Mucosal microbiome dysbiosis in gastric carcinogenesis

ObjectivesWe aimed to characterise the microbial changes associated with histological stages of gastric tumourigenesis.DesignWe performed 16S rRNA gene analysis of gastric mucosal samples from 81 cases including superficial gastritis (SG), atrophic gastritis (AG), intestinal metaplasia (IM) and gastric cancer (GC) from Xi’an, China, to determine mucosal microbiome dysbiosis across stages of GC. We validated the results in mucosal samples of 126 cases from Inner Mongolia, China.ResultsWe observed significant mucosa microbial dysbiosis in IM and GC subjects, with significant enrichment of 21 and depletion of 10 bacterial taxa in GC compared with SG (q<0.05). Microbial network analysis showed increasing correlation strengths among them with disease progression (p<0.001). Five GC-enriched bacterial taxa whose species identifications correspond to Peptostreptococcus stomatis, Streptococcus anginosus, Parvimonas micra, Slackia exigua and Dialister pneumosintes had significant centralities in the GC ecological network (p<0.05) and classified GC from SG with an area under the receiver-operating curve (AUC) of 0.82. Moreover, stronger interactions among gastric microbes were observed in Helicobacter pylori-negative samples compared with H. pylori-positive samples in SG and IM. The fold changes of selected bacteria, and strengths of their interactions were successfully validated in the Inner Mongolian cohort, in which the five bacterial markers distinguished GC from SG with an AUC of 0.81.ConclusionsIn addition to microbial compositional changes, we identified differences in bacterial interactions across stages of gastric carcinogenesis. The significant enrichments and network centralities suggest potentially important roles of P. stomatis, D. pneumosintes, S. exigua, P. micra and S. anginosus in GC progression.

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Association between the relative abundance of gastric microbiota and the risk of gastric cancer: a case-control study

Scientific Reports ◽

10.1038/s41598-019-50054-x ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 10

Author(s):

Madhawa Neranjan Gunathilake ◽

Jeonghee Lee ◽

Il Ju Choi ◽

Young-Il Kim ◽

Yongju Ahn ◽

...

Keyword(s):

Gastric Cancer ◽

Relative Abundance ◽

Protective Factor ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Logistic Regression Models ◽

Diverse Community ◽

H Pylori ◽

Study Participants ◽

Gastric Microbiota

Abstract The human gut hosts a diverse community of bacteria referred to as the gut microbiome. We investigated the association between the relative abundance of gastric microbiota and gastric cancer (GC) risk in a Korean population. The study participants included 268 GC patients and 288 controls. DNA was extracted from gastric biopsies, and 16S rRNA gene analysis was performed. Unconditional logistic regression models were used to observe the associations. Of the participants, those who had the highest level (highest tertile) of relative Helicobacter pylori and Propionibacterium acnes abundances showed a significantly higher risk for GC after adjusting for potential confounding variables (odds ratio (OR) = 1.86, 95% confidence interval (CI) = 1.17–2.97, p for trend = 0.017 and OR = 4.77, 95% CI = 2.94–7.74, p for trend <0.001, respectively). Subjects who carried Prevotella copri had a significantly higher risk of GC than noncarriers (OR = 2.54, 95% CI = 1.42–4.55, p for trend = 0.002). There was a lower risk of GC in subjects carrying Lactococcus lactis than in noncarriers (OR = 0.21, 95% CI = 0.10–0.44, p for trend <0.001). H. pylori, P. acnes and P. copri are strong risk factors, whereas L. lactis is a protective factor, for GC development in Koreans. Further microbiome studies are warranted to verify the findings of the current study.

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Alterations of Gastric Microbiota in Gastric Cancer and Precancerous Stages

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.559148 ◽

2021 ◽

Vol 11 ◽

Author(s):

Xinmei Zhang ◽

Chao Li ◽

Weijun Cao ◽

Zhenyu Zhang

Keyword(s):

