name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Bacteroides dorei	357276	S	251319	40675	291994	0.60084
Bacteroides caccae	47678	S	43459	702	44161	0.09087
Bacteroides vulgatus	821	S	27641	5944	33585	0.06911
Bacteroides ovatus	28116	S	9683	406	10089	0.02076
Bacteroides caecimuris	1796613	S	7084	504	7588	0.01561
Bacteroides fragilis	817	S	4149	474	4623	0.00951
Bacteroides thetaiotaomicron	818	S	3340	259	3599	0.00741
Bacteroides helcogenes	290053	S	2809	21	2830	0.00582
Bacteroides cellulosilyticus	246787	S	2046	51	2097	0.00432
Bacteroides heparinolyticus	28113	S	1426	186	1612	0.00332
Bacteroides salanitronis	376805	S	1384	31	1415	0.00291
Bacteroides zoogleoformans	28119	S	842	110	952	0.00196
Bacteroides coprosuis	151276	S	14	0	14	0.00003
Alistipes finegoldii	214856	S	3412	559	3971	0.00817
Alistipes shahii	328814	S	1786	352	2138	0.00440
Parabacteroides distasonis	823	S	1330	97	1427	0.00294
Parabacteroides sp. CT06	2025876	S	1183	408	1591	0.00327
Tannerella sp. oral taxon HOT-286	712710	S	20	0	20	0.00004
Tannerella forsythia	28112	S	12	0	12	0.00002
Odoribacter splanchnicus	28118	S	782	17	799	0.00164
Prevotella dentalis	52227	S	177	59	236	0.00049
Prevotella intermedia	28131	S	24	10	34	0.00007
Prevotella ruminicola	839	S	12	0	12	0.00002
Prevotella melaninogenica	28132	S	12	18	30	0.00006
Prevotella scopos	589437	S	9	20	29	0.00006
Prevotella jejuni	1177574	S	7	10	17	0.00003
Prevotella fusca	589436	S	5	4	9	0.00002
Barnesiella viscericola	397865	S	298	15	313	0.00064
Petrimonas mucosa	1642646	S	229	6	235	0.00048
Fermentimonas caenicola	1562970	S	5	0	5	0.00001
Muribaculum intestinale	1796646	S	40	0	40	0.00008
Proteiniphilum saccharofermentans	1642647	S	8	0	8	0.00002
Ornithobacterium rhinotracheale	28251	S	157	112	269	0.00055
Gramella flava	1486245	S	6	0	6	0.00001
Nonlabens sp. Hel1_33_55	1336802	S	7	0	7	0.00001
Dokdonia sp. 4H-3-7-5	983548	S	5	0	5	0.00001
Runella sp. HYN0085	2259595	S	5	0	5	0.00001
Aquiflexum balticum	280473	S	10	0	10	0.00002
Cardinium endosymbiont of Encarsia pergandiella	249402	S	11	0	11	0.00002
Anaerostipes hadrus	649756	S	17244	1845	19089	0.03928
[Eubacterium] rectale	39491	S	3735	392	4127	0.00849
Lachnospiraceae bacterium GAM79	2109691	S	1930	460	2390	0.00492
Lachnospiraceae bacterium Choco86	2109690	S	1212	146	1358	0.00279
Lachnospiraceae bacterium oral taxon 500	712991	S	11	0	11	0.00002
Roseburia hominis	301301	S	2128	533	2661	0.00548
Blautia hansenii	1322	S	962	195	1157	0.00238
Blautia sp. N6H1-15	1912897	S	322	47	369	0.00076
[Clostridium] bolteae	208479	S	201	34	235	0.00048
Lachnoclostridium sp. YL32	1834196	S	163	21	184	0.00038
Lachnoclostridium phocaeense	1871021	S	124	14	138	0.00028
