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Table 1 Variations observed among different types of microbial communities, and the extent of sequencing and sampling used

From: Direct sequencing of the human microbiome readily reveals community differences

Topic Number of subjects Number of samples sequenced Total number of 16S sequences in final analysis Average number of sequences per sample Study conclusions Reference
(a) Microbial communities associated with healthy humans
120 120 14,115 118 Collected saliva from 10 individuals at each of 12 globally widespread locations. They attributed approximately 13.5% of the total variation in the distribution of genera to differences between individuals and found little evidence for geographic structure: 11.7% of the variation was among individuals from the same location while just 1.8% was among individuals from different locations [38]
(tooth, tongue,
buccal mucosa, palate)
3 29 298,261 10,285 Collected samples from various oral niches of three individuals; 26% of the unique sequences and 47% of species-level phylotypes found in the study were found in all three subjects. Bacterial community composition was shaped primarily by oral niche: principal components analysis differentiated communities from shedding (tongue, cheek, palate) versus tooth surfaces [39]
Skin (right and left volar forearm) 6 20 2,038 102 Sampled the superficial left and right volar forearms of six healthy subjects (four of whom were sampled again 8 to 10 months later). Samples from the same subject at the same time point (left versus right) were not significantly different, whereas samples from the same subject at different time points could be significantly different [40]
(right and left palms)
51 102 351,630 3,251 Collected skin swabs from the left and right palms of 51 volunteers. On average, individuals shared only 17% of species-level phylotypes between their right and left palms, while only 13% of species-level phylotypes were shared between different individuals. (UniFrac similarity between hands from different individuals = 0.30, and the same individual = 0.36 to 0.38.) Palm surface bacterial community structure was determined by handedness, time since washing, and the individual's sex [5]
(20 skin sites, including moist, dry, and sebaceous sites)
10 300 112,283 374 Obtained samples from 20 skin sites on each of 10 individuals (half of whom were sampled twice). They found that interpersonal variation in community membership and structure depended on skin site, and that subjects were more similar to themselves (site-to-site) than to others. Four of the five re-sampled subjects were also more similar to themselves over time than they were to other volunteers. Bacterial community composition was shaped by microhabitat: sebaceous, moist, or dry [18]
Gut 3 18 11,831 657 Interpersonal and site-to-site variation in three subjects at six sites. Between subject dissimilarity was greater than within subject dissimilarity [4]
Gut 154 281 1,947,381 6,930 Interpersonal variation was found to be largest between unrelated individuals, smaller between children and their mothers, still smaller between twins, and dramatically smaller in the same individual over time. (Average UniFrac distance over time within-individual = 0.69 and between unrelated individuals = 0.80) [6]
(b) Microbial communities and human disease
Obesity 12 subjects
2 controls
50 18,348 367 Obese people have fewer Bacteroidetes (5%; P < 0.001) and more Firmicutes (85%; P = 0.002) than lean controls (25% Bacteroidetes and 75% Firmicutes). During the diet, the relative abundance of Bacteroidetes increased from 5 to 20% (P < 0.001) and the abundance of Firmicutes decreased from 85 to 75% (P = 0.002). Increased abundance of Bacteroidetes correlated with percentage loss of body weight (R2 = 0.8 for the CARB-R diet and 0.5 for the FAT-R diet, P < 0.05), and not with changes in dietary calorie content over time (R2 = 0.06 for the CARB-R diet and 0.09 for the FAT-R diet) [14]
Diabetes 10 Diabetic patients
10 healthy subjects*
20 382,229
37,001 The proportion of Firmicutes was significantly higher (P = 0.03) in the controls (mean 56.4%) compared to the diabetic group (mean 36.8%). Accordingly, phyla Bacteroidetes and Proteobacteria were somewhat but not significantly enriched in the diabetic group (50.4 and 4.1% in the diabetic group compared with 35.1 and 2.7% in the healthy group, respectively) [41]
Crohn's disease (CD) and ulcerative colitis (UC) 6 CD patients
5 UC patients
5 healthy subjects
16 1,590
207 Proteobacteria were significantly (P = 0.0007) increased in CD patients (13%) versus UC patients (9.4%) or healthy subjects (8.5%). Bacteroidetes were far less diverse than Firmicutes, containing only 32 phylotypes, versus 87 species-level phylotypes in the latter phylum, but were nevertheless the most abundant, representing over 70% of total clones. Bacteroidetes were significantly increased (75%) in CD patients versus UC patients (64.3%) or healthy subjects (67.4%) The increase in Bacteroidetes and Proteobacteria was accompanied by a significant (P = 0.0001) decrease in Firmicutes (CD,10%; UC, 25.8%; healthy subjects, 24%), all belonging to the class Clostridia in the CD group [42]
