name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Bacteroides dorei	357276	S	133139	19663	152802	0.34443
Bacteroides ovatus	28116	S	105847	3430	109277	0.24632
Bacteroides vulgatus	821	S	49349	8211	57560	0.12975
Bacteroides cellulosilyticus	246787	S	18848	440	19288	0.04348
Bacteroides fragilis	817	S	16315	815	17130	0.03861
Bacteroides thetaiotaomicron	818	S	13329	533	13862	0.03125
Bacteroides caecimuris	1796613	S	4239	277	4516	0.01018
Bacteroides helcogenes	290053	S	1228	8	1236	0.00279
Bacteroides caccae	47678	S	761	11	772	0.00174
Bacteroides heparinolyticus	28113	S	616	74	690	0.00156
Bacteroides zoogleoformans	28119	S	453	55	508	0.00115
Bacteroides salanitronis	376805	S	311	6	317	0.00071
Bacteroides coprosuis	151276	S	21	0	21	0.00005
Parabacteroides sp. CT06	2025876	S	2145	2719	4864	0.01096
Parabacteroides distasonis	823	S	1667	1916	3583	0.00808
Tannerella sp. oral taxon HOT-286	712710	S	21	0	21	0.00005
Tannerella forsythia	28112	S	19	4	23	0.00005
Odoribacter splanchnicus	28118	S	7706	297	8003	0.01804
Alistipes shahii	328814	S	2006	330	2336	0.00527
Alistipes finegoldii	214856	S	1490	197	1687	0.00380
Mucinivorans hirudinis	1433126	S	7	0	7	0.00002
Barnesiella viscericola	397865	S	710	35	745	0.00168
Prevotella intermedia	28131	S	18	4	22	0.00005
Prevotella dentalis	52227	S	16	2	18	0.00004
Prevotella enoeca	76123	S	11	4	15	0.00003
Prevotella fusca	589436	S	11	5	16	0.00004
Prevotella ruminicola	839	S	9	0	9	0.00002
Prevotella melaninogenica	28132	S	8	5	13	0.00003
Muribaculum intestinale	1796646	S	60	0	60	0.00014
Petrimonas mucosa	1642646	S	31	0	31	0.00007
Porphyromonas gingivalis	837	S	9	0	9	0.00002
Porphyromonas asaccharolytica	28123	S	5	0	5	0.00001
Fermentimonas caenicola	1562970	S	5	0	5	0.00001
Paludibacter propionicigenes	185300	S	8	0	8	0.00002
Alkalitalea saponilacus	889453	S	7	0	7	0.00002
Draconibacterium orientale	1168034	S	5	0	5	0.00001
Chryseobacterium gallinarum	1324352	S	279	6	285	0.00064
Ornithobacterium rhinotracheale	28251	S	288	176	464	0.00105
Gramella flava	1486245	S	5	0	5	0.00001
Aquiflexum balticum	280473	S	7	0	7	0.00002
Cardinium endosymbiont of Encarsia pergandiella	249402	S	7	0	7	0.00002
[Eubacterium] rectale	39491	S	12679	1132	13811	0.03113
Lachnospiraceae bacterium GAM79	2109691	S	2600	600	3200	0.00721
Lachnospiraceae bacterium Choco86	2109690	S	687	75	762	0.00172
Lachnospiraceae bacterium oral taxon 500	712991	S	9	0	9	0.00002
Anaerostipes hadrus	649756	S	2063	244	2307	0.00520
Roseburia hominis	301301	S	1916	456	2372	0.00535
[Clostridium] bolteae	208479	S	476	87	563	0.00127
Lachnoclostridium phocaeense	1871021	S	124	15	139	0.00031
Lachnoclostridium sp. YL32	1834196	S	123	17	140	0.00032
[Clostridium] saccharolyticum	84030	S	45	3	48	0.00011
Lachnoclostridium phytofermentans	66219	S	19	0	19	0.00004
