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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
Turnbaugh et al. 2009 [39, 100] 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
  1. Summary of the key experimental findings and the predominant phylogenetic data, and specific pathways and functional pathways highlighted by analysis from the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and clusters of orthologous groups (COG) analysis.
  2. CAZy, carbohydrate-active enzyme; DZ, dizygotic; DXP, deoxyxylulose 5-phosphate; IPP, isopenteryl pyrophosphate; MEP, 2-methyl-D-erythritol 4-phosphate; MZ, monozygotic; OUT, operational taxonomic unit.
  3. Applied Biosystems, Carlsbad, CA, USA; GE Healthcare, Piscataway, NJ, USA; Illumina, San Diego, CA, USA.