name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Streptococcus salivarius	1304	S	14	8	22	0.00009
Streptococcus suis	1307	S	36	38	74	0.00030
Anaerostipes hadrus	649756	S	5305	894	6199	0.02476
Turicibacter sp. H121	1712675	S	18	2	20	0.00008
Finegoldia magna	1260	S	8	0	8	0.00003
Streptococcus thermophilus	1308	S	27	5	32	0.00013
Ruminococcus albus	1264	S	21	1	22	0.00009
Bacteroides helcogenes	290053	S	1197	16	1213	0.00485
Streptococcus mitis	28037	S	5	1	6	0.00003
Clostridium novyi	1542	S	5	1	6	0.00002
Methanobrevibacter smithii	2173	S	304	4	308	0.00123
Ethanoligenens harbinense	253239	S	5	3	8	0.00004
Bacteroides thetaiotaomicron	818	S	21001	1356	22357	0.08928
Parabacteroides sp. CT06	2025876	S	1174	2485	3659	0.01461
Prevotella scopos	589437	S	8	6	14	0.00006
Bacteroides fragilis	817	S	3221	603	3824	0.01527
Flavonifractor plautii	292800	S	35	3	38	0.00016
Lachnoclostridium sp. YL32	1834196	S	106	12	118	0.00047
Streptococcus agalactiae	1311	S	22	2	24	0.00010
Bacteroides salanitronis	376805	S	533	19	552	0.00221
Clostridium botulinum	1491	S	21	23	44	0.00018
Clostridium butyricum	1492	S	13	1	14	0.00006
Clostridium cochlearium	1494	S	9	3	12	0.00005
Clostridioides difficile	1496	S	317	199	516	0.00206
[Clostridium] bolteae	208479	S	470	65	535	0.00214
Gottschalkia acidurici	1556	S	7	0	7	0.00003
Desulfovibrio fairfieldensis	44742	S	9	0	9	0.00004
Bifidobacterium pseudocatenulatum	28026	S	20	0	20	0.00008
Herbinix luporum	1679721	S	12	1	13	0.00005
[Eubacterium] cellulosolvens	29322	S	54	0	54	0.00022
Mageeibacillus indolicus	884684	S	9	1	10	0.00004
Prevotella melaninogenica	28132	S	5	4	9	0.00004
Prevotella intermedia	28131	S	134	34	168	0.00067
Phoenicibacter massiliensis	1944646	S	30	0	30	0.00012
Methanosphaera stadtmanae	2317	S	117	0	117	0.00047
Sebaldella termitidis	826	S	5	3	8	0.00003
Clostridium sp. SY8519	1042156	S	356	17	373	0.00149
Clostridium saccharoperbutylacetonicum	36745	S	8	3	11	0.00004
Blautia hansenii	1322	S	355	106	461	0.00184
Streptococcus acidominimus	1326	S	8	0	8	0.00004
Campylobacter coli	195	S	22	19	41	0.00017
Streptococcus anginosus	1328	S	78	11	89	0.00036
Microcystis aeruginosa	1126	S	5	1	6	0.00003
Parabacteroides phage YZ-2015b	1655645	S	11	0	11	0.00004
Roseburia hominis	301301	S	4036	971	5007	0.02000
Clostridium acetobutylicum	1488	S	5	0	5	0.00002
Bacteroides caecimuris	1796613	S	2678	317	2995	0.01196
Butyrivibrio hungatei	185008	S	23	10	33	0.00013
Prevotella sp. oral taxon 299	652716	S	23	4	27	0.00011
[Clostridium] saccharolyticum	84030	S	214	12	226	0.00090
Prevotella ruminicola	839	S	10	0	10	0.00004
[Eubacterium] hallii	39488	S	1837	264	2101	0.00839
Clostridium beijerinckii	1520	S	6	1	7	0.00003
[Clostridium] cellulolyticum	1521	S	6	1	7	0.00003
Bacillus cereus	1396	S	11	18	29	0.00012
Faecalitalea cylindroides	39483	S	416	183	599	0.00240
Ruminococcus champanellensis	1161942	S	71	5	76	0.00030
[Eubacterium] eligens	39485	S	5748	501	6249	0.02496
Porphyromonas asaccharolytica	28123	S	9	0	9	0.00004
Mobiluncus curtisii	2051	S	7	0	7	0.00003
Streptococcus intermedius	1338	S	9	9	18	0.00007
Christensenella massiliensis	1805714	S	47	4	51	0.00020