[Clostridium] sphenoides	29370	S	18	0	18	0.00004
Blautia sp. N6H1-15	1912897	S	185	47	232	0.00052
Blautia hansenii	1322	S	162	57	219	0.00049
Butyrivibrio fibrisolvens	831	S	19	1	20	0.00005
Butyrivibrio proteoclasticus	43305	S	12	1	13	0.00003
Butyrivibrio hungatei	185008	S	10	1	11	0.00002
Lachnoanaerobaculum umeaense	617123	S	17	0	17	0.00004
Herbinix luporum	1679721	S	14	1	15	0.00003
Anaerotignum propionicum	28446	S	14	0	14	0.00003
Cellulosilyticum lentocellum	29360	S	5	0	5	0.00001
Ruminococcus bicirculans	1160721	S	3422	77	3499	0.00789
Ruminococcus champanellensis	1161942	S	35	0	35	0.00008
Ruminococcus albus	1264	S	9	0	9	0.00002
Faecalibacterium prausnitzii	853	S	2696	329	3025	0.00682
Flavonifractor plautii	292800	S	148	5	153	0.00034
Ruminococcaceae bacterium CPB6	1572656	S	8	0	8	0.00002
[Eubacterium] hallii	39488	S	1508	130	1638	0.00369
[Eubacterium] eligens	39485	S	583	32	615	0.00139
[Eubacterium] cellulosolvens	29322	S	19	0	19	0.00004
Eubacterium limosum	1736	S	15	0	15	0.00003
Clostridiales bacterium CCNA10	2109688	S	542	103	645	0.00145
Monoglobus pectinilyticus	1981510	S	395	21	416	0.00094
Intestinimonas butyriciproducens	1297617	S	130	7	137	0.00031
Clostridium sporogenes	1509	S	416	244	660	0.00149
Clostridium sp. SY8519	1042156	S	136	3	139	0.00031
Clostridium perfringens	1502	S	16	0	16	0.00004
Clostridium butyricum	1492	S	9	0	9	0.00002
Clostridium baratii	1561	S	9	0	9	0.00002
Clostridium botulinum	1491	S	6	0	6	0.00001
Clostridium isatidis	182773	S	6	0	6	0.00001
Clostridium chauvoei	46867	S	6	0	6	0.00001
Clostridium septicum	1504	S	5	0	5	0.00001
Clostridium beijerinckii	1520	S	5	0	5	0.00001
Clostridium saccharobutylicum	169679	S	5	0	5	0.00001
Mordavella sp. Marseille-P3756	2086584	S	158	24	182	0.00041
Oscillibacter sp. PEA192	2109687	S	836	130	966	0.00218
Oscillibacter valericigenes	351091	S	12	0	12	0.00003
Clostridioides difficile	1496	S	497	47	544	0.00123
Paeniclostridium sordellii	1505	S	12	0	12	0.00003
Mageeibacillus indolicus	884684	S	20	1	21	0.00005
Mogibacterium diversum	114527	S	5	1	6	0.00001
[Eubacterium] sulci	143393	S	9	0	9	0.00002
Christensenella massiliensis	1805714	S	14	1	15	0.00003
Streptococcus salivarius	1304	S	277	95	372	0.00084
Streptococcus suis	1307	S	104	77	181	0.00041
Streptococcus agalactiae	1311	S	44	56	100	0.00023
Streptococcus parasanguinis	1318	S	34	1	35	0.00008
Streptococcus equinus	1335	S	23	15	38	0.00009
Streptococcus sp. FDAARGOS_192	1839799	S	18	16	34	0.00008
Streptococcus pasteurianus	197614	S	16	16	32	0.00007
Streptococcus mitis	28037	S	15	2	17	0.00004
Streptococcus thermophilus	1308	S	13	1	14	0.00003
Streptococcus sanguinis	1305	S	12	0	12	0.00003
Streptococcus anginosus	1328	S	5	3	8	0.00002
Streptococcus sp. oral taxon 431	712633	S	10	0	10	0.00002
Streptococcus oralis	1303	S	8	1	9	0.00002
Streptococcus acidominimus	1326	S	7	0	7	0.00002
