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Gut Sep 2020is associated with gastric inflammation, precancerous gastric atrophy (GA) and intestinal metaplasia (IM). We aimed to identify microbes that are associated with... (Randomized Controlled Trial)
Randomized Controlled Trial
OBJECTIVE
is associated with gastric inflammation, precancerous gastric atrophy (GA) and intestinal metaplasia (IM). We aimed to identify microbes that are associated with progressive inflammation, GA and IM 1 year after eradication.
DESIGN
A total of 587 -positive patients were randomised to receive eradication therapy (295 patients) or placebo (292 patients). Bacterial taxonomy was analysed on 404 gastric biopsy samples comprising 102 pairs before and after 1 year eradication and 100 pairs before and after 1 year placebo by 16S rRNA sequencing.
RESULTS
Analysis of microbial sequences confirmed the eradication of in treated group after 1 year. Principal component analysis revealed distinct microbial clusters reflected by increase in bacterial diversity (p<0.00001) after eradication. While microbial interactions remained largely unchanged after placebo treatment, microbial co-occurrence was less in treated group. , and were enriched while and were depleted in patients with persistent inflammation 1 year after eradication. A distinct cluster of oral bacteria comprising , , , and were associated with emergence and persistence of GA and IM. Probiotic was depleted in subjects who developed GA following eradication. Functional pathways including amino acid metabolism and inositol phosphate metabolism were enriched while folate biosynthesis and NOD-like receptor signalling decreased in atrophy/IM-associated gastric microbiota.
CONCLUSION
This study identified that gastric microbes contribute to the progression of gastric carcinogenesis after eradication.
Topics: Bacteria; Biopsy; Carcinogenesis; Disease Eradication; Disease Progression; Female; Gastritis, Atrophic; Helicobacter Infections; Helicobacter pylori; Humans; Male; Metaplasia; Microbial Interactions; Middle Aged; Sequence Analysis, RNA; Stomach
PubMed: 31974133
DOI: 10.1136/gutjnl-2019-319826 -
Microbes and Infection Jun 2003About 25% of humans with chronic gastritis are negative for Helicobacter pylori, suggesting that other bacteria are capable of causing inflammation. Bacterial overgrowth... (Review)
Review
About 25% of humans with chronic gastritis are negative for Helicobacter pylori, suggesting that other bacteria are capable of causing inflammation. Bacterial overgrowth may occur in the stomach under conditions of reduced acid secretion. In this review, we will explore what is generally known about non-H. pylori organisms and their ability to induce gastritis, with particular focus on Acinetobacter lwoffi.
Topics: Acinetobacter; Acinetobacter Infections; Gastric Mucosa; Gastritis; Helicobacter Infections; Helicobacter pylori; Humans; Models, Biological; Virulence Factors
PubMed: 12787741
DOI: 10.1016/s1286-4579(03)00099-6 -
Frontiers in Microbiology 2021A novel plasmid-encoded aminoglycoside 3''-nucleotidyltransferase ANT(3")-IId, was discovered in strain H7 isolated from a chick on an animal farm in Wenzhou, China....
A novel plasmid-encoded aminoglycoside 3''-nucleotidyltransferase ANT(3")-IId, was discovered in strain H7 isolated from a chick on an animal farm in Wenzhou, China. The whole-genome of H7 consisted of one chromosome and five plasmids (pH7-250, pH7-108, pH7-68, pH7-48, and pH7-11). was identified as being encoded on pH7-250, sharing the highest amino acid identity of 50.64% with a function-known resistance gene, (KB849358.1). Susceptibility testing and enzyme kinetic parameter analysis were conducted to determine the function of the aminoglycoside 3"-nucleotidyltransferase. The gene conferred resistance to spectinomycin and streptomycin [the minimum inhibitory concentration (MIC) levels of both increased 16-fold compared with the control strain]. Consistent with the MIC data, kinetic analysis revealed a narrow substrate profile including spectinomycin and streptomycin, with / ratios of 4.99 and 4.45×10M S, respectively. Sequencing analysis revealed that the gene was associated with insertion sequences (IS) element [ΔIS-ΔIS-hp-orf-orf-orf1-], and were identified in plasmids from various species. This study of the novel aminoglycoside 3"-nucleotidyltranferase ANT(3")-IId helps us further understand the functional and sequence characteristics of aminoglycoside 3"-nucleotidyltranferases, highlights the risk of resistance gene transfer among species and suggests that attention should be given to the emergence of new aminoglycoside 3"-nucleotidyltranferase genes.
