Table 1 Human metagenomic studies that have studied the distal gut microbiome
From: Gut microbiome-host interactions in health and disease
Study | Number of humans | Sequencing technology | Sequence length | Phylogenetic data and key findings | Gene function (for example, KEGG/COG-enriched processes) |
|---|---|---|---|---|---|
Gill et al. (2006) [2] | 2 (1 male, 1 female, healthy) | ABI 3730xl sequencer (Applied Biosystems) | 17,668 contigs; 14,572 scaffolds; 33,753,108 bp; 50,164 ORFs; 19,866 unique database matches predicted | 72 bacterial phylotypes identified; 1 archaeal phylotype (Methanobrevibacter smithii); 16 novel bacterial phylotypes. Phylotypes assigned: Firmicutes (62 phylotypes, 105 sequences) and the Actinobacteria (10 phylotypes, 27 sequences) | Energy production and conversion; carbohydrate transport and metabolism; amino acid transport and metabolism; coenzyme transport and metabolism; secondary metabolites biosynthesis, and transport and catabolism; MEP pathway for biosynthesis of DXP and IPP; β-glucuronidase activity induced |
Kurokawa et al. (2007) [37] | 7 adults, 2 children and 4 unweaned infants (Japanese and Japanese American) | ABI 3730 sequencers (Applied Biosystems) or the ET chemistry on MegaBACE4500 sequencers (GE Healthcare) | 1,057,481 shotgun reads representing sequences of 727 Mb; total length of the contigs and singletons from 13 samples was 478.8 Mb; identified 20,063 to 67,740 potential protein-encoding genes | 17% to 43% of predicted genes assigned to particular genera (35 to 65 genera, 121 in total). Adults and weaned children: Bacteroides and genera belonging to division Firmicutes (for example, Eubacterium, Ruminococcus and Clostridium, and the genus Bifidobacterium. Infants: Bifidobacterium and/or a few genera from the family Enterobacteriaceae, such as Escherichia, Raoultella and Klebsiella | Carbohydrate transport and metabolism; under-representation of those for 'lipid transport and metabolism'; defense mechanisms; cell motility, secondary metabolites biosynthesis, transport and catabolism and post-translational modification and protein turnover; pyruvate-formate lyase enriched; formate hydrogenlyase system under-represented |
154 (31 MZ and 23 DZ female twin pairs and their mothers n = 46, twins concordant for obesity or leanness) | 454 Pyrosequencing | 9,920 near full-length and 1,937,461 partial bacterial 16S rRNA sequences | Gut microbiome shared among family members; degree of co-variation between adult MZ and DZ twin pairs; no single abundant bacterial species shared by all 154 individuals; wide array of shared microbial genes in sampled general population: 'core microbiome' at the gene level. Lower proportion of Bacteroidetes and a higher proportion of Actinobacteria in obese subjects and reduced bacterial diversity. Altered representation of bacterial genes and metabolic pathways, including those involved in nutrient harvest | Total of 156 total CAZy families found within at least one human gut microbiome: 77 glycoside hydrolase, 21 carbohydrate-binding module, 35 glycosyltransferase, 12 polysaccharide lyase, 11 carbohydrate-esterase families. Carbohydrate metabolism pathways enriched in Bacteroidetes bins; transport systems in Firmicutes bins; transcription and translation pathways enriched; carbohydrate and amino acid metabolism; secretion systems, and membrane transport for import of nutrients, including sugars varied in their enrichment | |
Qin et al. (2010) [6] | 124 healthy, overweight and obese individual human adults; 21 ulcerative colitis, 4 Crohn's disease | Illumina GA | 6.58 million contigs (>500 bp giving a total contig length of 10.3 Gb); 576.7 Gb | Definition of minimal core microbiome: at 1% (40 kb) coverage, 18 species in all individuals, 57 in ≥90% and 75 in ≥50% of individuals; 99.96% of the phylogenetically assigned genes belonged to the bacteria and archaea. Bacteroidetes and Firmicutes had the highest abundance. Network analysis of 155 species in at least one individual at ≥1% coverage had prominent clusters for Bacteroidetes, Dorea/Eubacterium/Ruminococcus, Bifidobacteria, Proteobacteria and streptococci/lactobacilli groups | Genes related to adhesion and harvesting sugars of the globoseries glycolipids; phage-related proteins; biodegradation of complex sugars and glycans, for example, pectin (and its monomer, rhamnose) and sorbitol; three-quarters of prevalent gut functionalities from novel gene families; approximately 45% of functions present in <10% of the sequenced bacterial genomes |
Koenig et al. [101] | 1 infant over 2.5 years | 454 pyrosequencing | 318,620 16S rRNA gene sequences | Phylogenetic diversity correlates with age. Diversity changed gradually in four discrete phases: (1) days 1 to 92: Firmicute OTUs; (2) fever at day 92: proteobacterial and actinobacterial OTU abundances, suite of Firmicute OTUs differed; (3) exclusion of breast milk; and (4) introduction of peas and cefdinir use: increase in Bacteroidetes | Carbohydrate metabolism; amylose, arabinose and maltose degradation; virulence genes enriched; rhamnose, fructo-oligosaccahride and raffinose-utilization pathways, and xylose-degradation genes expressed; lactose/galactose and sucrose utilization; antibiotic resistance; vitamin biosynthesis; sialic acid metabolism, β-glucoronide utilization; polysaccharide metabolism (day 371: maltose, maltodextrin, xylose); xenobiotic degradation; benzoate catabolism and aromatic metabolism |