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

Das, Anubhav; Pereira, Verima; Saxena, Shruti; Ghosh, Tarini Shankar; Anbumani, D.; Bag, Satyabrata; Das, Bhabatosh; Nair, G. Balakrish; Abraham, Philip; Mande, Sharmila S.

doi:10.1038/s41598-017-15510-6

Cited by 56 publications

(57 citation statements)

References 25 publications

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“…However, 7 days after the salmon were rst symptomatic (T3), the environmental pressure was eased, and the structure of the microbial communities appeared less deterministic, driven instead by a competitive exclusion principle (the ecological principle whereby community assembly is unhindered, and is driven by competition amongst taxa). Those trends were previously observed in the literature, albeit in connection with a different disease [30]. At the same time, N. perurans concentrations, determined by qPCR pro les, sharply increased by T3.…”

Section: Impact Of Agd and Freshwater Bathing On The Gill Microbiomesupporting

confidence: 85%

Dynamic Gill and Mucous Microbiomes Track an Amoebic Gill Disease Episode in Farmed Atlantic Salmon

Birlanga¹,

McCormack²,

Ijaz³

et al. 2020

Preprint

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Background Amongst gill disorders in Atlantic salmon, amoebic gill disease (AGD) is currently one of the most common and virulent, resulting in large losses for the aquaculture industry. However, our understanding of the role of the gill microbiome during AGD development is limited. Thus, we undertook a longitudinal study with the main objective of characterising the microbiome of gill, and mucous, samples from farmed Atlantic salmon before, and during, an AGD episode. Using a newly optimised DNA extraction protocol, we sequenced rRNA genes from 90 Atlantic salmon gill microbiomes from a fish farm (West coast of Ireland) over the course of a summer season. The first aetiological agent of AGD, Neoparamoeba perurans , was quantified using PCR targeting 18S rRNA genes. The same analyses were done using mucous samples as suitable, non-lethal alternatives to gill samples. Microbiome features across the sampling campaign were distinguished, focusing on patterns before and during the AGD episode. Results The richness and balance of the prokaryotic community on gills were trending upwards prior to the first appearance of AGD symptoms. The microbiome changed significantly, with reduced diversity and balance, after the AGD episode was confirmed, and the changing bacterial community was driven by competitive exclusion. However, this trend was reversed with the application of a first, and a second, freshwater bath treatment. Mucous samples behaved similarly. The variance of the entire prokaryotic community from both gill and mucous samples was significantly affected by the abundance of N. perurans . Rubritalea sp. were abundant in every gill and mucous sample; however, other genera ( Dyadobacter, Shewanella and Pedobacter ) were maximally abundant in gill and mucous samples 12 days prior to the first detection of AGD symptoms. Conclusions Gill and mucous microbiomes changed significantly after the first AGD symptoms were evident, correlating with N. perurans concentrations and supporting a connection between the development of the AGD and the gill microbiome. Those changes, however, were reversed by the application of multiple freshwater treatments, which returned gills to a more healthy state. Despite differences between microbiome features from gill and mucous samples, the data establish mucous scrapings as suitable, non-lethal substitutes for partial characterisation of the whole prokaryotic community from fish gills. The genus Shewanella was widely present, and significantly more abundant, immediately before the first AGD symptoms than during the AGD episode, marking this out as a feasible, putative target in identifying proxies for early detection of AGD.

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Section: Impact Of Agd and Freshwater Bathing On The Gill Microbiomesupporting

confidence: 85%

Dynamic Gill and Mucous Microbiomes Track an Amoebic Gill Disease Episode in Farmed Atlantic Salmon

Birlanga¹,

McCormack²,

Ijaz³

et al. 2020

Preprint

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“…These include two studies from India, two studies from Europe (UK and Austria) and single studies from China, Japan and Nicaragua. [33][34][35][36][37][38][39] Changes in the gastric microbiome were noted in all studies in response to H. pylori infection or different pathological states however other than H. pylori infection, there was no consistent gastric microbiome signature detected probably reflecting the importance of environmental influences. All studies noted reduced microbial diversity in H. pylori-infected groups, with one of the studies from India highlighting the ability of H. pylori to shape the constitution of the gastric microbiome but suggesting that other members of the Helicobacteraceae could also similarly influence community structure.…”

Section: Helicobacter Pylori and The Gastric Microbiomementioning

confidence: 87%

“…Several articles have also looked at the gastric microbiome in noncancerous and premalignant conditions as a result of H. pylori infection. These include two studies from India, two studies from Europe (UK and Austria) and single studies from China, Japan and Nicaragua . Changes in the gastric microbiome were noted in all studies in response to H. pylori infection or different pathological states however other than H. pylori infection, there was no consistent gastric microbiome signature detected probably reflecting the importance of environmental influences.…”