Streptococcus sp. A12	1759399	S	6	0	6	0.00001
Streptococcus pneumoniae	1313	S	5	0	5	0.00001
Lactococcus lactis	1358	S	5	5	10	0.00002
Enterococcus faecium	1352	S	106	38	144	0.00032
Enterococcus cecorum	44008	S	7	0	7	0.00002
Lactobacillus ruminis	1623	S	10	0	10	0.00002
Lactobacillus agilis	1601	S	9	1	10	0.00002
Lactobacillus salivarius	1624	S	6	1	7	0.00002
Staphylococcus aureus	1280	S	322	30	352	0.00079
Bacillus cereus	1396	S	7	6	13	0.00003
Bacillus thuringiensis	1428	S	5	1	6	0.00001
Bacillus kochii	859143	S	5	0	5	0.00001
Erysipelotrichaceae bacterium GAM147	2109692	S	690	540	1230	0.00277
Turicibacter sp. H121	1712675	S	437	27	464	0.00105
Faecalitalea cylindroides	39483	S	308	61	369	0.00083
Veillonella parvula	29466	S	32	2	34	0.00008
Dialister sp. Marseille-P5638	2161821	S	10	3	13	0.00003
Dialister pneumosintes	39950	S	5	2	7	0.00002
Peptoniphilus sp. ING2-D1G	1912856	S	6	0	6	0.00001
Bifidobacterium adolescentis	1680	S	278	9	287	0.00065
Bifidobacterium longum	216816	S	123	25	148	0.00033
Bifidobacterium breve	1685	S	34	27	61	0.00014
Bifidobacterium bifidum	1681	S	9	1	10	0.00002
Bifidobacterium pseudocatenulatum	28026	S	6	0	6	0.00001
Collinsella aerofaciens	74426	S	142	3	145	0.00033
Adlercreutzia equolifaciens	446660	S	24	1	25	0.00006
Eggerthella sp. YY7918	502558	S	7	6	13	0.00003
Gordonibacter pamelaeae	471189	S	6	0	6	0.00001
Phoenicibacter massiliensis	1944646	S	5	0	5	0.00001
Acholeplasma brassicae	61635	S	5	1	6	0.00001
Klebsiella pneumoniae	573	S	445	373	818	0.00184
Klebsiella oxytoca	571	S	7	0	7	0.00002
Escherichia coli	562	S	125	31	156	0.00035
Enterobacter cloacae	550	S	47	5	52	0.00012
Proteus mirabilis	584	S	5	0	5	0.00001
Pasteurella multocida	747	S	247	9	256	0.00058
Haemophilus parainfluenzae	729	S	120	6	126	0.00028
Candidatus Portiera aleyrodidarum	91844	S	13	0	13	0.00003
Burkholderiales bacterium YL45	1834205	S	83	0	83	0.00019
Burkholderia pseudomallei	28450	S	64	128	192	0.00043
Burkholderia sp. IDO3	1705310	S	5	0	5	0.00001
Neisseria gonorrhoeae	485	S	79	2	81	0.00018
Campylobacter jejuni	197	S	13	14	27	0.00006
Campylobacter coli	195	S	8	0	8	0.00002
Lawsonia intracellularis	29546	S	5	0	5	0.00001
Desulfobulbus sp. ORNL	1986146	S	9	0	9	0.00002
Desulfobacter postgatei	2293	S	5	0	5	0.00001
Paracoccus mutanolyticus	1499308	S	36	8	44	0.00010
Yangia sp. CCB-MM3	1792508	S	11	2	13	0.00003
Victivallales bacterium CCUG 44730	2094242	S	267	1	268	0.00060
Treponema sp. OMZ 838	1539298	S	11	5	16	0.00004
Streptobacillus moniliformis	34105	S	6	1	7	0.00002
Cloacibacillus porcorum	1197717	S	11	1	12	0.00003
Methanosarcina barkeri	2208	S	5	1	6	0.00001
Human endogenous retrovirus K	45617	S	42	0	42	0.00009
BeAn 58058 virus	67082	S	8	0	8	0.00002
Glypta fumiferanae ichnovirus	419435	S	6	7	13	0.00003
Pandoravirus salinus	1349410	S	5	2	7	0.00002