A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation

Gharechahi, Javad; Salekdeh, Ghasem Hosseini

doi:10.1186/s13068-018-1214-9

Biotechnology for Biofuels and Bioproducts

Table 1 Basic genome characteristics of the recovered genome bins (GBs)

From: A metagenomic analysis of the camel rumen’s microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation

BinID	Genome size (Mbp)	GC content	No. contigs	No. GHs	No. CBMs	No. dockerin	No. cohesin	SLH domain	Taxonomic label (phylum)	Com^a	Con^b	Het^c	Abu^d
Bin48	4.08	38.53	270	38	16	0	0	0	Firmicutes	72.9	7.3	2.17	0.2
Bin49	3.6	52.96	125	176	33	11	0	0	Bacteroidetes	91.5	3.1	16.67	0.4
Bin53	3.59	42.52	93	61	16	1	0	0	Bacteroidetes	92.1	4.48	31.25	0.17
Bin55	3.34	49.81	53	70	6	0	0	0	Firmicutes	98.97	3.26	0.0	0.12
Bin58	3.48	48.22	132	166	29	11	0	0	Bacteroidetes	94.82	5.33	32	0.47
Bin60	3.18	50.68	199	51	7	0	1	0	Firmicutes	91.2	9.86	0.0	0.09
Bin61	3.16	44.99	168	82	6	0	0	0	Firmicutes	91.6	9.42	26.3	0.12
Bin62	3.15	47.7	70	102	16	1	0	0	Bacteroidetes	93.90	0.68	33.3	0.38
Bin63	3.13	47.02	85	54	9	0	0	0	Bacteroidetes	95.05	7.86	45	0.13
Bin64	3.2	54.78	127	90	19	0	0	0	Fibrobacteres	87.6	5.13	40	0.37
Bin65	3.02	48.36	104	132	8	0	0	0	Bacteroidetes	91.1	4.44	47.06	0.44
Bin68	3	43.04	181	25	29	0	0	0	Bacteroidetes	97.58	6.72	23.08	0.1
Bin69	3.1	42.78	57	66	13	0	0	0	Firmicutes	91.34	2.58	23.08	0.23
Bin70	2.98	42.76	165	60	1	0	0	1	Firmicutes	90.29	5.96	0.0	0.1
Bin73	2.9	48.96	51	34	63	0	1	0	Firmicutes	98.07	0.0	0.0	0.14
Bin75	2.9	54.38	88	155	36	0	0	0	Bacteroidetes	86.19	3.37	0.0	0.23
Bin81	2.84	49.39	149	67	28	21	4	0	Firmicutes	86.01	6.1	50	0.11
Bin82	2.97	50.1	88	118	11	3	0	0	Bacteroidetes	85.57	3.58	66.67	0.7
Bin83	2.88	46.06	56	47	4	0	0	0	Firmicutes	94.68	1.42	0.0	0.37
Bin86	2.75	44.2	101	73	4	5	0	0	Bacteroidetes	93.39	2.43	83.3	0.24
Bin87	2.67	50.13	143	159	23	0	0	0	Bacteroidetes	84.23	5.95	4.55	0.2
Bin88	2.63	53.33	82	96	36	0	0	0	Firmicutes	96.95	0.23	100	0.1
Bin91	2.6	56.08	144	83	3	0	0	0	Firmicutes	88.34	8.56	0.0	0.1
Bin93	2.6	50.99	93	63	15	0	0	0	Fibrobacteres	97	1.1	0.0	0.2
Bin94	2.59	36.01	100	37	4	1	1	0	Firmicutes	99.16	7.38	41.18	0.12
Bin96	2.57	43.38	53	68	5	0	0	0	Firmicutes	95.77	0.53	50	0.3
Bin97	2.55	43.25	358	74	8	0	0	0	Firmicutes	83.12	4.19	11.76	0.09
Bin98	2.54	67.77	178	21	11	0	0	0	Lentisphaerae	79.22	2.36	0.0	0.23
Bin99	2.51	52.29	102	171	15	0	0	0	Bacteroidetes	94.29	1.43	33.33	0.35
Bin100	2.51	47.13	199	42	5	0	0	78	Firmicutes	84.29	3.25	12.5	0.09
