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Genome Biology Aug 2018Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer,...
BACKGROUND
Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier integrity and increases susceptibility to infections. Herein, we hypothesize that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from 33 controls and 143 cancer cases, we conduct 16S ribosomal RNA (rRNA) bacterial gene sequencing, with RNA-sequencing data from lung cancer cases in The Cancer Genome Atlas serving as the validation cohort.
RESULTS
Overall, we demonstrate a lower alpha diversity in normal lung as compared to non-tumor adjacent or tumor tissue. In squamous cell carcinoma specifically, a separate group of taxa are identified, in which Acidovorax is enriched in smokers. Acidovorax temporans is identified within tumor sections by fluorescent in situ hybridization and confirmed by two separate 16S rRNA strategies. Further, these taxa, including Acidovorax, exhibit higher abundance among the subset of squamous cell carcinoma cases with TP53 mutations, an association not seen in adenocarcinomas.
CONCLUSIONS
The results of this comprehensive study show both microbiome-gene and microbiome-exposure interactions in squamous cell carcinoma lung cancer tissue. Specifically, tumors harboring TP53 mutations, which can impair epithelial function, have a unique bacterial consortium that is higher in relative abundance in smoking-associated tumors of this type. Given the significant need for clinical diagnostic tools in lung cancer, this study may provide novel biomarkers for early detection.
Topics: Adult; Aged; Biodiversity; Comamonadaceae; Female; Humans; Lung Neoplasms; Male; Microbiota; Middle Aged; Mutation; Neoplasms, Squamous Cell; Proteobacteria; Reproducibility of Results; Smokers; Tumor Suppressor Protein p53
PubMed: 30143034
DOI: 10.1186/s13059-018-1501-6 -
Revista Chilena de Infectologia :... Apr 2020
Topics: Bacterial Typing Techniques; Comamonas; DNA, Bacterial
PubMed: 32730480
DOI: 10.4067/s0716-10182020000200147 -
Diagnostics (Basel, Switzerland) Feb 2021Non-small cell lung cancer (NSCLC) is the number one cancer killer and its early detection can reduce mortality. Accumulating evidences suggest an etiopathogenic role of...
Non-small cell lung cancer (NSCLC) is the number one cancer killer and its early detection can reduce mortality. Accumulating evidences suggest an etiopathogenic role of microorganisms in lung tumorigenesis. Certain bacteria are found to be associated with NSCLC. Herein we evaluated the potential use of microbiome as biomarkers for the early detection of NSCLC. We used droplet digital PCR to analyze 25 NSCLC-associated bacterial genera in 31 lung tumor and the paired noncancerous lung tissues and sputum of 17 NSCLC patients and ten cancer-free smokers. Of the bacterial genera, four had altered abundances in lung tumor tissues, while five were aberrantly abundant in sputum of NSCLC patients compared with their normal counterparts (all < 0.05). Acidovorax and Veillonella were further developed as a panel of sputum biomarkers that could diagnose lung squamous cell carcinoma (SCC) with 80% sensitivity and 89% specificity. The use of Capnocytophaga as a sputum biomarker identified lung adenocarcinoma (AC) with 72% sensitivity and 85% specificity. The use of Acidovorax as a sputum biomarker had 63% sensitivity and 96% specificity for distinguishing between SCC and AC, the two major types of NSCLC. The sputum biomarkers were further validated for the diagnostic values in a different cohort of 69 NSCLC cases and 79 cancer-free controls. Sputum microbiome might provide noninvasive biomarkers for the early detection and classification of NSCLC.
PubMed: 33673596
DOI: 10.3390/diagnostics11030407 -
Environmental Science and Ecotechnology Jul 2023The potential release capacity of arsenic (As) from sediment was evaluated under a high level of exogenous organic matter (EOM) with both bioreactive and chemically...
The potential release capacity of arsenic (As) from sediment was evaluated under a high level of exogenous organic matter (EOM) with both bioreactive and chemically reactive organic matters (OMs). The OMs were characterized by FI, HIX, BIX, and SUVA fluorescence indices showing the biological activities were kept at a high level during the experimental period. At the genus level, Fe/Mn/As-reducing bacteria (, , , and ) and bacteria (, , , and ) that can participate in metabolic transformation using EOM were identified. The reducing condition occurs which promoted As, Fe, and Mn releases at very high concentrations of OM. However, As release increased during the first 15-20 days, followed by a decline contributed by secondary iron precipitation. The degree of As release may be limited by the reactivity of Fe (hydro)oxides. The EOM infiltration enhances As and Mn releases in aqueous conditions causing the risk of groundwater pollution, which could occur in specific sites such as landfills, petrochemical sites, and managed aquifer recharge projects.