Gastric Cancer ◽

Cancer Patients ◽

Gastric Carcinogenesis ◽

Oral Bacteria ◽

Rrna Gene ◽

Cardia Cancer ◽

Microbial Composition ◽

16S Rrna Gene Analysis ◽

Linear Discriminant ◽

Gastric Microbiota

ObjectiveMicrobial infections have been shown to contribute to gastric carcinogenesis, the knowledge of gastric microbiota alteration in this process may provide help in early diagnosis of gastric cancer. The aim of this study was to characterize the microbial changes and identify taxonomic biomarkers across stages of gastric carcinogenesis.MethodsThe gastric microbiota was investigated by 16S rRNA gene analysis in gastric mucosal specimens from 47 patients including superficial gastritis (SG), atrophic gastritis (AG), gastric intraepithelial neoplasia (GIN), and gastric cancer (GC). Differences in microbial composition across the disease stages, especially in GIN and GC were assessed using linear discriminant analysis effect size.ResultsThere was no gradual changing trend in the richness or diversity of the gastric microbiota across stages of gastric carcinogenesis. The relative abundance of dominant taxa at phylum and genus levels didn’t show a gradual shift pattern, and the only four taxa that continuously enriched from SG to GC were Slackia, Selenomonas, Bergeyella, and Capnocytophaga, all of which were oral bacteria. The most representative taxa which were enriched in GC patients were oral bacteria including Parvimonas, Eikenella and Prevotella-2, and environmental bacteria including Kroppenstedtia, Lentibacillus, and Oceanobacillus. The gastric microbiota in GIN patients were characterized by enrichment of intestinal commensals including Romboutsia, Fusicatenibacter, Prevotellaceae-Ga6A1-group, and Intestinimonas. Gastric cardia cancer and non-cardia cancer patients had significantly different microbiota profiles characterized by a higher abundance of Helicobacter in the cardia cancer patients.ConclusionsOur results provide insights on potential taxonomic biomarkers for gastric cancer and precancerous stages, and suggest that gastric microbiota might play different roles in the carcinogenesis of cardia cancer and non-cardia cancer.

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Unravelling a microbial synergy to boost caproate production via carboxylates chain elongation with ethanol

HKIE Transactions ◽

10.33430/v26n2thie-2018-0041 ◽

2019 ◽

Vol 26 (2) ◽

pp. 63-71

Author(s):

Ling Leng ◽

Ying Wang ◽

Peixian Yang ◽

Takashi Narihiro ◽

Masaru Konishi Nobu ◽

...

Keyword(s):

Fatty Acids ◽

Volatile Fatty Acids ◽

Microbial Consortia ◽

Chain Elongation ◽

Desulfovibrio Vulgaris ◽

Rrna Gene ◽

Selective Enrichment ◽

Microbial Network ◽

Cost Efficient ◽

Rrna Gene Sequencing

Chain elongation of volatile fatty acids for medium chain fatty acids production (e.g. caproate) is an attractive approach to treat wastewater anaerobically and recover resource simultaneously. Undefined microbial consortia can be tailored to achieve chain elongation process with selective enrichment from anaerobic digestion sludge, which has advantages over pure culture approach for cost-efficient application. Whilst the metabolic pathway of the dominant caproate producer, Clostridium kluyveri, has been annotated, the role of other coexisting abundant microbiomes remained unclear. To this end, an ethanol-acetate fermentation inoculated with fresh digestion sludge at optimal conditions was conducted. Also, physiological study, thermodynamics and 16 S rRNA gene sequencing to elucidate the biological process by linking the system performance and dominant microbiomes were integrated. Results revealed a possible synergistic network in which C. kluyveri and three co-dominant species, Desulfovibrio vulgaris, Fusobacterium varium and Acetoanaerobium sticklandii coexisted. D. vulgaris and A. sticklandii (F. varium) were likely to boost the carboxylates chain elongation by stimulating ethanol oxidation and butyrate production through a syntrophic partnership with hydrogen (H2) serving as an electron messenger. This study unveils a synergistic microbial network to boost caproate production in mixed culture carboxylates chain elongation.