[Clostridium] saccharolyticum	84030	S	58	3	61	0.00013
Lachnoclostridium phytofermentans	66219	S	21	0	21	0.00004
[Clostridium] sphenoides	29370	S	15	0	15	0.00003
Butyrivibrio fibrisolvens	831	S	27	2	29	0.00006
Butyrivibrio proteoclasticus	43305	S	20	3	23	0.00005
Butyrivibrio hungatei	185008	S	13	2	15	0.00003
Lachnoanaerobaculum umeaense	617123	S	16	0	16	0.00003
Cellulosilyticum lentocellum	29360	S	10	0	10	0.00002
Herbinix luporum	1679721	S	8	0	8	0.00002
Anaerotignum propionicum	28446	S	7	0	7	0.00001
Ruminococcus bicirculans	1160721	S	12525	178	12703	0.02614
Ruminococcus champanellensis	1161942	S	15	0	15	0.00003
Ruminococcus albus	1264	S	6	0	6	0.00001
Faecalibacterium prausnitzii	853	S	3610	422	4032	0.00830
Flavonifractor plautii	292800	S	370	12	382	0.00079
Ruminococcaceae bacterium CPB6	1572656	S	9	0	9	0.00002
[Eubacterium] eligens	39485	S	5355	279	5634	0.01159
[Eubacterium] hallii	39488	S	1506	121	1627	0.00335
Eubacterium limosum	1736	S	60	1	61	0.00013
[Eubacterium] cellulosolvens	29322	S	17	0	17	0.00003
Clostridium sporogenes	1509	S	4868	1993	6861	0.01412
Clostridium sp. SY8519	1042156	S	174	3	177	0.00036
Clostridium botulinum	1491	S	91	3	94	0.00019
Clostridium perfringens	1502	S	54	0	54	0.00011
Clostridium baratii	1561	S	49	0	49	0.00010
Clostridium butyricum	1492	S	47	0	47	0.00010
Clostridium taeniosporum	394958	S	31	0	31	0.00006
Clostridium septicum	1504	S	26	0	26	0.00005
Clostridium isatidis	182773	S	22	0	22	0.00005
Clostridium saccharobutylicum	169679	S	22	0	22	0.00005
Clostridium saccharoperbutylacetonicum	36745	S	20	0	20	0.00004
Clostridium beijerinckii	1520	S	19	0	19	0.00004
Clostridium bornimense	1216932	S	18	0	18	0.00004
Clostridium sp. DL-VIII	641107	S	17	0	17	0.00003
Clostridium pasteurianum	1501	S	16	0	16	0.00003
Clostridium chauvoei	46867	S	16	0	16	0.00003
Clostridium argentinense	29341	S	16	0	16	0.00003
Clostridium carboxidivorans	217159	S	11	0	11	0.00002
Clostridium novyi	1542	S	10	0	10	0.00002
Clostridium tetani	1513	S	10	0	10	0.00002
Clostridium estertheticum	238834	S	7	0	7	0.00001
Clostridium sp. JN500901	2068654	S	7	0	7	0.00001
Clostridium cellulovorans	1493	S	7	0	7	0.00001
Clostridium acetobutylicum	1488	S	7	0	7	0.00001
Clostridium tyrobutyricum	1519	S	6	0	6	0.00001
Clostridium cochlearium	1494	S	5	0	5	0.00001
Mordavella sp. Marseille-P3756	2086584	S	132	18	150	0.00031
Clostridiaceae bacterium 14S0207	2082193	S	5	0	5	0.00001
Clostridioides difficile	1496	S	798	54	852	0.00175
Paeniclostridium sordellii	1505	S	19	0	19	0.00004
Filifactor alocis	143361	S	10	0	10	0.00002
Acetoanaerobium sticklandii	1511	S	6	0	6	0.00001
Clostridiales bacterium CCNA10	2109688	S	201	35	236	0.00049
