name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Bacteroides ovatus	28116	S	36641	2292	38933	0.15134
Bacteroides thetaiotaomicron	818	S	17502	1376	18878	0.07338
Bacteroides cellulosilyticus	246787	S	12540	691	13231	0.05143
Bacteroides caccae	47678	S	9696	282	9978	0.03879
Bacteroides vulgatus	821	S	4741	2071	6812	0.02648
Bacteroides dorei	357276	S	3056	883	3939	0.01531
Bacteroides caecimuris	1796613	S	2888	422	3310	0.01287
Bacteroides fragilis	817	S	2694	607	3301	0.01283
Bacteroides salanitronis	376805	S	2000	114	2114	0.00822
Bacteroides helcogenes	290053	S	848	12	860	0.00334
Bacteroides heparinolyticus	28113	S	461	115	576	0.00224
Bacteroides zoogleoformans	28119	S	371	93	464	0.00180
Bacteroides coprosuis	151276	S	58	0	58	0.00023
Odoribacter splanchnicus	28118	S	12935	986	13921	0.05411
Alistipes shahii	328814	S	8984	1978	10962	0.04261
Alistipes finegoldii	214856	S	2208	301	2509	0.00975
Mucinivorans hirudinis	1433126	S	7	0	7	0.00003
Parabacteroides sp. CT06	2025876	S	2598	4716	7314	0.02843
Parabacteroides distasonis	823	S	2090	2839	4929	0.01916
Tannerella sp. oral taxon HOT-286	712710	S	38	7	45	0.00017
Tannerella forsythia	28112	S	27	1	28	0.00011
Prevotella intermedia	28131	S	3243	542	3785	0.01471
Prevotella denticola	28129	S	57	7	64	0.00025
Prevotella ruminicola	839	S	55	0	55	0.00021
Prevotella melaninogenica	28132	S	53	14	67	0.00026
Prevotella dentalis	52227	S	47	4	51	0.00020
Prevotella enoeca	76123	S	44	12	56	0.00022
Prevotella sp. oral taxon 299	652716	S	32	3	35	0.00014
Prevotella jejuni	1177574	S	27	6	33	0.00013
Prevotella scopos	589437	S	26	10	36	0.00014
Prevotella fusca	589436	S	24	4	28	0.00011
Barnesiella viscericola	397865	S	1143	151	1294	0.00503
Petrimonas mucosa	1642646	S	29	1	30	0.00012
Porphyromonas gingivalis	837	S	20	5	25	0.00010
Fermentimonas caenicola	1562970	S	18	0	18	0.00007
Muribaculum intestinale	1796646	S	60	1	61	0.00024
Proteiniphilum saccharofermentans	1642647	S	33	1	34	0.00013
Bacteroidales bacterium CF	1400053	S	22	2	24	0.00009
Candidatus Azobacteroides pseudotrichonymphae	511435	S	10	0	10	0.00004
Paludibacter propionicigenes	185300	S	26	0	26	0.00010
Alkalitalea saponilacus	889453	S	24	0	24	0.00009
Draconibacterium orientale	1168034	S	5	0	5	0.00002
Ornithobacterium rhinotracheale	28251	S	149	537	686	0.00267
Chryseobacterium gallinarum	1324352	S	36	13	49	0.00019
Chryseobacterium sp. T16E-39	2015076	S	6	1	7	0.00003
Flavobacterium columnare	996	S	10	1	11	0.00004
Flavobacterium sp. HYN0048	2162713	S	8	1	9	0.00003
Flavobacterium sp. HYN0059	2175091	S	6	0	6	0.00002
Capnocytophaga cynodegmi	28189	S	10	7	17	0.00007
Maribacter sp. HTCC2170	313603	S	10	1	11	0.00004
Flavobacteriaceae bacterium UJ101	1150389	S	8	3	11	0.00004
Formosa sp. Hel1_31_208	1798225	S	5	0	5	0.00002
Flagellimonas sp. HME9304	1383885	S	5	0	5	0.00002
Spirosoma radiotolerans	1379870	S	10	1	11	0.00004
Runella sp. HYN0085	2259595	S	9	1	10	0.00004
Fibrella sp. ES10-3-2-2	1834519	S	10	0	10	0.00004
Dyadobacter fermentans	94254	S	7	0	7	0.00003
Pontibacter korlensis	400092	S	8	0	8	0.00003
Pontibacter akesuensis	388950	S	7	0	7	0.00003
Algoriphagus machipongonensis	388413	S	5	0	5	0.00002
Chryseolinea sp. KIS68-18	2321403	S	5	0	5	0.00002
Pedobacter cryoconitis	188932	S	8	2	10	0.00004
Pedobacter steynii	430522	S	5	0	5	0.00002
Sphingobacterium sp. ML3W	1538644	S	7	4	11	0.00004
