Table 2. Studies analyzing the human gastric microbiota using 16S rRNA identification methods.
| Study | Method | # of samples | Age range | Gender | Ethnicity or Location | HP status | Phyla | Genera (OTUs) observed | Genus information | Clinical status | Comments |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Monstein et al. 2000 | Biopsy/TTGE/Sanger-sequenced 16S rDNA library | 13 of 22 | Pool: male (44–79), female (43–76) | Pool: 10 males, 12 females | Sweden | Pos. | Proteobacteria, Firmicutes, Actinobacteria | 11 | Proteobacteria (Pseudomonas), Firmicutes (Enterococcus, Staphylococcus, Streptococcus), and Actinobacteria (Rothia (prev. Stomatococcus)). Low abundance Proteobacteria (Acinetobacter, Brevundimonas, Enterobacter, Helicobacter (non HP), and Rhizobium) and Actinobacteria (Propionibacterium) | No gastritis(5) or no clinical gastritis (8) | Gastritis increased HP numbers and reduced detection of other bacteria. Detected other Helicobacters |
| Bik et al. 2006 | Biopsy/Sanger-sequenced 16S rDNA library | 23 | 42–78 | 22 males, 1 female | USA (13 Caucasian, 5 Hispanic, 5 African-American) | 12 of 23 Pos., but 7 of 11 Neg. had counts of HP | Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, and Fusobacteria | 128 | HP = 72% of reads in Pos. patients, but still 11% in Neg. patients. Non-HP genera in the overall library were Firmicutes (Streptococcus, Veilonella), Bacteroidetes (Prevotella), Actinobacteria (Rothia), Fusobacteria (Fusobacterium) |
Medically indicated gastroscopies. 8/23 on acid blockers. pH range from 2–7 | Only detected H. pylori from genus Helicobacter. H. pylori is dominant but does not affect underlying structure and diversity. HP samples had relative lack of Bacteroidetes phylotypes |
| Andersson et al. 2008 | Biopsy/454 pyrosequencing of V6 of 16S rRNA amplicons | 3 | 61–76 | N/A | Sweden | Neg. | Actinobacteria (46.8%), Firmicutes (29.6%), Bacteroidetes (11.1%), Proteobacteria (10.8%), Fusobacteria (1.1%) | 262 | Firmicutes (Streptococcus, Gemella), Actinobacteria (Actinomyces), Bacteroidetes (Prevotella) | Healthy | Only 33 of 262 seen in all three Neg. samples. H. pylori reduced diversity. Found many throat organisms, so may be transients. Non-throat organisms were Proteobacteria |
| 3 | 61–76 | N/A | Sweden | Pos. | Proteobacteria (96%), Firmicutes (1.8%), Actinobacteria (1.1%), Bacteroidetes (0.8%) and Fusobacteria (0.1%) | 33 | HP 93–97% | Healthy | HP dominates with 93–97% of reads | ||
| Dicksved et al. 2009 | Biopsy/T-RFLP/Sanger-sequenced 16S rRNA library | 10 | 52–88 | 8 males, 2 females | Sweden | 8 of 10 | Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria | 102 | Firmicutes (Streptococcus, Lactobacillus and Veilonella) and Bacteroidetes:Prevotella | Gastric cancer (intestinal- and diffuse-type) | Low abundance of HP. Did not find disease related association from clustering of T-RFLP data from dyspepsia and GC samples |
| Biopsy/T-RFLP | 5 | 52–88 | 2 males, 3 females | Sweden | 0 of 5 | Firmicutes, Bacteroidetes, Actinobacteria | Firmicutes (Veilonella, Streptococcus) and Bacteroidetes (Prevotella) | Dyspepsia | |||
