Gastric bacterial Flora in patients Harbouring Helicobacter pylori with or without chronic dyspepsia: analysis with matrix-assisted laser desorption ionization time-of-flight mass spectroscopy.

BACKGROUND: The gastric microbiota has recently been implicated in the causation of organic/structural gastroduodenal diseases (gastric and duodenal ulcers, gastric cancer) in patients with Helicobacter pylori (H. pylori) infection. We aimed to ascertain, in patients harbouring H. pylori, the role of the gastric microbiota in the causation of symptoms (chronic dyspepsia) in the absence of organic disease. METHODS: Seventy-four gastric biopsy samples obtained at endoscopy from patients with (n = 21) or without (n = 53) chronic dyspepsia, and that tested positive by the bedside rapid urease test for H. pylori infection, were cultured for detection of H. pylori and non-H. pylori organisms. The cultured organisms were identified by matrix-assisted laser desorption ionization time-of-flight mass spectroscopy (MALDI-TOF MS). RESULTS: A total of 106 non-H. pylori isolates were obtained from 74 patients' samples. This included 33 isolates (median 2, range 1-2 per patient) from dyspeptic and 73 (median 2, range 1-2 per patient) from non-dyspeptic patients. These were identified from the Bruker Biotyper 2 database as Staphylococcus spp., Streptococcus spp., Lactobacillus spp., Micrococcus spp., Enterococcus spp., Pseudomonas spp., Escherichia spp., Klebsiella spp. and Bacillus spp., Staphylococcus and Lactobacillus were identified significantly more commonly in dyspeptics and Streptococcus, Pseudomonas, Escherichia coli and Klebsiella pneumoniae in non-dyspeptics. All identified organisms belonged to the phyla Firmicutes and Proteobacteria. CONCLUSIONS: There is a qualitative difference in the gastric microbial spectrum between patients harbouring H. pylori with and without chronic dyspepsia. Whether these organisms have an independent role in the development or prevention of dyspepsia or act in concurrence with H. pylori needs study.

Gastric microbiome of Indian patients with Helicobacter pylori infection, and their interaction networks.

The gastric microbiome is suspected to have a role in the causation of diseases by Helicobacter pylori. Reports on their relative abundance vis-à-vis H. pylori are available from various ethnic and geographic groups, but little is known about their interaction patterns. Endoscopic mucosal biopsy samples from the gastric antrum and corpus of 39 patients with suspected H. pylori infection were collected and microbiomes were analyzed by 16S rDNA profiling. Four groups of samples were identified, which harbored Helicobacter as well as a diverse group of bacteria including Lactobacillus, Halomonas and Prevotella. There was a negative association between the microbiome diversity and Helicobacter abundance. Network analyses showed that Helicobacter had negative interactions with members of the gastric microbiome, while other microbes interacted positively with each other, showing a higher tendency towards intra-cluster co-occurrence/co-operation. Cross-geographic comparisons suggested the presence of region-specific microbial abundance profiles. We report the microbial diversity, abundance variation and interaction patterns of the gastric microbiota of Indian patients with H. pylori infection and present a comparison of the same with the gastric microbial ecology in samples from different geographic regions. Such microbial abundance profiles and microbial interactions can help in understanding the pathophysiology of gastric ailments and can thus help in development of new strategies to curb it.

An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples.

To explore the natural microbial community of any ecosystems by high-resolution molecular approaches including next generation sequencing, it is extremely important to develop a sensitive and reproducible DNA extraction method that facilitate isolation of microbial DNA of sufficient purity and quantity from culturable and uncultured microbial species living in that environment. Proper lysis of heterogeneous community microbial cells without damaging their genomes is a major challenge. In this study, we have developed an improved method for extraction of community DNA from different environmental and human origin samples. We introduced a combination of physical, chemical and mechanical lysis methods for proper lysis of microbial inhabitants. The community microbial DNA was precipitated by using salt and organic solvent. Both the quality and quantity of isolated DNA was compared with the existing methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved method has been named as the THSTI method to depict the Institute where the method was developed.