PubMed: 34531844
DOI: 10.3389/fmicb.2021.728216 -
Frontiers in Microbiology 2021Phenol is a common environmental contaminant. The purpose of this study was to isolate phenol-degrading microorganisms from wastewater in the sections of the Chinese...
Phenol is a common environmental contaminant. The purpose of this study was to isolate phenol-degrading microorganisms from wastewater in the sections of the Chinese Medicine Manufactory. The phenol-degrading NL1 was identified based on a combination of biochemical characteristics and 16S rRNA genes. To analyze the molecular mechanism, the whole genome of . NL1 was sequenced, yielding 3499 genes on one circular chromosome and three plasmids. Enzyme activity analysis showed that . NL1 degraded phenol the -cleavage rather than the -cleavage pathway. Key genes encoding phenol hydroxylase and catechol 1,2-dioxygenase were located on a megaplasmid (pNL1) and were found to be separated by mobile genetic elements; their function was validated by heterologous expression in and quantitative real-time PCR. . NL1 could degrade 0.5 g/L phenol within 12 h and tolerate a maximum of 1.1 g/L phenol, and showed resistance against multiple antibiotics and heavy metal ions. Overall, this study shows that . NL1 can be potentially used for efficient phenol degradation in heavy metal wastewater treatment.
PubMed: 34566929
DOI: 10.3389/fmicb.2021.725755 -
Resistance of Permafrost and Modern Strains to Heavy Metals and Arsenic Revealed by Genome Analysis.BioMed Research International 2016We performed whole-genome sequencing of five permafrost strains of (frozen for 15-3000 thousand years) and analyzed their resistance genes found in plasmids and...
We performed whole-genome sequencing of five permafrost strains of (frozen for 15-3000 thousand years) and analyzed their resistance genes found in plasmids and chromosomes. Four strains contained multiple plasmids (8-12), which varied significantly in size (from 4,135 to 287,630 bp) and genetic structure; the fifth strain contained only two plasmids. All large plasmids and some medium-size and small plasmids contained genes encoding resistance to various heavy metals, including mercury, cobalt, zinc, cadmium, copper, chromium, and arsenic compounds. Most resistance genes found in the ancient strains of . had their closely related counterparts in modern clinical . strains that were also located on plasmids. The vast majority of the chromosomal resistance determinants did not possess complete sets of the resistance genes or contained truncated genes. Comparative analysis of various . and of . strains discovered a number of differences between them: (i) chromosome sizes in . exceeded those in . by about 20%; (ii) on the contrary, the number of plasmids in . and their total size were much higher than those in . ; (iii) heavy metal resistance genes in the environmental . strains surpassed those in . strains in the number and diversity and were predominantly located on plasmids. Possible reasons for these differences are discussed.
Topics: Acinetobacter; Arsenic; Biological Evolution; Cell Survival; Chromosome Mapping; Drug Resistance, Microbial; Genetic Variation; Genome, Bacterial; Metals, Heavy; Permafrost; Species Specificity
PubMed: 27795957
DOI: 10.1155/2016/3970831 -
International Journal of Molecular... Nov 2023Microorganism-based methods have been widely applied for the treatment of phenol-polluted environments. The previously isolated NL1 strain could completely degrade 0.5...
