Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

Maus, Irena; Bremges, Andreas; Stolze, Yvonne; Hahnke, Sarah; Cibis, Katharina G.; Koeck, Daniela E.; Kim, Yong S.; Kreubel, Jana; Hassa, Julia; Wibberg, Daniel; Weimann, Aaron; Off, Sandra; Stantscheff, Robbin; Zverlov, Vladimir V.; Schwarz, Wolfgang H.; König, Helmut; Liebl, Wolfgang; Scherer, Paul; McHardy, Alice C.; Sczyrba, Alexander; Klocke, Michael; Pühler, Alfred; Schlüter, Andreas

doi:10.1186/s13068-017-0947-1

Biotechnology for Biofuels and Bioproducts

Table 2 Genome features of 22 bacterial and archaeal strains used in this study

From: Genomics and prevalence of bacterial and archaeal isolates from biogas-producing microbiomes

Species and strain	Assembly status		Genome size (bp)	GC content (%)	No. of genes	No. of rrn operons	No. of tRNA genes	No. of protein coding genes	EBI accession no.	References
Species and strain	Genome structure	No. of contigs	Genome size (bp)	GC content (%)	No. of genes	No. of rrn operons	No. of tRNA genes	No. of protein coding genes	EBI accession no.	References
Bacteria
Clostridium cellulosi DG5	CCC	n.a.	2,229,578	44.15	2088	6	59	2017	ERP006074	[53]
Clostridium sp. N3C	Draft genome	109	3,037,440	32.43	2880	3	66	2880	FMJL01000001–FMJL01000109	This study
Clostridium bornimense M2/40^T	CCC	n.a.	2,917,864	29.78	2694	8	56	2613	HG917868	[37]
Clostridium bornimense M2/40^T	Chromid	n.a.	699,161	28.09	680	0	0	680	HG917869	[37]
Clostridium thermocellum BC1	Draft genome	139	3,454,918	39.10	3094	4	52	3095	CBQ0010000001–CBQ0010000139	[61]
Proteiniborus sp. DW1^a	Draft genome	62	3,121,392	32.44	2795	3	40	1793	FMDO01000001–FMDO01000062	This study
Sporanaerobacter sp. PP17-6a	Draft genome	53	3,296,672	33.45	3148	1	46	3148	FMIF01000001–FMIF01000053	This study
Herbinix hemicellulosilytica T3/55^T	Draft genome	35	3,037,031	36.69	2681	4	35	1726	CVTD020000001–CVTD020000035	[24]
Herbinix luporum SD1D^T	CCC	n.a.	2,609,352	35.25	2362	4	53	1517	LN879430	[78]
Peptoniphilaceae bacterium str. ING2-D1G	CCC	n.a.	1,601,846	34.85	1541	4	53	1476	LM997412	[22]
Propionispora sp. 2/2–37	Draft genome	43	4,122,013	45.58	3690	1	76	2685	CYSP01000001–CYSP01000043	[29]
Bacillus thermoamylovorans 1A1	Draft genome	106	3,708,331	37.28	3472	10	59	2957	CCRF01000001–CCRF01000106	[79]
Proteiniphilum saccharofermentans M3/6^T	CCC	n.a.	4,414,963	43.63	3450	3	48	3447	LT605205	This study
Fermentimonas caenicola ING2-E5B^T	CCC	n.a.	2,808,926	37.30	2455	2	44	2405	LN515532	[25]
Petrimonas mucosa ING2-E5A^T	CCC	n.a.	3,362,317	48.24	2693	2	46	2693	ERS1319466	This study
Defluviitoga tunisiensis L3	CCC	n.a.	2,053,097	31.38	1881	3	47	1815	LN824141	[23]
Archaea
Methanobacterium formicicum MF^T	CCC	n.a.	2,478,074	41.23	2409	2	44	2100	LN515531	[80]
Methanobacterium formicicum Mb9	CCC	n.a.	2,494,510	41.14	2416	2	43	2126	ERS549551	This study
Methanobacterium sp. Mb1	CCC	n.a.	2,029,766	39.74	2021	2	41	1689	HG425166	[19]
Methanobacterium congolense Buetzberg	CCC	n.a.	2,459,553	38.48	2351	3	41	2351	LT607756	This study
Methanobacterium congolense Buetzberg	Plasmid	n.a.	18,118	36.05	24	0	0	24	LT607757	This study
Methanothermobacter wolfeii SIV6	CCC	n.a.	1,686,891	48.89	1793	2	36	1444	ERS1319767	This study
Methanoculleus bourgensis MS2^T	CCC	n.a.	2,789,773	60.64	2586	1	45	2586	HE964772	[81]
Methanoculleus chikugoensis L21-II-0	Draft genome	70	2,649,997	61.83	2671	1	45	2671	FMID01000001–FMID01000070	This study

CCC, circulary closed chromosome; n.a., not applicable
^aThe strain Proteiniborus sp. DW1 was cultivated together with Methanobacterium sp. Mb1; the DW1 genome sequence was recovered from sequencing of a mixed culture consisting of strains DW1 and Mb1

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