Table 1. Studies analyzing the human gastric microbiota using culture-based methods.
| Study | Method | # of samples | Age range | Gender | Ethnicity or Location | HP status | Phyla | Genera observed | Genus information | Clinical presentation | Comments |
|---|---|---|---|---|---|---|---|---|---|---|---|
| Savage 1977 | N/A | N/A | N/A | N/A | Various | N/A | Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, and yeasts | 9+ | Firmicutes (Lactobacillus), Firmicutes (Streptococcus), Actinobacteria (Bifidobacterium), Firmicutes (Clostridium), Firmicutes (Veillonella), Proteobacteria (Coliforms), other bacteria (Firmicutes (Peptostreptococcus, Staphylococcus) Bacteroidetes (Bacteroides), and Actinobacteria (Actinobacillus)) and yeasts | N/A | Review |
| Sharma et al. 1984 | Gastric juice culture | 10 | 19–26 (mean 22.6) | Male | England | N/A | Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria | 9 | Actinobacteria (Corynebacterium), Firmicutes (Staphylococcus), Proteobacteria (Neisseria), Firmicutes (Lactobacillus, Veilonella, Streptococcus,Bacillus), Bacteroidetes (Bacteroides), Proteobacteria (Acinetobacter) | Omeprazole daily for 2 weeks on healthy patients | OMP increased bacterial load and nitrite levels but returned to normal after Tx discontinued |
| Stock-bruegger 1985 | N/A | N/A | N/A | N/A | Various | N/A | Firmicutes, Proteobacteria, Bacteroidetes | 7 | Proteobacteria (Enterobacteriaceae), Firmicutes (Enterococcus), Firmicutes (Streptococcus), Firmicutes (Staphylococcus), Firmicutes (Lactobacillus), Firmicutes (Clostridium), Bacteroidetes (Bacteroides) | Hypochlorhydria | Review |
| Sjostedt et al. 1985 | Gastric juice culture | 10 | Pool: 28–74 | Pool: 39 males, 21 females | Sweden | N/A | Firmicutes, Proteobacteria, Actinobacteria | 6 | Firmicutes (Staphylococcus), Proteobacteria (Neisseria), Firmicutes (Streptococcus), Actinobacteria/Firmicutes (Bifidobacterium/Lactobacillus), Firmicutes (Veilonella), Bacteroidetes (Bacteroides) | Healthy | Only 1–4 of 10 patients had cultures of each |
| Gastric juice culture | 10 | Pool: 28–74 | Pool: 39 males, 21 females | Sweden | N/A | Proteobacteria, Firmicutes, Actinobacteria | 9 | Firmicutes (Streptococcus), Actinobacteria/Firmicutes (Bifidobacterium/Lactobacillus) and Firmicutes (Veilonella). Also observed Proteobacteria (Klebsiella, Escherichia, Pseudomonas), Firmicutes (Bacillus), Candida spp | Gastric cancer | 2–6 of 10 patients had cultures of each | |
| Thorens et al. 1996 | Gastric juice culture | 37 | 20–60 (mean 42) | 39 males, 8 females | Switzerland | N/A | Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes | 11 | Firmicutes (Streptococcus), Actinobacteria (Corynebacterium), Proteobacteria (Neisseria), Actinobacteria (Micrococcus), Bacteroidetes (Bacteroides), Firmicutes (Staphylococcus), Proteobacteria (Escherichia coli), Proteobacteria (Klebsiella), Actinobacteria (Rothia (previously Stomatococcus)), Firmicutes (Enterococcus, Lactobacillus) | Patients with routine endoscopy with Omeprazole and Cimetidine | Bacterial overgrowth on acid suppression. Oral and intestinal microbes seen |
| Adamsson et al. 1999 | Culture - Biochemistry, Gas chromatography | 30 | 35–75 (mean 58.5) | 14 males, 16 females | Sweden | Pos. | Firmicutes (58%), Proteobacteria (22.2%), Actinobacteria (14.3%), Bacteroidetes (3.8%) and Fusobacterium (1.5%). | 12 to 13 | Firmicutes (Streptococcus), Proteobacteria (Neisseria), Proteobacteria (Haemophilus), Firmicutes (Staphylococcus), Firmicutes (Peptostreptococcus), Firmicutes (Veilonella), Actinobacteria (Actinomyces), Actinobacteria (Micrococcus), Bacteroidetes (Prevotella-Bacteroides), Proteobacteria (Enterobacteriaceae), Yeasts, Firmicutes / Actinobacteria (Lactobacillus and Bifidobacterium), Fusobacteria (Fusobacterium) | Non-ulcer dyspepsia treated with anti-HP triple therapies (omeprazole, metronidazole and either amoxicillin or clarithromycin) | Data presented prior to antibiotics. HP eradicated. |
| Mowat et al. 2000 | Gastric juice culture | 18 | HP neg 20–45 (mean 27) | N/A | Scotland | Neg. | Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria | 11 | Firmicutes (Streptococcus), Firmicutes (Staphylococcus), Proteobacteria (Neisseria), Firmicutes (Lactobacillus), Proteobacteria (Haemophilus), Bacteroidetes (Bacteroides), Firmicutes (Clostridium), Firmicutes (Veilonella), Proteobacteria (Coliform), Actinobacteria (Corynebacterium), Proteobacteria (Moraxella (previously Branhamella)), Yeast | Healthy | Samples collected during omeprazole treatment (pH 3). |