CD and UC 20 CD patients
15 UC patients
14 healthy subjects
49 809
35 The results obtained from CD and healthy subject samples did not differ (P > 0.05). Bacterial numbers associated with non-inflamed and inflamed mucosa within CD and UC groups did not differ (P > 0.05). The ratio of Actinobacteria:Bacteroidetes:Firmicutes: Proteobacteria differed between healthy (approximately 1:27:53:6%), UC (approximately 0.3:34:48:7%) and CD subjects (approximately 0.5:34:40.5:6%) [43]
CD and UC 190 CD, UC or healthy patients (around equal numbers) 190 15,172 80 Bacteroidetes (10%, P = 0.001) and Firmicutes (20%, P = 0.001) were greatly depleted while Actinobacteria (10%, P = 0.001) and Proteobacteria (50%, P = 0.001) were substantially more abundant in the inflammatory bowel disease (IBD) subset samples, relative to control subset samples (approximately 20% Bacteroidetes, approximately 50% Firmicutes, approximately 5% Actinobacteria, approximately 10% Proteobacteria) [44]
Necrotizing enterocolitis (NEC) 10 infants with NEC and 10 healthy infants 21 5,354 255 For the control infants four phyla were present: Proteobacteria, (34.97% relative abundance), Firmicutes (57.79%), Bacteroidetes (2.45%) and Fusobacteria (0.54%) with 4.25% unclassified bacteria. However, NEC patients had only two phyla, Proteobacteria (90.72%) and Firmicutes (9.12%) with 0.16% unclassified bacteria. The average proportion of Proteobacteria was significantly increased and the average proportion of Firmicutes was significantly decreased compared to controls (P = 0.001) [45]
Clostridium difficile-associated diarrhea (CDAD) 4 ICD patients
3 RCD patients
3 healthy subjects
10 581
143 Using rarefaction curves, species richness in the patients with ICD (initial episode of antibiotic-associated diarrhea due to C. difficile) was similar to that in the control subjects, with the shape of the curve revealing that the total richness of the microbial community had not been completely sampled (minimum of 20 phylotypes). However, the species richness in the patients with RCD (recurrent antibiotic associated diarrhea due to C. difficile) was consistently lower (around ten phylotypes) than both that in the patients with ICD and that in the control subjects [46]
Gastric cancer 10 non-cardia gastric cancer patients
5 control patients
15 140 9 No significant differences in microbial compositions were found between cancer patients and controls [47]
Helicobacter pylori colonization 19 H. pylori (+) subjects
4 H. pylori (-) subjects
23 1,833 80 Subjects negative for H. pylori had twice as many Fusobacteria as H. pylori-positive subjects (10% compared to 5%, respectively). Twenty percent of the clone libraries derived from H. pylori-positive patients were non-H. pylori Proteobacteria compared with 10% in the control subjects; this was also the case for Bacteroidetes (20% compared with 10% in the control) [48]
(c) Experimentally manipulated microbial communities
Restoration of wetland soils 3 agriculture wetlands, 3 restored wetlands and 3 reference wetlands 13 1,235 95 A significant difference in the Proteobacteria:Acidobacteria ratio from around 0.6 to around 0.4 was observed between agricultural and reference wetlands, respectively (P < 0.001). A difference was also found in the relative abundance of β-Proteobacteria from 14 to 3% in the same soils (P < 0.001) [22]
Soil moisture 4 wet and 4 dry soils 8 665 83 The relative abundance of Proteobacteria decreased from 48 to 36% in wet versus dry plots (P < 0.05). Acidobacteria increased in relative abundance from 7 to 23% in the same soils (P < 0.01) [21]
Antibiotic effects on piglet gut microbiota 6 control pigs and 6 pigs treated with chlor-tetracycline 12 1,900 171 An effect of antibiotics was seen on the overall community composition (P < 0.03) [23]
Effects of a 24-hour fast on mouse gut microbiota 4 to 5 fasted and control mice 38 145,428 3,827 The fast resulted in a significant increase in the proportion of Bacteroidetes (approximately 21 to approximately 42%, P = 0.01) and a significant decrease in the fraction of Firmicutes (approximately 77 to around 53%, P = 0.007) within the gut microbial community [49]
Effects of diet and genotype on murine gut microbiota 5 individuals from 2 genotypes fed standard or low-fat chow 20 25,790 1,290 The relative abundance of Bacteroidetes decreased (around 90% versus around 40%) in animals fed the high-fat diet regardless of genotype (P < 0.001). Likewise, mice fed the standard chow diet showed a lower relative abundance of Firmicutes (around 7 versus around 42) independent of genotype (P < 0.001) [50]
Antibiotic effects on canine gut microbiota 5 dogs sampled three times 15 44,096 2,940 Enterococcus-like organisms, Pasteurella species, and Dietzia species all increased significantly (P < 0.05) following tylosin treatment [51]
  1. *The entire study consisted of 36 subjects of which only 20 were selected for pyrosequencing.