Microorganism-based methods have been widely applied for the treatment of phenol-polluted environments. The previously isolated NL1 strain could completely degrade 0.5 g/L phenol within 12 h, but not higher concentrations of phenol. In this study, we developed an evolutionary strain NL115, through adaptive laboratory evolution, which possessed improved degradation ability and was able to degrade 1.5 g/L phenol within 12 h. Compared with that of the starting strain NL1, the concentration of degradable phenol by the developed strain increased three-fold; its phenol tolerance was also enhanced. Furthermore, comparative genomics showed that sense mutations mainly occurred in genes encoding alkyl hydroperoxide reductase, phenol hydroxylase, 30S ribosomal protein, and mercury resistance operon. Comparative transcriptomics between NL115 and NL1 revealed the enrichment of direct degradation, stress resistance, and vital activity processes among the metabolic responses of adapted to phenol stress. Among these, all the upregulated genes (logfold-change > 5) encoded peroxidases. A phenotypic comparison of NL1 and NL115 found that the adapted strain NL115 exhibited strengthened antioxidant capacity. Furthermore, the increased enzymatic activities of phenol hydroxylase and alkyl hydroperoxide reductase in NL115 validated their response to phenol. Overall, this study provides insight into the mechanism of efficient phenol degradation through adaptive microbial evolution and can help to drive improvements in phenol bioremediation.
Topics: Transcriptome; Phenols; Phenol; Biodegradation, Environmental; Genomics; Peroxiredoxins
PubMed: 38003719
DOI: 10.3390/ijms242216529 -
Allergy May 2023Early-life exposure to certain environmental bacteria including Acinetobacter lwoffii (AL) has been implicated in protection from chronic inflammatory diseases including...
BACKGROUND
Early-life exposure to certain environmental bacteria including Acinetobacter lwoffii (AL) has been implicated in protection from chronic inflammatory diseases including asthma later in life. However, the underlying mechanisms at the immune-microbe interface remain largely unknown.
METHODS
The effects of repeated intranasal AL exposure on local and systemic innate immune responses were investigated in wild-type and Il6 , Il10 , and Il17 mice exposed to ovalbumin-induced allergic airway inflammation. Those investigations were expanded by microbiome analyses. To assess for AL-associated changes in gene expression, the picture arising from animal data was supplemented by in vitro experiments of macrophage and T-cell responses, yielding expression and epigenetic data.
RESULTS
The asthma preventive effect of AL was confirmed in the lung. Repeated intranasal AL administration triggered a proinflammatory immune response particularly characterized by elevated levels of IL-6, and consequently, IL-6 induced IL-10 production in CD4 T-cells. Both IL-6 and IL-10, but not IL-17, were required for asthma protection. AL had a profound impact on the gene regulatory landscape of CD4 T-cells which could be largely recapitulated by recombinant IL-6. AL administration also induced marked changes in the gastrointestinal microbiome but not in the lung microbiome. By comparing the effects on the microbiota according to mouse genotype and AL-treatment status, we have identified microbial taxa that were associated with either disease protection or activity.
CONCLUSION
These experiments provide a novel mechanism of Acinetobacter lwoffii-induced asthma protection operating through IL-6-mediated epigenetic activation of IL-10 production and with associated effects on the intestinal microbiome.
Topics: Animals; Mice; Interleukin-10; Administration, Intranasal; Interleukin-6; Disease Models, Animal; Asthma; Lung; Inflammation; Microbiota; Mice, Inbred BALB C; Ovalbumin
PubMed: 36458896
DOI: 10.1111/all.15606 -
Biomedical Papers of the Medical... Jun 2019Various food-producing animals have been recognized in recent years as a potential reservoir for the spread of antibiotic resistant bacteria that may pose a risk to...
BACKGROUND
Various food-producing animals have been recognized in recent years as a potential reservoir for the spread of antibiotic resistant bacteria that may pose a risk to human health and therefore their dissemination in the food production chain needs to be assessed.
METHODS
In this study, 450 boot swabs from chicken farms were analyzed for the presence of antimicrobial resistance with a focus on β-lactams resistance in Acinetobacter species.
RESULTS
Two β-lactamase-encoding genes were first time identified in Acinetobacter lwoffii and Acinetobacter schindleri isolates. The deduced amino acid sequence of OXA-496 shared 93.8% identity with OXA-363. The second OXA-134-like enzyme, OXA-537, had the highest sequence identity (97.8%) with OXA-235 and OXA-237.