PubMed: 36896144
DOI: 10.1016/j.ese.2023.100243 -
Frontiers in Microbiology 2021Bacterial fruit blotch and seedling blight, caused by , is one of the most destructive diseases of melon and watermelon in many countries. Pathogen-free seed and...
Bacterial fruit blotch and seedling blight, caused by , is one of the most destructive diseases of melon and watermelon in many countries. Pathogen-free seed and cultural practices are major pillars of the disease control. However, use of bacteriophages as natural biocontrol agents might also contribute to the disease management. Therefore, we isolated 12 bacteriophages specific to , from phyllosphere and rhizosphere of diseased watermelon plants. The phage strains were characterized based on their host range, plaque and virion morphology, thermal inactivation point, adsorption rate, one step growth curve, restriction fragment length polymorphism (RFLP), and genomic analysis. Transmission electron microscopy of three phage strains indicated that they belong to the order , family All phages lysed 30 out of 32 tested strains isolated in Serbia, and did not lyse other less related bacterial species. They produced clear plaques, 2 mm in diameter, on bacterial lawns of different strains after 24 h of incubation. The thermal inactivation point was 66 or 67°C. They were stable at pH 5-9, but were sensitive to chloroform and inactivated in either 5 or 10 min exposure to ultraviolet (UV) light. RFLP analysis using RI, I and HI enzymes did not show genetic differences among the tested phages. Adsorption rate and one step growth curve were determined for the phage ACF1. Draft genome sequence of the ACF1 phage was 59.377 bp in size, with guanine-cytosine (GC) content 64.5%, including 89 open reading frames. This phage shared a very high genomic identity with phage ACPWH, isolated in South Korea. Evaluation of systemic nature of ACF1 strain showed that it can be absorbed by roots and translocated to upper parts of watermelon plants where it survived up to 10 days.
PubMed: 35185829
DOI: 10.3389/fmicb.2021.803789 -
Frontiers in Plant Science 2014Plant growth is highly dependent on bacteria, saprophytic, and mycorrhizal fungi which facilitate the cycling and mobilization of nutrients. Over 95% of the sulfur (S)... (Review)
Review
Plant growth is highly dependent on bacteria, saprophytic, and mycorrhizal fungi which facilitate the cycling and mobilization of nutrients. Over 95% of the sulfur (S) in soil is present in an organic form. Sulfate-esters and sulfonates, the major forms of organo-S in soils, arise through deposition of biological material and are transformed through subsequent humification. Fungi and bacteria release S from sulfate-esters using sulfatases, however, release of S from sulfonates is catalyzed by a bacterial multi-component mono-oxygenase system. The asfA gene is used as a key marker in this desulfonation process to study sulfonatase activity in soil bacteria identified as Variovorax, Polaromonas, Acidovorax, and Rhodococcus. The rhizosphere is regarded as a hot spot for microbial activity and recent studies indicate that this is also the case for the mycorrhizosphere where bacteria may attach to the fungal hyphae capable of mobilizing organo-S. While current evidence is not showing sulfatase and sulfonatase activity in arbuscular mycorrhiza, their effect on the expression of plant host sulfate transporters is documented. A revision of the role of bacteria, fungi and the interactions between soil bacteria and mycorrhiza in plant S supply was conducted.
PubMed: 25566295
DOI: 10.3389/fpls.2014.00723 -
Journal of Oleo Science Apr 2021A total of 100 environmental samples were investigated for their ability to degrade 1 g/L surfactin as a substrate. Among them, two enrichment cultures, which exhibited...
A total of 100 environmental samples were investigated for their ability to degrade 1 g/L surfactin as a substrate. Among them, two enrichment cultures, which exhibited microbial growth as well as surfactin degradation, were selected and further investigated. After several successive cultivations, nanopore sequencing of full-length 16S rRNA genes with MinION was used to analyze the bacterial species in the enrichment cultures. Variovorax spp., Caulobacter spp., Sphingopyxis spp., and Pseudomonas spp. were found to be dominant in these surfactin-degrading mixed cultures. Finally, one strain of Pseudomonas putida was isolated as a surfactin-degrading bacterium. This strain degraded 1 g/L surfactin below a detectable level within 14 days, and C surfactin was degraded faster than C surfactin.
Topics: Biodegradation, Environmental; Caulobacter; Comamonadaceae; Lipopeptides; Peptides, Cyclic; Pseudomonas putida; Sphingomonadaceae; Surface-Active Agents
PubMed: 33692244
DOI: 10.5650/jos.ess20331 -
RSC Advances Jan 2022A series of quinoxaline derivatives were designed, synthesized and evaluated as antimicrobial agents against plant pathogenic bacteria and fungi. Some of these compounds...