Bin101	2.49	45.35	104	43	7	0	0	0	Spirochaetes	93.01	0.12	0.0	0.09
Bin103	2.48	43.12	227	39	9	0	0	0	Spirochaetes	75.12	1.4	33.33	0.06
Bin104	2.48	66.95	126	20	9	0	0	0	Lentisphaerae	87.17	4.08	0.0	0.12
Bin105	2.47	50.54	64	40	3	0	1	0	Firmicutes	93.35	1.58	0.0	0.09
Bin106	2.47	44.91	320	65	9	0	1	0	Firmicutes	87.75	6.81	33.33	0.1
Bin108	2.45	56.29	94	69	8	0	0	0	Bacteroidetes	87.84	6.06	35	0.29
Bin110	2.32	38.96	79	36	9	0	0	0	Firmicutes	92.16	7.9	1.89	0.11
Bin112	2.3	56.63	54	108	3	1	0	0	Bacteroidetes	92.92	0.95	0.0	0.5
Bin113	2.3	38.95	325	60	6	0	1	0	Firmicutes	78.15	6.32	20	0.08
Bin114	2.3	50.06	47	20	9	0	0	0	Bacteroidetes	87.37	2.8	41.67	0.18
Bin115	2.27	49.96	85	39	5	0	0	0	Firmicutes	97	7.62	21.43	0.2
Bin117	2.2	47.78	238	74	4	0	0	0	Firmicutes	89.85	5.53	14.29	0.13
Bin119	2.18	54.56	77	93	3	0	0	0	Bacteroidetes	95.38	1.52	25	0.42
Bin121	2.19	43.55	76	82	7	2	0	0	Bacteroidetes	70.16	7.76	40	0.2
Bin122	2.14	52.71	54	94	3	1	0	0	Bacteroidetes	95.08	0.19	0.0	0.3
Bin123	2.27	54.48	91	100	12	1	0	0	Bacteroidetes	91.19	4.05	36.36	0.62
Bin124	2.1	46.44	33	26	8	0	0	0	Bacteroidetes	92.1	0.81	0.0	0.22
Bin128	2.08	51.55	249	19	2	0	0	9	Firmicutes	86.78	4.08	30	0.09
Bin129	2.07	50.58	165	82	6	0	2	0	Bacteroidetes	84.21	2.7	54.55	0.29
Bin131	2.16	44.49	52	93	6	0	0	0	Bacteroidetes	79.7	1.98	50	0.53
Bin133	2.07	55.82	50	83	6	0	0	0	Bacteroidetes	87.62	0.95	100	0.51
Bin134	2.03	49.33	60	25	11	0	0	0	Bacteroidetes	90.14	3.15	76.19	0.17
Bin136	2.01	49.87	42	54	16	5	1	0	Bacteroidetes	75.56	2.79	43.75	0.25
Bin138	2.09	49.53	31	51	12	0	0	0	Bacteroidetes	94.29	0.66	0.0	0.45
Bin140	1.96	55.28	33	97	7	0	0	0	Bacteroidetes	93.4	2.06	0.0	0.36
Bin142	2.15	55.36	80	97	11	0	0	0	Bacteroidetes	89.52	0.48	0.0	0.81
Bin143	1.94	48.69	55	14	7	0	0	0	Bacteroidetes	92.74	0.0	0.0	0.29
Bin145	2.02	50.62	105	26	24	0	0	0	Bacteroidetes	93.2	3.4	0.0	0.26
Bin147	1.83	50.55	205	61	10	0	0	0	Bacteroidetes	85.77	0.71	0.0	0.27
Bin154	1.76	48.53	183	14	5	0	0	0	Bacteroidetes	83.69	5.1	0.0	0.13
Bin164	1.58	33.65	25	10	4	0	0	0	Tenericutes	97.33	1.33	0.0	0.16
Bin165	1.56	48.77	153	22	3	0	0	1	Firmicutes	82.89	4.26	0.0	0.07
Bin174	1.35	48.57	147	8	4	0	0	0	Spirochaetes	90.8	4.6	40	0.12
Bin187	1.2	55.2	45	1	2	2	0	0	Euryarchaeota	80.65	0.81	0.0	0.15
Bin206	0.98	37.13	144	4	2	1	0	0	Elusimicrobia	83.6	4.25	0.0	0.08

GBs were taxonomy assigned at the phylum level using universally conserved marker proteins using CheckM
^aCompeletness, ^b contamination, ^c strain heterogeneity, ^d abundance

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