Section: Gastric Microbiomementioning

confidence: 93%

“…Changes in the gastric microbiome were noted in all studies in response to H. pylori infection or different pathological states however other than H. pylori infection, there was no consistent gastric microbiome signature detected probably reflecting the importance of environmental influences. All studies noted reduced microbial diversity in H. pylori‐ infected groups, with one of the studies from India highlighting the ability of H. pylori to shape the constitution of the gastric microbiome but suggesting that other members of the Helicobacteraceae could also similarly influence community structure . In addition, the study from Austria stratified the H. pylori‐ positive patient samples based on CagA status which potentially suggested that CagA expression might be influencing H. pylori proliferation within the stomach, although larger studies are needed to confirm it .…”

Section: Gastric Microbiomementioning

confidence: 99%

“…All studies noted reduced microbial diversity in H. pylori-infected groups, with one of the studies from India highlighting the ability of H. pylori to shape the constitution of the gastric microbiome but suggesting that other members of the Helicobacteraceae could also similarly influence community structure. 34 In addition, the study from Austria stratified the H. pylori-positive patient samples based on CagA status which potentially suggested that CagA expression might be influencing H. pylori proliferation within the stomach, although larger studies are needed to confirm it. 35 The first study to assess active gastric microbiome using metatranscriptomics (derived from RNA rather than genomic DNA) was published in 2017.…”

Section: Helicobacter Pylori and The Gastric Microbiomementioning

confidence: 99%

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Other Helicobacters and the gastric microbiome

Kupčinskas

Hold

2018

Helicobacter

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The current article is a review of the most important, accessible, and relevant literature published between April 2017 and March 2018 on other Helicobacters and the gastric microbiome. The first part of the review focuses on literature describing non-Helicobacter pylori-Helicobacter (NHPH) infections in humans and animals whilst the subsequent section focuses specifically on the human gastric microbiome. Novel diagnostic methods as well as new NHPHs species have been identified in recent studies. Furthermore, our knowledge about the pathogenesis of NHPH infections has been further enhanced by important fundamental studies in cell lines and animal models. Over the last year, additional insights over the prevalence and potential prevention strategies of NHPHs have also been reported. With regard to understanding the gastric microbiome, new information detailing the structure of the gastric microbiota at different stages of H. pylori infection, within different patient geographical locations, was documented. There was also a study detailing the impact of proton-pump inhibitor usage and the effect on the gastric microbiome. Newer analysis approaches including defining the active microbiome through analysis of RNA rather than DNA-based sequencing were also published allowing the first assessments of the functional capabilities of the gastric microbiome.

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Helicobacter pylori infection affects the human gastric microbiome, as revealed by metagenomic sequencing

Wang

Zhang

et al. 2022

FEBS Open Bio

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Helicobacter pylori infection is a prevalent infectious disease, associated with many gastric diseases, including gastritis, gastric ulcer, and gastric cancer. To reveal the characteristics of the gastric microbiome in patients infected with H. pylori, we performed metagenomic shotgun sequencing of stomach swab samples from 96 patients and then conducted metagenomic association analyses between alterations in the gastric microbiome and H. pylori infection status. The overall composition of the gastric microbiota in H. pylori‐infected individuals was distinctly different from the negative controls; H. pylori became the dominant species after colonizing the human stomach and significantly decreased the α‐diversity of the gastric community (P < 0.05, Wilcoxon rank‐sum test). We also identified 6 HPI‐associated microbial species (FDR < 0.05, Wilcoxon rank‐sum test): Stenotrophomonas maltophilia, Stenotrophomonas unclassified, Chryseobacterium unclassified, Pedobacter unclassified, Variovorax unclassified, and Pseudomonas stutzeri. Furthermore, 55 gastric microbial pathways were enriched in the H. pylori‐positive group, whereas only 2 pathways were more abundant in the H. pylori‐negative group: dTDP‐L‐rhamnose biosynthesis and tetrapyrrole biosynthesis (FDR < 0.05, Wilcoxon rank‐sum test). Gastritis was not associated with non‐H. pylori species in the stomach (P > 0.05, Wilcoxon rank‐sum test). This study revealed alterations in gastric microbial taxa and function associated with HPI in the Chinese population, which provides an insight into gastric microbial interactions and their potential role in the pathological process of gastric diseases.

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

Cited by 56 publications

References 25 publications

Dynamic Gill and Mucous Microbiomes Track an Amoebic Gill Disease Episode in Farmed Atlantic Salmon

Dynamic Gill and Mucous Microbiomes Track an Amoebic Gill Disease Episode in Farmed Atlantic Salmon

Other Helicobacters and the gastric microbiome

Helicobacter pylori infection affects the human gastric microbiome, as revealed by metagenomic sequencing

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