A series of quinoxaline derivatives were designed, synthesized and evaluated as antimicrobial agents against plant pathogenic bacteria and fungi. Some of these compounds exhibited significant antibacterial and antifungal activities . Compound 5k displayed good antibacterial activity against (). Compounds 5j and 5t exhibited the most potent anti- () activity, with the corresponding EC values of 8.54 and 12.01 μg mL, respectively, which are superior to that of the commercial azoxystrobin (26.17 μg mL). Further, the scanning electron microscopy results proved that compound 5j had certain effects on the cell morphology of . Moreover, an bioassay also demonstrated that the anti- activity of compound 5j could effectively control rice sheath blight. These results indicate that quinoxaline derivatives could be promising agricultural bactericides and fungicides.
PubMed: 35425241
DOI: 10.1039/d1ra07559d -
Functional and structural characterization of AntR, an Sb(III) responsive transcriptional repressor.Molecular Microbiology Aug 2021The ant operon of the antimony-mining bacterium Comamonas testosterone JL40 confers resistance to Sb(III). The operon is transcriptionally regulated by the product of...
The ant operon of the antimony-mining bacterium Comamonas testosterone JL40 confers resistance to Sb(III). The operon is transcriptionally regulated by the product of the first gene in the operon, antR. AntR is a member of ArsR/SmtB family of metal/metalloid-responsive repressors resistance. We purified and characterized C. testosterone AntR and demonstrated that it responds to metalloids in the order Sb(III) = methylarsenite (MAs(III) >> As(III)). The protein was crystallized, and the structure was solved at 2.1 Å resolution. The homodimeric structure of AntR adopts a classical ArsR/SmtB topology architecture. The protein has five cysteine residues, of which Cys103 from one monomer and Cys113 from the other monomer, are proposed to form one Sb(III) binding site, and Cys113 and Cys103 forming a second binding site. This is the first report of the structure and binding properties of a transcriptional repressor with high selectivity for environmental antimony.
Topics: Amino Acid Sequence; Antimony; Arsenic; Arsenicals; Binding Sites; Comamonas testosteroni; Gene Expression Regulation, Bacterial; Protein Conformation; Repressor Proteins; Transcription Factors; Transcription, Genetic
PubMed: 33786926
DOI: 10.1111/mmi.14721 -
Frontiers in Cellular and Infection... 2023The present study aims to investigate the effect of (Hp) infection on gastric mucosal microbiota in patients with chronic gastritis.
OBJECTIVE
The present study aims to investigate the effect of (Hp) infection on gastric mucosal microbiota in patients with chronic gastritis.
METHODS
Here recruited a population of 193 patients with both chronic gastritis and positive rapid urease, including 124 patients with chronic atrophic gastritis (CAG) and 69 patients with chronic non-atrophic gastritis (nCAG). Immunoblotting was used to detect four serum Hp antibodies (UreA, UreB, VacA and CagA) to determine the types of virulent Hp-I and avirulent Hp-II infections. Gastric microbiota was profiled by 16S rRNA gene V3-V4 region, and R software was used to present the relationship between the microbial characteristics and the type of Hp infection.
RESULTS
In the stomach of patients with Hp-positive gastritis, the dominant gastric bacterial genera included (23.94%), (20.28%), (9.99%), (9.21%), (5.05%), and (4.75%). The proportion of Hp-I infection was significantly higher in CAG patients (91.1%) than in nCAG patients (71.0%) ( < 0.001). The gastric microbiota richness index (observed OTUs, Chao) was significantly lower in CAG patients than in nCAG patients (0.05). Compared with avirulent Hp-II infection, virulent Hp-I infection significantly decreased the Shannon index in CAG patients (0.05). In nCAG patients, Hp-I infected patients had lower abundances of several dominant gastric bacteria (, , , , ) than Hp-II infected patients. Meanwhile, in CAG patients, Hp-I infected patients occupied lower abundances of several dominant oral bacteria (, and ) than Hp-II infected patients. In addition, bile reflux significantly promoted the colonization of dominant oral microbiota (, and ) in the stomach of CAG patients. There was no significant symbiotic relationship between bacteria and non- bacteria in the stomach of nCAG patients, while bacteria distinctly linked with the non- bacteria (, , , and ) in CAG patients.
CONCLUSIONS
Virulent Hp infection alters the gastric microbiota, reduces microbial diversity, and enhances the symbiotic relationship between the bacteria and non- bacteria in patients with chronic gastritis. The data provides new evidence for treating Hp infection by improving the gastric microbiota.
Topics: Humans; Helicobacter pylori; Helicobacter Infections; RNA, Ribosomal, 16S; Gastritis
PubMed: 37662018
DOI: 10.3389/fcimb.2023.1221433