CONCLUSIONS
The results of this study illustrate the occurrence of new OXA-134-like β-lactamases, called OXA-496 and OXA-537, carrying strains of Acinetobacter lwoffii and Acinetobacter schindleri in chicken farm litter, and highlight the possible role of Acinetobacter as a reservoir of resistance genes.
Topics: Acinetobacter; Animals; Chickens; Czech Republic; Drug Resistance, Bacterial; Farms; Microbial Sensitivity Tests; beta-Lactam Resistance; beta-Lactamases
PubMed: 30150791
DOI: 10.5507/bp.2018.037 -
Plasmid Jul 2020Emerging important Acinetobacter strains commonly accommodate a plethora of mobile elements including plasmids of different size. Plasmids, apart from encoding modules...
Emerging important Acinetobacter strains commonly accommodate a plethora of mobile elements including plasmids of different size. Plasmids, apart from encoding modules enabling their self-replication and/or transmission, can carry a diverse number of genes, allowing the host cell to survive in an environment that would otherwise be lethal or restrictive for growth. The present study characterizes the plasmidome generated from an arsenic-resistant strain named ZS207, classified as Acinetobacter lwoffii. Sequencing effort revealed the presence of nine plasmids in the size between 4.3 and 38.4 kb as well as one 186.6 kb megaplasmid. All plasmids, except the megaplasmid, do apparently not confer distinguishing phenotypic features. In contrast, the megaplasmid carries arsenic and heavy metals resistance regions similar to those found in permafrost A. lwoffii strains. In-depth in silico analyses have shown a significant similarity between the regions from these plasmids, especially concerning multiple transposable elements, transfer and mobilization genes, and toxin-antitoxin systems. Since ars genes encode proteins of major significance in terms of potential use in bioremediation, arsenic resistance level of ZS207 was determined and the functionality of selected ars genes was examined. Additionally, we checked the functionality of plasmid-encoded toxin-antitoxin systems and their impact on the formation of persister cells.
Topics: Acinetobacter; Arsenic; Bacterial Proteins; Computational Biology; DNA Transposable Elements; DNA, Bacterial; Genome, Bacterial; Gold; Mining; Plasmids; Toxin-Antitoxin Systems; Whole Genome Sequencing
PubMed: 32380021
DOI: 10.1016/j.plasmid.2020.102505 -
Biology Sep 2021Microbial life can be supported at subzero temperatures in permafrost up to several million years old. Genome analysis of strains isolated from permafrost provides a...
Genome Analysis of Strains Isolated from Permafrost Soils Aged from 15 Thousand to 1.8 Million Years Revealed Their Close Relationships with Present-Day Environmental and Clinical Isolates.
Microbial life can be supported at subzero temperatures in permafrost up to several million years old. Genome analysis of strains isolated from permafrost provides a unique opportunity to study microorganisms that have not previously come into contact with the human population. is a typical soil bacterium that has been increasingly reported as hospital pathogens associated with bacteremia. In order to identify the specific genetic characteristics of ancient permafrost-conserved strains of and their differences from present-day clinical isolates, we carried out a genome-wide analysis of five strains of isolated from permafrost aged from 15 thousand to 1.8 million years. Surprisingly, we did not identify chromosomal genetic determinants that distinguish permafrost strains from clinical isolates and strains from other natural habitats. Phylogenetic analysis based on whole genome sequences showed that permafrost strains do not form a separate cluster and some of them are most closely related to clinical isolates. The genomes of clinical and permafrost strains contain similar mobile elements and prophages, which indicates an intense horizontal transfer of genetic material. Comparison of plasmids of modern and permafrost strains showed that plasmids from the modern strains are enriched with antibiotic resistance genes, while the content of genes for resistance to heavy metals and arsenic is nearly the same. The thawing of permafrost caused by global warming could release new potentially pathogenic strains of .
PubMed: 34571748
DOI: 10.3390/biology10090871