name	taxonomy_id	taxonomy_lvl	kraken_assigned_reads	added_reads	new_est_reads	fraction_total_reads
Streptococcus suis	1307	S	37	40	77	0.00051
Anaerostipes hadrus	649756	S	2134	497	2631	0.01735
Turicibacter sp. H121	1712675	S	22	3	25	0.00017
Chryseobacterium gallinarum	1324352	S	25	1	26	0.00018
Ruminococcus albus	1264	S	21	0	21	0.00014
Draconibacterium orientale	1168034	S	5	1	6	0.00004
Methanobrevibacter millerae	230361	S	18	0	18	0.00012
Bacteroides helcogenes	290053	S	253	6	259	0.00171
Veillonella parvula	29466	S	5	0	5	0.00003
Hymenobacter sedentarius	1411621	S	6	1	7	0.00005
Methanobrevibacter smithii	2173	S	17754	108	17862	0.11779
Ethanoligenens harbinense	253239	S	5	0	5	0.00004
Akkermansia muciniphila	239935	S	217	2	219	0.00145
Bacteroides thetaiotaomicron	818	S	5891	761	6652	0.04387
Acidaminococcus intestini	187327	S	7796	369	8165	0.05385
Parabacteroides sp. CT06	2025876	S	2572	6294	8866	0.05847
Prevotella scopos	589437	S	70	140	210	0.00139
Prevotella fusca	589436	S	19	18	37	0.00025
Bacteroides fragilis	817	S	1185	483	1668	0.01100
Bacteroides caccae	47678	S	2664	115	2779	0.01833
Lachnoclostridium sp. YL32	1834196	S	85	9	94	0.00062
Streptococcus agalactiae	1311	S	72	8	80	0.00053
Carboxydothermus hydrogenoformans	129958	S	5	0	5	0.00003
Bacteroides salanitronis	376805	S	1005	80	1085	0.00716
Adlercreutzia equolifaciens	446660	S	31	3	34	0.00023
Clostridium botulinum	1491	S	8	13	21	0.00014
Clostridium butyricum	1492	S	6	0	6	0.00005
Clostridium cochlearium	1494	S	22	7	29	0.00019
Bacteroides caecimuris	1796613	S	2136	445	2581	0.01703
Dialister pneumosintes	39950	S	5	1	6	0.00004
Olsenella sp. Marseille-P2300	1805478	S	5	3	8	0.00005
[Clostridium] bolteae	208479	S	1075	139	1214	0.00801
Bifidobacterium pseudocatenulatum	28026	S	17	2	19	0.00013
Lactobacillus salivarius	1624	S	5	1	6	0.00004
Herbinix luporum	1679721	S	7	1	8	0.00006
[Eubacterium] cellulosolvens	29322	S	27	0	27	0.00018
Mageeibacillus indolicus	884684	S	11	1	12	0.00009
Prevotella melaninogenica	28132	S	28	56	84	0.00056
Prevotella intermedia	28131	S	76	51	127	0.00084
Phoenicibacter massiliensis	1944646	S	20	1	21	0.00014
Clostridium sp. SY8519	1042156	S	104	7	111	0.00074
Parabacteroides distasonis	823	S	1467	2789	4256	0.02807
Blautia hansenii	1322	S	320	95	415	0.00274
Capnocytophaga sputigena	1019	S	5	11	16	0.00011
Tannerella sp. oral taxon HOT-286	712710	S	10	0	10	0.00007
Campylobacter coli	195	S	65	5	70	0.00047
Tenacibaculum dicentrarchi	669041	S	5	5	10	0.00007
Streptococcus anginosus	1328	S	37	5	42	0.00028
Roseburia hominis	301301	S	2425	883	3308	0.02182
Fibrobacter succinogenes	833	S	5	0	5	0.00003
Butyrivibrio hungatei	185008	S	9	1	10	0.00007
Methanobrevibacter sp. YE315	1609968	S	15	0	15	0.00010
Prevotella sp. oral taxon 299	652716	S	24	11	35	0.00024
Candidatus Izimaplasma sp. HR1	1541959	S	7	0	7	0.00005
[Clostridium] saccharolyticum	84030	S	107	9	116	0.00077
Prevotella ruminicola	839	S	42	0	42	0.00028
Gemella sp. oral taxon 928	1785995	S	5	0	5	0.00004
[Eubacterium] hallii	39488	S	836	154	990	0.00653
Selenomonas sp. oral taxon 126	712528	S	5	1	6	0.00005
Leuconostoc carnosum	1252	S	5	0	5	0.00003
Prevotella denticola	28129	S	50	33	83	0.00055
Bacillus coagulans	1398	S	7	1	8	0.00006
Bacillus cereus	1396	S	7	11	18	0.00012
Faecalitalea cylindroides	39483	S	414	162	576	0.00380
Ruminococcus champanellensis	1161942	S	69	1	70	0.00046
[Eubacterium] eligens	39485	S	2843	381	3224	0.02126
Porphyromonas asaccharolytica	28123	S	5	0	5	0.00003
Candidatus Azobacteroides pseudotrichonymphae	511435	S	7	0	7	0.00005
Prevotella enoeca	76123	S	41	30	71	0.00047
Christensenella massiliensis	1805714	S	194	24	218	0.00144
Desulfotomaculum gibsoniae	102134	S	8	0	8	0.00005
Fermentimonas caenicola	1562970	S	6	0	6	0.00004
Burkholderiales bacterium YL45	1834205	S	12	59	71	0.00047
Desulfovibrio vulgaris	881	S	7	0	7	0.00005