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Increased Production of Matrix Metalloproteinases in Helicobacter pylori Infection that Stimulates Gastric Cancer Stem Cells

International Journal of Veterinary Science ◽

10.37422/ijvs/20.043 ◽

2020 ◽

Keyword(s):

Gastric Cancer ◽

Stem Cells ◽

Helicobacter Pylori ◽

Cancer Stem Cells ◽

Histopathological Examination ◽

Physiological Saline ◽

Rrna Gene ◽

Peptic Ulcers ◽

Gastric Cancer Stem Cells ◽

H Pylori

Background and aim: Helicobacter pylori (H. pylori) is an incriminated pathogen causing diseases in both animals and humans and considered a zoonotic pathogen. H. pylori infection is considered a cause of gastric cancer, which rests a significant health care challenge. This study analyzes the expression pattern of matrix metalloprotein 2 (MMP-2) in patients with Helicobacter pylori-associated gastritis and the effect of H. pylori on gastric cancer stem cells, as well as study the role of helicon bacteriosis in dog in transmission of H. pylori infection to human. Materials and methods: Fifty-five of each sample (gastric biopsy, blood and stool) were collected from patients suffering from dyspepsia, chronic vomiting and perforated peptic ulcers and also from apparent healthy dogs. The investigation detected H. pylori by serological and histopathological examination. Biopsies were stored in physiological saline for identification of H. pylori by conventional time PCR. MMP-2 and Gastric cancer stem cells were then identified by immunohistochemistry. Results: Serological identification for H. pylori Antigen and Antibodies revealed (63% human, 50% dogs) and (87% human, 90% dogs) respectively were positive. Genotyping of H. pylori based on 16S rRNA gene showed 54.5% of human and 35% of dogs were positive. Immunohistochemistry revealed strong expression of CD44 in H. pylori- associated gastric cancer cases, MMP-2 expression was observed in all neoplastic lesions associated with H. pylori infection. Conclusion: H. pylori infection affects gastric mucosa and induces changes in gastric stem cells altering their differentiation and increased expression of MMP’s and CD44with a resultant potentiation of oncogenic alteration. In addition the up-regulation of both markers could be an instrumental to interpret the origination of gastric cancer.

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Microbiome of Odontogenic Abscesses

Microorganisms ◽

10.3390/microorganisms9061307 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1307

Author(s):

Sebastian Böttger ◽

Silke Zechel-Gran ◽

Daniel Schmermund ◽

Philipp Streckbein ◽

Jan-Falco Wilbrand ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Oral Microbiome ◽

Minor Role ◽

Rrna Gene ◽

Sequencing Analysis ◽

Bacterial Strains ◽

16S Rrna Gene Analysis ◽

Odontogenic Infections ◽

Odontogenic Abscess

Severe odontogenic abscesses are regularly caused by bacteria of the physiological oral microbiome. However, the culture of these bacteria is often prone to errors and sometimes does not result in any bacterial growth. Furthermore, various authors found completely different bacterial spectra in odontogenic abscesses. Experimental 16S rRNA gene next-generation sequencing analysis was used to identify the microbiome of the saliva and the pus in patients with a severe odontogenic infection. The microbiome of the saliva and the pus was determined for 50 patients with a severe odontogenic abscess. Perimandibular and submandibular abscesses were the most commonly observed diseases at 15 (30%) patients each. Polymicrobial infections were observed in 48 (96%) cases, while the picture of a mono-infection only occurred twice (4%). On average, 31.44 (±12.09) bacterial genera were detected in the pus and 41.32 (±9.00) in the saliva. In most cases, a predominantly anaerobic bacterial spectrum was found in the pus, while saliva showed a similar oral microbiome to healthy individuals. In the majority of cases, odontogenic infections are polymicrobial. Our results indicate that these are mainly caused by anaerobic bacterial strains and that aerobic and facultative anaerobe bacteria seem to play a more minor role than previously described by other authors. The 16S rRNA gene analysis detects significantly more bacteria than conventional methods and molecular methods should therefore become a part of routine diagnostics in medical microbiology.

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2,4-Dichlorophenoxyacetic acid degradation in methanogenic mixed cultures obtained from Brazilian Amazonian soil samples

Biodegradation ◽

10.1007/s10532-021-09940-3 ◽

2021 ◽

Author(s):

Gunther Brucha ◽

Andrea Aldas-Vargas ◽

Zacchariah Ross ◽

Peng Peng ◽

Siavash Atashgahi ◽

...

