Archaea and the human gut: New beginning of an old story

Table 2 Possible association between several human diseases and methanogens

Pathology	Pros for a role or an association	Cons
Colorectal cancer	80% of colorectal cancer patients are methane producers[127]	No significant relation with the amount of breath methane[48,71,129-131]
	Methane production increases with the severity of colorectal cancer[128]	Native Africans with high level of methanogenic archaea are less susceptible to sporadic colorectal cancer[48]
Obesity	Higher levels of methanogens in obese[132]	Decreased proportion of M. smithii in obese[72,73,133]
Anorexia	Higher levels of M. smithii in anorexic people (adaption to diet restriction?)[134]
IBD	Lower proportion of methane-producers/methanogen carriers in patients with IBD[104,135]
IBS	Correlation with higher production of methane (also compared to IBD patients)[136]	No significant difference in methane production with controls[137]
Diverticulosis	Subjects with diverticulosis often with high level of methanogens[45]
Constipation	Association with chronic constipation/transit time[138,139]	No significant difference between constipated children and controls[144]
	Level of methane significantly associated with the severity of constipation[136,140]
	Association with IBS constipation/increase of transit time[141-143]
Periodontitis	Possible pathogenic role and increased proportions of hydrogenotrophs and methanogens in severe cases[24,145,146]
	After therapy, decrease in the prevalence of archaea[147]

IBD: Inflammatory bowel disease; IBS: Irritable bowel disease.

Table 1 Available genomics data (GenBank, March 2014) from methanogens of the human gut

Species	Strain (DSMZ collection number)	Status1	Size (Mb)	GC%	mta	BSH	Accession	Genome reference
					ABC	gene	number
Methanobacteriales
Methanobrevibacter smithii	PS (DSM 861)	Chromosome	1.85	31.0	1	1	CP000678.1	[54]
	F1 (DSM 2374)	Scaffolds	1.73	31.3	0	1	ABYV00000000	[126]
	ALI (DSM 2375)	Scaffolds	1.71	31.3	1	1	ABYW00000000	[126]
	TS145A	Contigs	1.78	31.1	12	12	AEKU00000000	[55]
	TS145B	Contigs	1.80	31.1	12	12	AELL00000000
	TS146A	Contigs	1.79	31.2	12	12	AELM00000000
	TS146B	Contigs	1.79	31.1	12	12	AELN00000000
	TS146C	Contigs	1.95	31.2	12	12	AELO00000000
	TS146D	Contigs	1.71	31.1	12	12	AELP00000000
	TS146E	Contigs	1.95	30.4	12	12	AELQ00000000
	TS147A	Contigs	2.01	30.5	12	12	AELR00000000
	TS147B	Contigs	1.97	30.4	12	12	AELS00000000
	TS147C	Contigs	1.97	30.4	12	12	AELT00000000
	TS94A	Contigs	1.89	30.2	12	12	AELU00000000
	TS94B	Contigs	1.89	30.2	12	12	AELV00000000
	TS94C	Contigs	1.91	30.3	12	12	AELW00000000
	TS95A	Contigs	1.99	30.2	12	12	AELX00000000
	TS95B	Contigs	1.97	30.2	12	12	AELY00000000
	TS95C	Contigs	1.98	30.2	12	12	AELZ00000000
	TS95D	Contigs	2.01	30.2	12	12	AEMA00000000
	TS96A	Contigs	1.98	30.3	12	12	AEMB00000000
	TS96B	Contigs	1.87	30.2	12	12	AEMC00000000
	TS96C	Contigs	1.82	31.1	12	12	AEMD00000000
Methanobrevibacter arboriphilus	ANOR1	Scaffolds	2.22	25.5	12	22	CBVX000000000	[83]
Methanobrevibacter oralis	JMR01	Scaffolds	2.11	27.8	2	2	CBWS000000000	[63]
Methanosphaera stadtmanae	(DSM 3091)	Chromosome	1.77	27.6	4	1	CP000102	[58]
Methanomassiliicoccales
Methanomassiliicoccus luminyensis	B10 (DSM 25720)	Contigs	2.62	60.5	33	0	CAJE00000000	[88]
Ca. Methanomassiliicoccus intestinalis	Issoire-Mx1	Chromosome	1.93	41.3	33	0	CP005934	[87]
Ca. Methanomethylophilus alvus	Mx1201	Chromosome	1.67	55.6	13	1	CP004049	[86]

¹As given by genbank, March 2014;

²Original analysis from this work: a tblasn of the protein sequence of mtaA (YP_447810), mtaB (YP_447248), mtaC (YP_447249) and the BSH (Bile Salt Hydrolase) gene (YP_447796) from Methanosphaera stadtmanae on the draft genome sequence of Methanobrevibacter arboriphilus ANOR1, Methanobrevibacter oralis JMR01 and Methanobrevibacter smithii strains from[55].

³Numbers of mtaBC genes detected, homologues of mtaA genes are also present in the 3 Methanomassiliicoccales genomes but their specific implication in either methanol and/or methylamines utilization pathways has not yet been determined.