Desulfovibrio piger	901	S	418	53	471	0.00311
Acidaminococcus fermentans	905	S	7	0	7	0.00005
Bacteroides vulgatus	821	S	11510	6316	17826	0.11755
Acholeplasma brassicae	61635	S	6	0	6	0.00004
Clostridium kluyveri	1534	S	5	0	5	0.00003
Aeromonas salmonicida	645	S	6	12	18	0.00012
Trueperella pyogenes	1661	S	5	0	5	0.00003
[Eubacterium] rectale	39491	S	5416	1356	6772	0.04466
Paludibacter propionicigenes	185300	S	11	0	11	0.00007
Enterococcus cecorum	44008	S	40	4	44	0.00029
Klebsiella pneumoniae	573	S	7	75	82	0.00054
Flavonifractor plautii	292800	S	138	13	151	0.00100
Lachnoclostridium phocaeense	1871021	S	226	30	256	0.00169
Eggerthella lenta	84112	S	12	2	14	0.00009
Streptococcus pasteurianus	197614	S	24	7	31	0.00021
Acholeplasma palmae	38986	S	8	3	11	0.00008
Taterapox virus	28871	S	6	0	6	0.00004
Dyadobacter fermentans	94254	S	7	1	8	0.00006
Murdochiella vaginalis	1852373	S	32	10	42	0.00028
Ornithobacterium rhinotracheale	28251	S	346	1025	1371	0.00904
Tenacibaculum jejuense	584609	S	13	3	16	0.00011
Eubacterium limosum	1736	S	48	0	48	0.00032
Barnesiella viscericola	397865	S	1674	297	1971	0.01300
Clostridium pasteurianum	1501	S	8	3	11	0.00007
Eggerthella sp. YY7918	502558	S	12	1	13	0.00009
Bifidobacterium thermophilum	33905	S	8	0	8	0.00005
Alistipes finegoldii	214856	S	1946	598	2544	0.01678
Campylobacter jejuni	197	S	41	109	150	0.00099
Enterococcus faecium	1352	S	395	145	540	0.00357
Escherichia coli	562	S	19	42	61	0.00041
Geobacter uraniireducens	351604	S	12	1	13	0.00009
Myxococcus hansupus	1297742	S	5	2	7	0.00005
Muricauda ruestringensis	111501	S	7	0	7	0.00005
Treponema succinifaciens	167	S	6	4	10	0.00007
Clostridioides difficile	1496	S	578	393	971	0.00641
Myroides odoratimimus	76832	S	8	2	10	0.00007
Oscillibacter valericigenes	351091	S	51	1	52	0.00034
Butyrivibrio proteoclasticus	43305	S	19	2	21	0.00014
Brochothrix thermosphacta	2756	S	8	1	9	0.00006
Ruminococcus bicirculans	1160721	S	10072	804	10876	0.07172
Flavobacterium gilvum	1492737	S	7	0	7	0.00005
Bacteroides cellulosilyticus	246787	S	3041	230	3271	0.02158
Mucinivorans hirudinis	1433126	S	5	0	5	0.00003
Clostridium saccharobutylicum	169679	S	5	1	6	0.00004
Haemophilus parainfluenzae	729	S	9	5	14	0.00009
Intestinimonas butyriciproducens	1297617	S	483	65	548	0.00361
uncultured crAssphage	1211417	S	11267	0	11267	0.07430
Francisella sp. TX077310	573570	S	5	2	7	0.00005
Selenomonas sputigena	69823	S	5	0	5	0.00004
Streptococcus pyogenes	1314	S	90	238	328	0.00216
Bifidobacterium catenulatum	1686	S	5	1	6	0.00004
Anaerotignum propionicum	28446	S	6	0	6	0.00004
Mesotoga prima	1184387	S	6	0	6	0.00004
Microbacterium sp. No. 7	1714373	S	6	7	13	0.00009
Faecalibaculum rodentium	1702221	S	14	3	17	0.00011
Alistipes shahii	328814	S	2289	912	3201	0.02111
Sneathia amnii	187101	S	19	1	20	0.00014
Lachnoclostridium phytofermentans	66219	S	12	0	12	0.00008
Prevotella dentalis	52227	S	129	33	162	0.00107
Petrimonas mucosa	1642646	S	24	2	26	0.00017
Proteiniphilum saccharofermentans	1642647	S	9	0	9	0.00006
Bacteroides coprosuis	151276	S	33	0	33	0.00022
Ruminococcaceae bacterium CPB6	1572656	S	19	2	21	0.00014
Vibrio vulnificus	672	S	5	1	6	0.00004
Bifidobacterium longum	216816	S	380	247	627	0.00414
BeAn 58058 virus	67082	S	7	0	7	0.00005
Porphyromonas gingivalis	837	S	6	0	6	0.00005
Megamonas hypermegale	158847	S	315	9	324	0.00214
Olsenella uli	133926	S	5	1	6	0.00004
Lactobacillus agilis	1601	S	12	4	16	0.00011
Bacteroides dorei	357276	S	5606	2350	7956	0.05247
Bifidobacterium bifidum	1681	S	22	6	28	0.00019
Bifidobacterium adolescentis	1680	S	1657	106	1763	0.01163
Bifidobacterium angulatum	1683	S	11	1	12	0.00008
Bacteroides ovatus	28116	S	4316	358	4674	0.03082
Bifidobacterium breve	1685	S	27	27	54	0.00036
Tannerella forsythia	28112	S	19	6	25	0.00017
Odoribacter splanchnicus	28118	S	3270	496	3766	0.02483