Mucilaginibacter gotjawali	1550579	S	6	0	6	0.00002
Niabella soli	446683	S	5	3	8	0.00003
Melioribacter roseus	1134405	S	5	0	5	0.00002
Fibrobacter succinogenes	833	S	6	0	6	0.00002
Lachnospiraceae bacterium GAM79	2109691	S	39875	4459	44334	0.17233
[Eubacterium] rectale	39491	S	3787	168	3955	0.01537
Lachnospiraceae bacterium Choco86	2109690	S	460	28	488	0.00190
Lachnospiraceae bacterium oral taxon 500	712991	S	12	0	12	0.00005
Roseburia hominis	301301	S	3181	424	3605	0.01401
[Clostridium] bolteae	208479	S	1354	82	1436	0.00558
Lachnoclostridium sp. YL32	1834196	S	92	4	96	0.00037
Lachnoclostridium phocaeense	1871021	S	88	6	94	0.00037
[Clostridium] saccharolyticum	84030	S	41	1	42	0.00016
[Clostridium] sphenoides	29370	S	20	0	20	0.00008
Lachnoclostridium phytofermentans	66219	S	18	0	18	0.00007
Anaerostipes hadrus	649756	S	1241	97	1338	0.00520
Blautia sp. N6H1-15	1912897	S	165	43	208	0.00081
Blautia hansenii	1322	S	116	40	156	0.00061
Butyrivibrio fibrisolvens	831	S	15	0	15	0.00006
Butyrivibrio hungatei	185008	S	14	1	15	0.00006
Butyrivibrio proteoclasticus	43305	S	10	0	10	0.00004
Anaerotignum propionicum	28446	S	8	0	8	0.00003
Lachnoanaerobaculum umeaense	617123	S	6	0	6	0.00002
Herbinix luporum	1679721	S	6	0	6	0.00002
[Eubacterium] eligens	39485	S	22351	608	22959	0.08924
[Eubacterium] hallii	39488	S	703	38	741	0.00288
Eubacterium limosum	1736	S	34	0	34	0.00013
[Eubacterium] cellulosolvens	29322	S	14	0	14	0.00005
Faecalibacterium prausnitzii	853	S	9875	748	10623	0.04129
Ruminococcus bicirculans	1160721	S	287	16	303	0.00118
Ruminococcus champanellensis	1161942	S	67	2	69	0.00027
Ruminococcus albus	1264	S	12	0	12	0.00005
Flavonifractor plautii	292800	S	356	6	362	0.00141
Ruminococcaceae bacterium CPB6	1572656	S	14	0	14	0.00005
[Clostridium] cellulosi	29343	S	13	0	13	0.00005
Ethanoligenens harbinense	253239	S	12	0	12	0.00005
Intestinimonas butyriciproducens	1297617	S	756	34	790	0.00307
Clostridiales bacterium CCNA10	2109688	S	606	59	665	0.00258
Monoglobus pectinilyticus	1981510	S	85	4	89	0.00035
Clostridium sporogenes	1509	S	250	222	472	0.00183
Clostridium sp. SY8519	1042156	S	32	0	32	0.00012
Clostridium perfringens	1502	S	16	0	16	0.00006
Clostridium chauvoei	46867	S	15	0	15	0.00006
Clostridium baratii	1561	S	10	0	10	0.00004
Clostridium butyricum	1492	S	7	0	7	0.00003
Clostridium botulinum	1491	S	6	0	6	0.00002
Clostridium saccharoperbutylacetonicum	36745	S	6	0	6	0.00002
Clostridium septicum	1504	S	6	0	6	0.00002
Clostridium estertheticum	238834	S	5	0	5	0.00002
Clostridium argentinense	29341	S	5	0	5	0.00002
Clostridium isatidis	182773	S	5	0	5	0.00002
Mordavella sp. Marseille-P3756	2086584	S	249	22	271	0.00105
Oscillibacter sp. PEA192	2109687	S	610	53	663	0.00258
Oscillibacter valericigenes	351091	S	24	0	24	0.00009
Clostridioides difficile	1496	S	610	67	677	0.00263
Paeniclostridium sordellii	1505	S	7	0	7	0.00003
Christensenella massiliensis	1805714	S	74	3	77	0.00030
Desulfofarcimen acetoxidans	58138	S	9	1	10	0.00004
Desulfallas gibsoniae	102134	S	8	1	9	0.00003
Dehalobacterium formicoaceticum	51515	S	6	5	11	0.00004
Mageeibacillus indolicus	884684	S	14	1	15	0.00006
Ruminiclostridium cellulolyticum	1521	S	10	1	11	0.00004
Heliobacterium modesticaldum	35701	S	12	2	14	0.00005
Mogibacterium diversum	114527	S	5	1	6	0.00002
Moorella thermoacetica	1525	S	5	0	5	0.00002
Mahella australiensis	252966	S	6	0	6	0.00002