Keyword(s):

Microbial Community Composition ◽

High Mobility ◽

16S Rrna Gene Sequencing ◽

Dichlorophenoxyacetic Acid ◽

Rrna Gene ◽

Deep Soil ◽

Anoxic Environments ◽

Top Soil ◽

Significant Enrichment ◽

2,4 Dichlorophenoxyacetic Acid

Abstract2,4-Dichlorophenoxyacetic acid (2,4-D) is the third most applied pesticide in Brazil to control broadleaf weeds in crop cultivation and pastures. Due to 2,4-D’s high mobility and long half-life under anoxic conditions, this herbicide has high probability for groundwater contamination. Bioremediation is an attractive solution for 2,4-D contaminated anoxic environments, but there is limited understanding of anaerobic 2,4-D biodegradation. In this study, methanogenic enrichment cultures were obtained from Amazonian top soil (0—40 cm) and deep soil (50 -80 cm below ground) that biotransform 2,4-D (5 µM) to 4-chlorophenol and phenol. When these cultures were transferred (10% v/v) to fresh medium containing 40 µM or 160 µM 2,4-D, the rate of 2,4-D degradation decreased, and biotransformation did not proceed beyond 4-chlorophenol and 2,4-dichlorophenol in the top and deep soil cultures, respectively. 16S rRNA gene sequencing and qPCR of a selection of microbes revealed no significant enrichment of known organohalide-respiring bacteria. Furthermore, a member of the genus Cryptanaerobacter was identified as possibly responsible for phenol conversion to benzoate in the top soil inoculated culture. Overall, these results demonstrate the effect of 2,4-D concentration on biodegradation and microbial community composition, which are both important factors when developing pesticide bioremediation technologies.

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Gastric Cancer Microbiome

Pathobiology ◽

10.1159/000512833 ◽

2021 ◽

Vol 88 (2) ◽

pp. 156-169

Author(s):

Williams Fernandes Barra ◽

Dionison Pereira Sarquis ◽

André Salim Khayat ◽

Bruna Cláudia Meireles Khayat ◽

Samia Demachki ◽

...

Keyword(s):

Gastric Cancer ◽

Small Sample Size ◽

Total Sample ◽

Clinical Situation ◽

Gastric Carcinogenesis ◽

Comprehensive Analysis ◽

Small Sample ◽

Metagenomic Data ◽

Clinical Scenarios ◽

H Pylori

Identifying a microbiome pattern in gastric cancer (GC) is hugely debatable due to the variation resulting from the diversity of the studied populations, clinical scenarios, and metagenomic approach. H. pylori remains the main microorganism impacting gastric carcinogenesis and seems necessary for the initial steps of the process. Nevertheless, an additional non-H. pylori microbiome pattern is also described, mainly at the final steps of the carcinogenesis. Unfortunately, most of the presented results are not reproducible, and there are no consensual candidates to share the H. pylori protagonists. Limitations to reach a consistent interpretation of metagenomic data include contamination along every step of the process, which might cause relevant misinterpretations. In addition, the functional consequences of an altered microbiome might be addressed. Aiming to minimize methodological bias and limitations due to small sample size and the lack of standardization of bioinformatics assessment and interpretation, we carried out a comprehensive analysis of the publicly available metagenomic data from various conditions relevant to gastric carcinogenesis. Mainly, instead of just analyzing the results of each available publication, a new approach was launched, allowing the comprehensive analysis of the total sample amount, aiming to produce a reliable interpretation due to using a significant number of samples, from different origins, in a standard protocol. Among the main results, Helicobacter and Prevotella figured in the “top 6” genera of every group. Helicobacter was the first one in chronic gastritis (CG), gastric cancer (GC), and adjacent (ADJ) groups, while Prevotella was the leader among healthy control (HC) samples. Groups of bacteria are differently abundant in each clinical situation, and bacterial metabolic pathways also diverge along the carcinogenesis cascade. This information may support future microbiome interventions aiming to face the carcinogenesis process and/or reduce GC risk.