| Gastric juice culture | 11 | HP pos 21–45 (mean 29) | N/A | Scotland | Pos. | Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria. HP decreased Firmicutes and increases in Proteobacteria/Bacteroidetes | 11 | Firmicutes (Streptococcus), Proteobacteria (Neisseria), Firmicutes (Staphylococcus), Bacteroidetes (Bacteroides), Firmicutes (Veilonella), Proteobacteria (Haemophilus), Firmicutes (Clostridium), Proteobacteria (HP), Proteobacteria (Moraxella (previously Branhamella)), Firmicutes (Lactobacillus), Actinobacteria (Corynebacterium).# | Healthy | Samples collected during omeprazole treatment (pH 8). Nitrosating bacteria found. HP presence was not high. | |
| Kato et al. 2006 | Biopsy, Gastric juice culture with qPCR | 10 | 9 to 16 | 3 males, 7 females | Japan | Pos. | Firmicutes, Actinobacteria, Bacteroidetes | 5 | Firmicutes (Lactobacillus), Actinobacteria (Bifidobacterium), Firmicutes (Eubacterium), Bacteroidetes (Bacteroides), Firmicutes (Faecalibacterium (previously Fusobacteria) prausnitzii) | Children (gastritis, duodenal ulcer, reflux esophagitis, non-ulcer dyspepsia). | Did not culture HP. Only recovered bacteria from 2 children |
| Biopsy, Gastric juice culture with qPCR | 10 | 9 to 16 | 3 males, 7 females | Japan | Neg. | 1 | Firmicutes (Lactobacillus) | Did not culture HP. Only recovered from 1 child with highest pH | |||
| Biopsy, Gastric juice culture with qPCR | 10 | 33–79 | 4 males, 6 females | Japan | Pos. | Firmicutes, Proteobacteria, Bacteroidetes | 9 | Firmicutes (Streptococcus), Firmicutes (Bacillus), Firmicutes (Veilonella), Proteobacteria (Neisseria), Firmicutes (Lactobacillus), Bacteroidetes (Bacteroides), Firmicutes (Peptostreptococcus), Firmicutes (Staphylococcus) | Adults (gastritis, gastric ulcer, early gastric cancer, gastric adenoma, non-ulcer dyspepsia) | Did not culture HP. Higher bacterial load (100 fold) correlated with higher pH | |
| Biopsy, Gastric juice culture with qPCR | 10 | 33–79 | 4 males, 6 females | Japan | Neg. | Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria | 9 | Firmicutes (Bacillus), Firmicutes (Streptococcus), Firmicutes (Staphylococcus), Proteobacteria (Neisseria), Firmicutes (Veilonella), Bacteroidetes (Bacteroides), Fusobacteria (Fusobacterium) | Adults (gastritis, gastric ulcer, early gastric cancer, gastric adenoma, non-ulcer dyspepsia) | Did not culture HP | |
| Zilberstein et al. 2007 | Biopsy, Culture | 20 | Mean age 42 | 8 males, 12 females | Brazil | N/A | Firmicutes, Proteobacteria, Actinobacteria, Fusobacteria, Bacteroidetes | 18 | Firmicutes (Lactobacillus) (41.6%), Firmicutes (Veilonella) (41.6%), Firmicutes (Clostridium) (33.3%), Actinobacteria (Corynebacterium) (25%), Proteobacteria (Escherichia) (16%), Bacteroidetes (Bacteroides) (16%), Proteobacteria (Klebsiella) (16%), Firmicutes (Peptococcus) (16%). Other genera observed were Fusobacteria (Fusobacterium), Actinobacteria (Propionibacterium), Firmicutes (Peptostreptococcus, Staphylococcus, and Streptococcus), Proteobacteria (Proteus and Enterobacter) and yeast | Healthy | Found acid resistant strains. Proteobacteria likely from lower bowel |
| Hu et al. 2012 | Biopsy, Culture + MALDI-TOF mass spectrometry | 67 samples from 103 patients | 81 patients < 50 y old | 51 males, 52 females | China | Pos. | Firmicutes, Proteobacteria, Actinobacteria | Proteobacteria (Neisseria), Firmicutes (Streptococcus), Actinobacteria (Rothia), Firmicutes (Staphylococcus) | Upper GI diseases (duodenal ulcers, gastric ulcers, gastritis, dyspepsia, esophagitis) | Detected Acinetobacter lwoffi | |
| Delgado et al. 2013 | Biopsy, Culture | 12 | Mean age 60.5 | 6 males, 6 females | Spain | Neg. | Firmicutes, Actinobacteria, Proteobacteria | 9 | Actinobacteria (Propionibacterium), Firmicutes (Lactobacillus), Firmicutes (Staphylococcus) | Dyspeptic without PPI | P. acnes was surprising but it has shown in other studies (Monstein et al.) |
*
N/A, not available; Pos., positive; Neg., negative; #, underlined values are altered by HP infection compared to negative controls