Faecalitalea cylindroides	39483	S	474	186	660	0.00257
Erysipelotrichaceae bacterium GAM147	2109692	S	310	369	679	0.00264
Turicibacter sp. H121	1712675	S	24	2	26	0.00010
Streptococcus agalactiae	1311	S	63	52	115	0.00045
Streptococcus thermophilus	1308	S	53	5	58	0.00023
Streptococcus salivarius	1304	S	32	7	39	0.00015
Streptococcus suis	1307	S	25	28	53	0.00021
Streptococcus parasanguinis	1318	S	10	0	10	0.00004
Streptococcus pasteurianus	197614	S	8	8	16	0.00006
Streptococcus pneumoniae	1313	S	7	1	8	0.00003
Streptococcus sanguinis	1305	S	6	0	6	0.00002
Streptococcus acidominimus	1326	S	6	0	6	0.00002
Lactococcus lactis	1358	S	8	13	21	0.00008
Enterococcus faecalis	1351	S	57	12	69	0.00027
Enterococcus faecium	1352	S	52	47	99	0.00038
Enterococcus cecorum	44008	S	46	4	50	0.00019
Lactobacillus salivarius	1624	S	7	1	8	0.00003
Lactobacillus sp. CBA3606	2099789	S	6	13	19	0.00007
Bacillus jeotgali	129985	S	5	10	15	0.00006
Paenibacillus sp. FSL R5-0345	1536770	S	9	19	28	0.00011
Staphylococcus aureus	1280	S	9	8	17	0.00007
Staphylococcus lutrae	155085	S	5	2	7	0.00003
Megasphaera stantonii	2144175	S	6	2	8	0.00003
Veillonella parvula	29466	S	5	3	8	0.00003
Acidaminococcus fermentans	905	S	9	14	23	0.00009
Selenomonas ruminantium	971	S	5	1	6	0.00002
Murdochiella vaginalis	1852373	S	6	0	6	0.00002
Parvimonas micra	33033	S	5	0	5	0.00002
Bifidobacterium longum	216816	S	38	27	65	0.00025
Bifidobacterium animalis	28025	S	20	2	22	0.00009
Bifidobacterium breve	1685	S	16	16	32	0.00012
Bifidobacterium bifidum	1681	S	13	9	22	0.00009
Bifidobacterium adolescentis	1680	S	7	0	7	0.00003
Adlercreutzia equolifaciens	446660	S	16	0	16	0.00006
Eggerthella sp. YY7918	502558	S	10	5	15	0.00006
Collinsella aerofaciens	74426	S	6	3	9	0.00003
Mycoplasma fermentans	2115	S	23	0	23	0.00009
Thermomicrobium roseum	500	S	7	0	7	0.00003
Akkermansia muciniphila	239935	S	1329	4	1333	0.00518
Victivallales bacterium CCUG 44730	2094242	S	117	1	118	0.00046
Escherichia coli	562	S	14	520	534	0.00208
Klebsiella pneumoniae	573	S	10	38	48	0.00019
Chania multitudinisentens	1639108	S	7	0	7	0.00003
Providencia alcalifaciens	126385	S	11	0	11	0.00004
Marinobacter salarius	1420917	S	8	1	9	0.00003
Mannheimia varigena	85404	S	5	0	5	0.00002
Aggregatibacter aphrophilus	732	S	5	0	5	0.00002
Kangiella profundi	1561924	S	7	3	10	0.00004
Luteibacter rhizovicinus	242606	S	6	0	6	0.00002
Legionella spiritensis	452	S	7	0	7	0.00003
Rhodobacter sphaeroides	1063	S	5	39	44	0.00017
Magnetospirillum gryphiswaldense	55518	S	5	11	16	0.00006
Erythrobacter atlanticus	1648404	S	5	8	13	0.00005
Campylobacter jejuni	197	S	43	23	66	0.00026
Campylobacter coli	195	S	23	1	24	0.00009
Helicobacter cetorum	138563	S	6	4	10	0.00004
Desulfovibrio piger	901	S	6	2	8	0.00003
Pelobacter acetylenicus	29542	S	5	1	6	0.00002
Sutterella sp. 6FBBBH3	2259134	S	8	15	23	0.00009
Neisseria sp. 10023	1853278	S	12	5	17	0.00007
Bacteriovorax stolpii	960	S	12	0	12	0.00005
Treponema denticola	158	S	150	393	543	0.00211
Treponema succinifaciens	167	S	8	0	8	0.00003
Treponema sp. OMZ 838	1539298	S	5	0	5	0.00002
Streptobacillus moniliformis	34105	S	8	0	8	0.00003
Cloacibacillus porcorum	1197717	S	17	0	17	0.00007
Calditerrivibrio nitroreducens	477976	S	5	0	5	0.00002
Methanobrevibacter smithii	2173	S	8143	15	8158	0.03171
Orgyia leucostigma nucleopolyhedrovirus	490711	S	6	0	6	0.00002