| Li et al. 2009 | Biopsy/Sanger-sequenced 16S rDNA library | 5 | Pool - 40–87 | Female | Hong Kong | Neg. | Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, Fusobacteria | 133 | Proteobacteria (Neisseria), Bacteroidetes (Prevotella), Firmicutes (Streptococcus), Proteobacteria (Haemophilus), Bacteroidetes (Porphyromonas) | Asymptomatic | Found 1–2 dominant genera per phyla. Neisseria and Haemophilus higher in asymptomatic patients |
| 5 | Pool - 40–87 | Female | Hong Kong | Neg. | Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Fusobacteria | 133 | Firmicutes (Streptococcus), Bacteroidetes (Prevotella), Proteobacteria (Neisseria, Haemophilus), Bacteroidetes (Porphyromonas) | Gastritis | Streptococcus higher in gastritis. Streptococcus and Prevotella levels correspond with Bik et al. | ||
| Maldonado-Contreras et al. 2010 | Biopsy/PhyloChip | 4 | 37–80 | 2 males, 2 females | 4 Amerindians | Neg. | Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes | 154 (family) | Gastritis | ||
| 8 | 21–59 | 4 males, 4 females | 6 Amerindians, 2 USA (South Asia and Africa) | Pos. | Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes | 137 (family) | Dyspepsia, GERD, Gastritis | No differences on taxonomic complexity but HP increases relative abundance of non-Helicobacter bacteria from Proteobacteria, Spirochetes, and Acidobacteria. Decreased abundance of Actinobacteria, Bacteroidetes and Firmicutes. | |||
| Stearns et al. 2011 | Biopsy/V3 16S rRNA sequencing (Sanger and Illumina) (data for males and females) | 4 | > 50 | 2 males, 2 females | Canada | Unk. | Overall antrum Proteobacteria (50.66%), Firmicutes (35.7%), Bacteroidetes (13.47%). Overall corpus Firmicutes (69.0%), Proteobacteria (16.7%), Fusobacteria (8.1%) | 23 antrum 24 body | Healthy undergoing gastroscopy | High variability between subjects and between antrum and corpus. Data hard to interpret as they only report phyla and genera present in all 4 samples. | |
| Same data (only males) | 2 | > 50 | Male | Canada | Unk. | Antrum: Male (avg) Proteobacteria 99.6%. Corpus Male 1 Proteobacteria (45.0%), Fusobacteria (22.1%), Firmicutes (16.0%), Bacteroidetes (14.9%) and SR1 (2.0%). Corpus Male 2 Firmicutes (Parvimonas) (99.44%) | Antrum: Males = 99% Proteobacteria - no genus data (HP?) Corpus: Male 1 = Firmicutes (Parvimonas) (99.4%), Male 2 = Proteobacteria (no data) (45%), Fusobacteria (no data) (22.1%), Firmicutes (Streptococcus, Veilonella, other) (16%), Bacteroidetes (Prevotella, Porphyromonas, other) (14.9%), SR1 (no data) (2%) | Healthy undergoing gastroscopy | n = 2 per site | ||
| Same data (only females) | 2 | > 50 | Female | Canada | Unk. | Female antrum: Firmicutes, Bacteroidetes. Female corpus: Firmicutes. | Antrum: Female = Firmicutes (Streptococcus) (72.6%) and Bacteroidetes (Prevotella) (27.3%). Corpus: Female = Firmicutes [Veilonella, Streptococcus and Oribacterium] (99.9%) | Healthy undergoing gastroscopy | n = 1 per site | ||
| Delgado et al. 2013 | Biopsy/454 pyrosequencing of 16S rDNA amplicons | 4 sequenced | Mean age 60.5 | Pool: 6 males, 6 females | Spain | Neg. | Firmicutes, Proteobacteria, Actinobacteria with small proportions of Deinococcus-Thermus, Bacteroidetes and Gemmatimonadetes | 19 core. 69 total | Firmicutes (Streptococcus, Lactobacillus), Actinobacteria (Propionibacterium), and Proteobacteria (Methylobacterium) were dominant. Dominant genera varied by sample. | dyspeptic without PPI | High variability between subjects |
*
N/A, Not available, Pos., positive, Neg., negative, Unk., unknown H. pylori status