	759620	S	7	0	7	0.00005
Hymenobacter sp. DG25B	1385664	S	6	2	8	0.00006
Eggerthella lenta	84112	S	11	1	12	0.00009
Eubacterium limosum	1736	S	49	1	50	0.00037
Barnesiella viscericola	397865	S	703	106	809	0.00590
Clostridium pasteurianum	1501	S	7	0	7	0.00005
Eggerthella sp. YY7918	502558	S	13	1	14	0.00011
[Eubacterium] sulci	143393	S	6	0	6	0.00005
Alistipes finegoldii	214856	S	886	188	1074	0.00784
Campylobacter jejuni	197	S	108	72	180	0.00132
Enterococcus faecium	1352	S	98	64	162	0.00118
Escherichia coli	562	S	19	18	37	0.00027
Prochlorococcus marinus	1219	S	5	7	12	0.00009
Clostridium carboxidivorans	217159	S	6	2	8	0.00006
Lactobacillus ruminis	1623	S	5	1	6	0.00004
Anaerolineaceae bacterium oral taxon 439	1889813	S	14	0	14	0.00010
Oscillibacter valericigenes	351091	S	33	0	33	0.00024
Butyrivibrio proteoclasticus	43305	S	16	3	19	0.00015
Ruminococcus bicirculans	1160721	S	237	95	332	0.00243
Flavobacterium gilvum	1492737	S	30	1	31	0.00023
Bacteroides cellulosilyticus	246787	S	9101	576	9677	0.07061
Filimonas lacunae	477680	S	5	0	5	0.00004
Clostridium saccharobutylicum	169679	S	8	0	8	0.00006
Haemophilus parainfluenzae	729	S	16	2	18	0.00013
Endomicrobium proavitum	1408281	S	5	3	8	0.00006
Intestinimonas butyriciproducens	1297617	S	305	32	337	0.00246
uncultured crAssphage	1211417	S	631	0	631	0.00460
Filifactor alocis	143361	S	5	1	6	0.00005
Treponema denticola	158	S	488	827	1315	0.00960
Enterobacter cloacae	550	S	118	302	420	0.00307
BeAn 58058 virus	67082	S	30	0	30	0.00022
Streptococcus pyogenes	1314	S	96	338	434	0.00317
Caulobacter sp. K31	366602	S	5	19	24	0.00018
Clostridium sp. BNL1100	755731	S	8	1	9	0.00007
Alistipes shahii	328814	S	2439	698	3137	0.02289
Lachnoclostridium phytofermentans	66219	S	12	0	12	0.00009
Prevotella dentalis	52227	S	79	13	92	0.00067
Clostridium baratii	1561	S	21	1	22	0.00017
Proteiniphilum saccharofermentans	1642647	S	5	0	5	0.00004
Ruminococcaceae bacterium CPB6	1572656	S	6	10	16	0.00012
Bifidobacterium longum	216816	S	112	122	234	0.00171
Streptococcus parasanguinis	1318	S	12	0	12	0.00009
[Clostridium] cellulosi	29343	S	5	4	9	0.00007
Clostridium argentinense	29341	S	5	0	5	0.00004
Megamonas hypermegale	158847	S	12	0	12	0.00009
Lactobacillus agilis	1601	S	5	4	9	0.00007
Bacteroides dorei	357276	S	10372	3806	14178	0.10345
Bifidobacterium bifidum	1681	S	5	1	6	0.00004
Bifidobacterium adolescentis	1680	S	7	0	7	0.00005
Bacteroides ovatus	28116	S	2704	195	2899	0.02115
Bifidobacterium breve	1685	S	22	17	39	0.00029
Tannerella forsythia	28112	S	20	5	25	0.00019
Enterobacter ludwigii	299767	S	6	24	30	0.00022
Odoribacter splanchnicus	28118	S	9761	775	10536	0.07688