Fermentimonas caenicola	1562970	S	7	0	7	0.00003
Burkholderiales bacterium YL45	1834205	S	22	5	27	0.00011
Veillonella parvula	29466	S	7	0	7	0.00003
Prevotella denticola	28129	S	6	1	7	0.00003
Megasphaera elsdenii	907	S	10	2	12	0.00005
Acidaminococcus fermentans	905	S	8	1	9	0.00004
Bacteroides vulgatus	821	S	85502	30083	115585	0.46158
Clostridium kluyveri	1534	S	6	0	6	0.00003
Parabacteroides distasonis	823	S	1117	2308	3425	0.01368
Marivirga tractuosa	1006	S	5	3	8	0.00003
[Eubacterium] rectale	39491	S	15274	2391	17665	0.07055
Paludibacter propionicigenes	185300	S	6	0	6	0.00002
[Clostridium] clariflavum	288965	S	5	0	5	0.00002
Bacteroides caccae	47678	S	1644	46	1690	0.00675
Lachnoclostridium phocaeense	1871021	S	103	11	114	0.00046
Streptococcus pasteurianus	197614	S	14	10	24	0.00010
Murdochiella vaginalis	1852373	S	14	4	18	0.00008
Clostridium perfringens	1502	S	39	6	45	0.00018
Ornithobacterium rhinotracheale	28251	S	108	219	327	0.00131
Eubacterium limosum	1736	S	26	0	26	0.00011
Barnesiella viscericola	397865	S	199	15	214	0.00086
Clostridium pasteurianum	1501	S	12	1	13	0.00005
Alistipes finegoldii	214856	S	486	90	576	0.00230
Campylobacter jejuni	197	S	18	20	38	0.00015
Lactococcus lactis	1358	S	6	2	8	0.00003
Enterococcus faecium	1352	S	88	30	118	0.00047
Enterococcus faecalis	1351	S	8	3	11	0.00004
Prochlorococcus marinus	1219	S	5	0	5	0.00002
Cellulosilyticum lentocellum	29360	S	6	0	6	0.00002
Spiroplasma diminutum	216936	S	6	1	7	0.00003
Treponema succinifaciens	167	S	6	7	13	0.00005
Lactobacillus ruminis	1623	S	10	2	12	0.00005
Oscillibacter valericigenes	351091	S	19	0	19	0.00008
Butyrivibrio proteoclasticus	43305	S	25	9	34	0.00014
Ruminococcus bicirculans	1160721	S	286	61	347	0.00139
Bacteroides cellulosilyticus	246787	S	33751	1162	34913	0.13942
Clostridium saccharobutylicum	169679	S	7	1	8	0.00003
Intestinimonas butyriciproducens	1297617	S	153	23	176	0.00070
uncultured crAssphage	1211417	S	566	0	566	0.00226
Histophilus somni	731	S	20	4	24	0.00010
Streptococcus pyogenes	1314	S	19	71	90	0.00036
Anaerotignum propionicum	28446	S	6	0	6	0.00002
Faecalibaculum rodentium	1702221	S	9	2	11	0.00005
Clostridium sp. BNL1100	755731	S	5	0	5	0.00002
Alistipes shahii	328814	S	539	118	657	0.00263
Lachnoclostridium phytofermentans	66219	S	24	0	24	0.00010
Prevotella dentalis	52227	S	28	3	31	0.00012
Clostridium baratii	1561	S	5	1	6	0.00003
Brachyspira pilosicoli	52584	S	30	0	30	0.00012
Escherichia coli	562	S	42	55	97	0.00039
Petrimonas mucosa	1642646	S	106	4	110	0.00044
Bifidobacterium catenulatum	1686	S	9	0	9	0.00004
Bacteroides coprosuis	151276	S	176	1	177	0.00071
Bifidobacterium longum	216816	S	101	61	162	0.00065
Streptococcus parasanguinis	1318	S	7	0	7	0.00003
Clostridium argentinense	29341	S	5	0	5	0.00002
Porphyromonas gingivalis	837	S	19	1	20	0.00008
Megamonas hypermegale	158847	S	69	2	71	0.00029
Bacteroides dorei	357276	S	6384	1797	8181	0.03267
Bacteroides ovatus	28116	S	2630	154	2784	0.01112
Bifidobacterium breve	1685	S	24	8	32	0.00013
Tannerella forsythia	28112	S	14	1	15	0.00006
Odoribacter splanchnicus	28118	S	2947	238	3185	0.01272