name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Streptococcus salivarius	1304	S	179	56	235	0.00114
Desulfotomaculum acetoxidans	58138	S	12	0	12	0.00006
Streptococcus suis	1307	S	180	155	335	0.00162
Anaerostipes hadrus	649756	S	4066	483	4549	0.02206
Streptococcus gordonii	1302	S	14	1	15	0.00007
Chryseobacterium gallinarum	1324352	S	28	1	29	0.00014
Streptococcus thermophilus	1308	S	44	4	48	0.00024
Ruminococcus albus	1264	S	12	0	12	0.00006
Bacteroides dorei	357276	S	5359	1850	7209	0.03496
Bacteroides helcogenes	290053	S	956	18	974	0.00472
Acholeplasma oculi	35623	S	5	0	5	0.00003
Veillonella parvula	29466	S	6	4	10	0.00005
Turicibacter sp. H121	1712675	S	24	2	26	0.00013
Methanobrevibacter smithii	2173	S	32	0	32	0.00016
Ethanoligenens harbinense	253239	S	6	0	6	0.00003
Bacteroides thetaiotaomicron	818	S	4669	455	5124	0.02485
Citrobacter freundii	546	S	60	26	86	0.00042
Parabacteroides sp. CT06	2025876	S	2728	5923	8651	0.04195
Prevotella scopos	589437	S	29	18	47	0.00023
Prevotella fusca	589436	S	7	2	9	0.00004
Parvimonas micra	33033	S	5	0	5	0.00003
Bacteroides fragilis	817	S	1117	392	1509	0.00732
Lactobacillus ruminis	1623	S	23	1	24	0.00012
Bacteroides caccae	47678	S	4452	164	4616	0.02239
Streptococcus pneumoniae	1313	S	5	1	6	0.00003
Lachnoclostridium sp. YL32	1834196	S	107	16	123	0.00060
Streptococcus agalactiae	1311	S	70	6	76	0.00037
Campylobacter hominis	76517	S	7	0	7	0.00003
Bacteroides salanitronis	376805	S	521	24	545	0.00264
Adlercreutzia equolifaciens	446660	S	15	7	22	0.00011
Clostridium botulinum	1491	S	21	36	57	0.00028
Clostridium butyricum	1492	S	16	3	19	0.00009
Clostridium cellulovorans	1493	S	9	1	10	0.00005
Polaribacter vadi	1774273	S	6	0	6	0.00003
Clostridioides difficile	1496	S	301	141	442	0.00215
Akkermansia muciniphila	239935	S	677	12	689	0.00334
[Clostridium] bolteae	208479	S	815	140	955	0.00463
Bifidobacterium pseudocatenulatum	28026	S	26	2	28	0.00014
Herbinix luporum	1679721	S	14	1	15	0.00008
[Eubacterium] cellulosolvens	29322	S	16	0	16	0.00008
Mageeibacillus indolicus	884684	S	7	0	7	0.00004
Prevotella melaninogenica	28132	S	8	5	13	0.00006
Prevotella intermedia	28131	S	19	4	23	0.00011
Owenweeksia hongkongensis	253245	S	5	0	5	0.00002
Phoenicibacter massiliensis	1944646	S	9	1	10	0.00005
Raoultella ornithinolytica	54291	S	6	24	30	0.00015
Clostridium sp. SY8519	1042156	S	190	7	197	0.00096
Parabacteroides distasonis	823	S	2566	5391	7957	0.03859
Blautia hansenii	1322	S	405	76	481	0.00234
Streptococcus pyogenes	1314	S	124	364	488	0.00237
Tannerella sp. oral taxon HOT-286	712710	S	30	0	30	0.00015
Campylobacter coli	195	S	67	26	93	0.00046
Streptococcus anginosus	1328	S	27	4	31	0.00015
Campylobacter fetus	196	S	5	0	5	0.00002
Spirosoma rigui	564064	S	7	4	11	0.00005
Bacteroides caecimuris	1796613	S	1703	247	1950	0.00946
Streptococcus sp. I-G2	1156431	S	6	2	8	0.00004
Fibrobacter succinogenes	833	S	6	0	6	0.00003
Butyrivibrio hungatei	185008	S	7	3	10	0.00005
Lysinibacillus fusiformis	28031	S	6	1	7	0.00004
Porphyromonas gingivalis	837	S	34	3	37	0.00018
Candidatus Izimaplasma sp. HR1	1541959	S	8	0	8	0.00004
[Clostridium] saccharolyticum	84030	S	261	9	270	0.00131
Lactobacillus curvatus	28038	S	8	4	12	0.00006
Prevotella ruminicola	839	S	8	0	8	0.00004
[Eubacterium] hallii	39488	S	1319	123	1442	0.00699
Paraphotobacterium marinum	1755811	S	5	2	7	0.00004
Prevotella denticola	28129	S	9	1	10	0.00005
Campylobacter jejuni	197	S	13	14	27	0.00013
Faecalitalea cylindroides	39483	S	454	177	631	0.00306
Ruminococcus champanellensis	1161942	S	74	1	75	0.00036
[Eubacterium] eligens	39485	S	10361	570	10931	0.05301
Porphyromonas asaccharolytica	28123	S	5	0	5	0.00002
Desulfatibacillum alkenivorans	259354	S	8	1	9	0.00004