Intestinimonas butyriciproducens	1297617	S	89	4	93	0.00019
Monoglobus pectinilyticus	1981510	S	37	1	38	0.00008
Oscillibacter sp. PEA192	2109687	S	144	22	166	0.00034
Mageeibacillus indolicus	884684	S	26	1	27	0.00006
Christensenella massiliensis	1805714	S	7	0	7	0.00001
Erysipelotrichaceae bacterium GAM147	2109692	S	1310	777	2087	0.00429
Faecalitalea cylindroides	39483	S	581	138	719	0.00148
Turicibacter sp. H121	1712675	S	107	6	113	0.00023
Faecalibaculum rodentium	1702221	S	6	1	7	0.00001
Streptococcus salivarius	1304	S	126	23	149	0.00031
Streptococcus pasteurianus	197614	S	60	58	118	0.00024
Streptococcus parasanguinis	1318	S	59	1	60	0.00012
Streptococcus agalactiae	1311	S	43	33	76	0.00016
Streptococcus suis	1307	S	28	17	45	0.00009
Streptococcus thermophilus	1308	S	17	3	20	0.00004
Streptococcus mitis	28037	S	12	1	13	0.00003
Streptococcus equinus	1335	S	10	3	13	0.00003
Streptococcus sp. FDAARGOS_192	1839799	S	10	4	14	0.00003
Streptococcus acidominimus	1326	S	8	0	8	0.00002
Streptococcus equi	1336	S	8	0	8	0.00002
Streptococcus sanguinis	1305	S	8	0	8	0.00002
Streptococcus pneumoniae	1313	S	6	3	9	0.00002
Streptococcus mutans	1309	S	5	0	5	0.00001
Streptococcus cristatus	45634	S	5	0	5	0.00001
Enterococcus faecium	1352	S	57	8	65	0.00013
Enterococcus cecorum	44008	S	16	1	17	0.00003
Enterococcus faecalis	1351	S	15	8	23	0.00005
Lactobacillus ruminis	1623	S	29	3	32	0.00007
Lactobacillus murinus	1622	S	11	4	15	0.00003
Lactobacillus coryniformis	1610	S	8	0	8	0.00002
Leuconostoc mesenteroides	1245	S	6	1	7	0.00001
Weissella koreensis	165096	S	5	0	5	0.00001
Paenibacillus larvae	1464	S	7	0	7	0.00001
Veillonella parvula	29466	S	14	0	14	0.00003
Dialister sp. Marseille-P5638	2161821	S	9	3	12	0.00002
Finegoldia magna	1260	S	6	0	6	0.00001
Parvimonas micra	33033	S	5	0	5	0.00001
Bifidobacterium longum	216816	S	259	23	282	0.00058
Bifidobacterium breve	1685	S	63	12	75	0.00015
Bifidobacterium pseudocatenulatum	28026	S	16	0	16	0.00003
Bifidobacterium bifidum	1681	S	13	1	14	0.00003
Bifidobacterium kashiwanohense	630129	S	7	0	7	0.00001
Bifidobacterium catenulatum	1686	S	5	0	5	0.00001
Phoenicibacter massiliensis	1944646	S	21	0	21	0.00004
Eggerthella lenta	84112	S	18	0	18	0.00004
Synechococcus lividus	33070	S	5	2	7	0.00001
Escherichia coli	562	S	99	121	220	0.00045
Haemophilus parainfluenzae	729	S	33	6	39	0.00008
Vibrio campbellii	680	S	7	5	12	0.00002
Campylobacter jejuni	197	S	22	26	48	0.00010
Campylobacter coli	195	S	9	0	9	0.00002
Desulfovibrio piger	901	S	19	4	23	0.00005
Treponema azotonutricium	150829	S	14	0	14	0.00003
Treponema sp. OMZ 838	1539298	S	6	1	7	0.00001
Cloacibacillus porcorum	1197717	S	5	1	6	0.00001
Streptococcus virus phiAbc2	633135	S	6	4	10	0.00002