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Spontaneous Mutations That Confer Antibiotic Resistance inHelicobacter pylori

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.45.3.727-733.2001 ◽

2001 ◽

Vol 45 (3) ◽

pp. 727-733 ◽

Cited By ~ 91

Author(s):

Ge Wang ◽

Trevor J. M. Wilson ◽

Qin Jiang ◽

Diane E. Taylor

Keyword(s):

Mutant Allele ◽

Rapid Development ◽

Mutagenic Effect ◽

Serial Passage ◽

Sublethal Dose ◽

23S Rrna ◽

Rrna Gene ◽

Spontaneous Mutations ◽

H Pylori

ABSTRACT In this study, we systematically examined in vitro frequencies and spectra of the spontaneous mutations in Helicobacter pylori that confer resistance to clarithromycin (Clar), metronidazole (Mtzr), amoxicillin (Amxr), ciprofloxacin (Cipr), and rifampin (Rifr). The mutation rate of Rifror Cipr determined in a fluctuation assay is 1 × 10−8 to 2 × 10−8 per cell per division. In contrast, the mutation rates of Clar, Mtzr, and Amxr are much lower (<10−9). However, Mtzr mutants could be readily selected in vitro by using the serial passage method, suggesting that the mutagenic effect and selective effect of a sublethal dose of metronidazole contribute to the rapid development of Mtzr. Analysis of spontaneous Rifr, Clar, and Cipr mutants confirmed previous results indicating that mutations within therpoB gene, the 23S rRNA gene, and thegyrA gene, respectively, are responsible; also, several new mutant alleles were identified. Mtzrmutants resulted most frequently, but not always, from mutations in the rdxA gene. DNA fragments containing each mutant allele could readily transform susceptibleH. pylori strains to resistance, confirming that each mutant allele is responsible for the resistance phenotype.

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Correction: H. pylori CagL-Y58/E59 Prime Higher Integrin α5β1 in Adverse pH Condition to Enhance Hypochlorhydria Vicious Cycle for Gastric Carcinogenesis

PLoS ONE ◽

10.1371/journal.pone.0101912 ◽

2014 ◽

Vol 9 (6) ◽

pp. e101912 ◽

Cited By ~ 1

Author(s):

Yi-Chun Yeh ◽

Hsiu-Chi Cheng ◽

Hsiao-Bai Yang ◽

Wei-Lun Chang ◽

Bor-Shyang Sheu

Keyword(s):

Gastric Carcinogenesis ◽

Vicious Cycle ◽

Integrin Α5β1 ◽

H Pylori

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Biogeochemical Modelling of Uranium Immobilization and Aquifer Remediation Strategies Near NCCP Sludge Storage Facilities

Applied Sciences ◽

10.3390/app11062875 ◽

2021 ◽

Vol 11 (6) ◽

pp. 2875

Author(s):

A.V. Safonov ◽

A.E. Boguslavsky ◽

O.L. Gaskova ◽

K.A. Boldyrev ◽

O.S. Shvartseva ◽

...

Keyword(s):

Sandy Loam ◽

Influential Factor ◽

Rrna Gene ◽

16S Rrna Gene Analysis ◽

Long Term Stability ◽

Microbial Biofilms ◽

Remediation Strategies ◽

Reducing Bacteria ◽

Nitrate Reducing Bacteria ◽

Storage Facilities

Nitrate is a substance which influences the prevailing redox conditions in groundwater, and in turn the behaviour of U. The study of groundwater in an area with low-level radioactive sludge storage facilities has shown their contamination with sulphate and nitrate anions, uranium, and some associated metals. The uranyl ion content in the most contaminated NO3–Cl–SO4–Na borehole is 2000 times higher (1.58 mg/L) than that in the background water. At the same time, assessment of the main physiological groups of microorganisms showed a maximum number of denitrifying and sulphate-reducing bacteria (e.g., Sulfurimonas) in the water from the same borehole. Biogenic factors of radionuclide immobilization on sandy rocks of upper aquifers have been experimentally investigated. Different reduction rates of NO3-, SO42-, Fe(III) and U(VI) with stimulated microbial activity were dependent on the pollution degree. Moreover, 16S rRNA gene analysis of the microbial community after whey addition revealed a significant decrease in microbial diversity and the activation of nonspecific nitrate-reducing bacteria (genera Rhodococcus and Rhodobacter). The second influential factor can be identified as the formation of microbial biofilms on the sandy loam samples, which has a positive effect on U sorption (an increase in Kd value is up to 35%). As PHREEQC physicochemical modelling numerically confirmed, the third most influential factor that drives U mobility is the biogenic-mediated formation of a sulphide redox buffer. This study brings important information, which helps to assess the long-term stability of U in the environment of radioactive sludge storage facilities.

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