Candidatus Azobacteroides pseudotrichonymphae	511435	S	5	0	5	0.00002
Christensenella massiliensis	1805714	S	71	4	75	0.00037
Fermentimonas caenicola	1562970	S	22	1	23	0.00011
Haemophilus parainfluenzae	729	S	10	5	15	0.00008
Acidaminococcus fermentans	905	S	14	9	23	0.00011
Bacteroides vulgatus	821	S	19693	9032	28725	0.13930
Fusobacterium hwasookii	1583098	S	5	2	7	0.00004
Finegoldia magna	1260	S	7	0	7	0.00004
Alcaligenes faecalis	511	S	7	8	15	0.00007
[Eubacterium] rectale	39491	S	34953	3276	38229	0.18539
Paludibacter propionicigenes	185300	S	7	0	7	0.00003
Enterococcus cecorum	44008	S	6	0	6	0.00003
Klebsiella pneumoniae	573	S	9	61	70	0.00034
Flavonifractor plautii	292800	S	145	9	154	0.00075
Lachnoclostridium phocaeense	1871021	S	158	12	170	0.00082
Streptococcus pasteurianus	197614	S	30	10	40	0.00019
Acholeplasma palmae	38986	S	6	0	6	0.00003
Clostridium chauvoei	46867	S	8	2	10	0.00005
Murdochiella vaginalis	1852373	S	13	2	15	0.00008
Tenacibaculum sp. LPB0136	1850252	S	5	0	5	0.00003
Ornithobacterium rhinotracheale	28251	S	95	264	359	0.00174
Fusobacterium nucleatum	851	S	19	6	25	0.00012
Helicobacter pylori	210	S	8	0	8	0.00004
Eubacterium limosum	1736	S	102	2	104	0.00051
Barnesiella viscericola	397865	S	217	20	237	0.00115
Clostridium pasteurianum	1501	S	29	7	36	0.00018
Eggerthella sp. YY7918	502558	S	5	2	7	0.00004
Alistipes finegoldii	214856	S	2576	404	2980	0.01445
Mycoplasma fermentans	2115	S	8	0	8	0.00004
Hafnia alvei	569	S	7	0	7	0.00004
Lactococcus lactis	1358	S	12	3	15	0.00008
Enterococcus faecium	1352	S	70	34	104	0.00051
Enterococcus faecalis	1351	S	5	0	5	0.00003
Clostridium carboxidivorans	217159	S	8	10	18	0.00009
Caldicellulosiruptor obsidiansis	717609	S	10	4	14	0.00007
Parabacteroides phage YZ-2015b	1655645	S	5	0	5	0.00002
Oscillibacter valericigenes	351091	S	65	0	65	0.00032
Butyrivibrio proteoclasticus	43305	S	16	5	21	0.00011
Ruminococcus bicirculans	1160721	S	18159	940	19099	0.09262
Bacteroides cellulosilyticus	246787	S	12669	527	13196	0.06400
Carnobacterium maltaromaticum	2751	S	7	0	7	0.00003
Anoxybacillus gonensis	198467	S	5	6	11	0.00005
Clostridium perfringens	1502	S	10	2	12	0.00006
Intestinimonas butyriciproducens	1297617	S	388	33	421	0.00205
Filifactor alocis	143361	S	11	1	12	0.00006
Flavobacterium columnare	996	S	5	0	5	0.00002
Bifidobacterium catenulatum	1686	S	11	1	12	0.00006
Anaerotignum propionicum	28446	S	5	0	5	0.00002
Faecalibaculum rodentium	1702221	S	13	4	17	0.00009
Clostridium sp. BNL1100	755731	S	10	1	11	0.00005
Alistipes shahii	328814	S	4975	984	5959	0.02890
Lachnoclostridium phytofermentans	66219	S	11	0	11	0.00005
Prevotella dentalis	52227	S	21	2	23	0.00011
Brachyspira pilosicoli	52584	S	8	0	8	0.00004
Escherichia coli	562	S	45	121	166	0.00081
Petrimonas mucosa	1642646	S	11	0	11	0.00006
Proteiniphilum saccharofermentans	1642647	S	35	1	36	0.00018
Bacteroides coprosuis	151276	S	14	0	14	0.00007
Treponema sp. OMZ 838	1539298	S	5	14	19	0.00009
Arachidicoccus sp. BS20	1850526	S	6	0	6	0.00003
Ruminococcaceae bacterium CPB6	1572656	S	13	0	13	0.00007
Bifidobacterium longum	216816	S	206	137	343	0.00166
Streptococcus parasanguinis	1318	S	30	1	31	0.00015
Clostridium argentinense	29341	S	10	1	11	0.00006
Megamonas hypermegale	158847	S	28	2	30	0.00015
Citrobacter braakii	57706	S	215	101	316	0.00153
Ureaplasma urealyticum	2130	S	7	4	11	0.00006
Roseburia hominis	301301	S	4300	699	4999	0.02424
Bifidobacterium bifidum	1681	S	8	2	10	0.00005
Bifidobacterium adolescentis	1680	S	27	1	28	0.00014
Bacteroides ovatus	28116	S	22872	1814	24686	0.11971
Bifidobacterium breve	1685	S	36	14	50	0.00025
Tannerella forsythia	28112	S	20	4	24	0.00012
Streptococcus sp. A12	1759399	S	12	1	13	0.00006
Odoribacter splanchnicus	28118	S	3325	158	3483	0.01689