-
Microbial Genomics Sep 2022is a diverse betaproteobacterial genus with many strains having agricultural and industrial relevance, including plant-growth promotion, bioremediation of...
is a diverse betaproteobacterial genus with many strains having agricultural and industrial relevance, including plant-growth promotion, bioremediation of hydrocarbon-contaminated soils, and heavy metal immobilization. spp. are broadly distributed in the environment, and have been isolated from plant hosts as well as healthy and diseased animal hosts, yet the genetic basis of this ecological versatility has not been characterized. Here, we present a phylogenomic comparison of published genomes and show that the genus is divided into two well-supported clades: one '' clade with isolates from soils and plant rhizospheres, and a second ' and ' clade with isolates from humans and sludge. The pan-genome inferred from 61 genomes contained over 28 000 genes, of which only 884 were found in all genomes. Analysis of industrially relevant functions highlighted the ecological versatility of and supported their role as generalists.
Topics: Animals; DNA, Bacterial; Delftia; Humans; Metals, Heavy; Phylogeny; Sequence Analysis, DNA; Sewage; Soil
PubMed: 36107145
DOI: 10.1099/mgen.0.000864 -
Frontiers in Cellular and Infection... 2022Periodontitis and rheumatoid arthritis (RA) are two widespread chronic inflammatory diseases with a previously suggested association. The objective of the current study...
OBJECTIVES
Periodontitis and rheumatoid arthritis (RA) are two widespread chronic inflammatory diseases with a previously suggested association. The objective of the current study was to compare the oral microbial composition and host´s inflammatory mediator profile of saliva samples obtained from subjects with periodontitis, with and without RA, as well as to predict biomarkers, of bacterial pathogens and/or inflammatory mediators, for classification of samples associated with periodontitis and RA.
METHODS
Salivary samples were obtained from 53 patients with periodontitis and RA and 48 non-RA with chronic periodontitis. The microbial composition was identified using 16S rRNA gene sequencing and compared across periodontitis patients with and without RA. Levels of inflammatory mediators were determined using a multiplex bead assay, compared between the groups and correlated to the microbial profile. The achieved data was analysed using PCoA, DESeq2 and two machine learning algorithms, OPLS-DA and sPLS-DA.
RESULTS
Differential abundance DESeq2 analyses showed that the four most highly enriched (log2 FC >20) amplicon sequence variants (ASVs) in the non-RA periodontitis group included sp., sp., sp., and sp. whereas sp., sp., sp., and were the most highly enriched ASVs (log2 FC >20) in the RA group. OPLS-DA with log2 FC analyses demonstrated that the top ASVs with the highest importance included sp. having a positive correlation with non-RA group, and seven ASVs belonging to , sp., , , spp. and with a positive correlation with RA group. Among the detected inflammatory mediators in saliva samples, TWEAK/TNFSF12, IL-35, IFN-α2, pentraxin-3, gp130/sIL6Rb, sIL-6Ra, IL-19 and sTNF-R1 were found to be significantly increased in patients with periodontitis and RA compared to non-RA group with periodontitis. Moreover, correlations between ASVs and inflammatory mediators using sPLS-DA analysis revealed that TWEAK/TNFSF12, pentraxin-3 and IL-19 were positively correlated with the ASVs sp., , sp., and sp.
CONCLUSION
Our results suggest that the combination of microbes and host inflammatory mediators could be more efficient to be used as a predictable biomarker associated with periodontitis and RA, as compared to microbes and inflammatory mediators alone.
Topics: Arthritis, Rheumatoid; Chronic Periodontitis; Humans; Inflammation Mediators; Microbiota; RNA, Ribosomal, 16S
PubMed: 35360114
DOI: 10.3389/fcimb.2022.841139 -
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 2023The composition of resident microbes in the human body is linked to various diseases and their treatment outcomes. Although studies have identified pancreatic ductal...
The composition of resident microbes in the human body is linked to various diseases and their treatment outcomes. Although studies have identified pancreatic ductal adenocarcinoma (PDAC)-associated bacterial communities in the oral and gut samples, herein, we hypothesize that the prevalence of microbiota in pancreatic tumor tissues is different as compared with their matched adjacent, histologically normal appearing tissues, and these microbial molecular signatures can be highly useful for PDAC diagnosis/prognosis. In this study, we performed comparative profiling of bacterial populations in pancreatic tumors and their respective adjacent normal tissues using 16S rRNA-based metagenomics analysis. This study revealed a higher abundance of Proteobacteria and Actinomycetota in tumor tissues compared with adjacent normal tissues. Interestingly, the linear discriminant analysis (LDA) scores unambiguously revealed an enrichment of Delftia in tumor tissues, whereas Sphingomonas, Streptococcus, and Citrobacter exhibited a depletion in tumor tissues. Furthermore, we analyzed the microbial composition between different groups of patients with different tumor differentiation stages. The bacterial genera, Delftia and Staphylococcus, were very high at the G1 stages (well differentiated) compared with G2 (well to moderate/moderately differentiated) and G3/G4 (poorly differentiated) stages. However, the abundance of Actinobacter and Cloacibacterium was found to be very high in G2 and G3, respectively. Additionally, we evaluated the correlation of programmed death-ligand (PDL1) expression with the abundance of bacterial genera in tumor lesions. Our results indicated that three genera such as Streptomyces, Cutibacterium, and Delftia have a positive correlation with PD-L1 expression. Collectively, these findings demonstrate that PDAC lesions harbor relatively different microbiota compared with their normal tumor adjacent tissues, and this information may be helpful for the diagnosis and prognosis of PADC patients.
PubMed: 38179448
DOI: 10.3389/fmicb.2023.1275374 -
Plants (Basel, Switzerland) Oct 2022We investigated the role of two different plant growth-promoting probiotic bacteria in conferring cadmium (Cd) tolerance in rapeseed ( cv. BARI Sarisha-14) through...
We investigated the role of two different plant growth-promoting probiotic bacteria in conferring cadmium (Cd) tolerance in rapeseed ( cv. BARI Sarisha-14) through improving reactive oxygen species scavenging, antioxidant defense, and glyoxalase system. Soil, as well as seeds of rapeseed, were separately treated with probiotic bacteria, BRRh-4 and sp. BTL-M2. Fourteen-day-old seedlings were exposed to 0.25 and 0.5 mM CdCl for two weeks. Cadmium-treated plants resulted in a higher accumulation of hydrogen peroxide, increased lipid peroxidation, electrolyte leakage, chlorophyll damage, and impaired antioxidant defense and glyoxalase systems. Consequently, it reduced plant growth and biomass production, and yield parameters. However, probiotic bacteria-inoculated plants significantly ameliorated the Cd toxicity by enhancing the activities of antioxidant enzymes (ascorbate peroxidase, dehydroascorbate reductase, monodehydroascorbate reductase, glutathione reductase, glutathione peroxidase, and catalase) and glyoxalase enzymes (glyoxalase I and glyoxalase II) which led to the mitigation of oxidative damage indicated by reduced hydrogen peroxide, lipid peroxidation, and electrolyte leakage that ultimately improved growth, physiology, and yield of the bacterial inoculants rapeseed plants. When taken together, our results demonstrated the potential role of the plant probiotic bacteria, BRRh-4 and BTL-M2, in mitigating the Cd-induced damages in rapeseed plants.
PubMed: 36297762
DOI: 10.3390/plants11202738 -
Microbiology Spectrum Aug 2022Delftia acidovorans () is a Gram-negative bacteria and an uncommon cause of human infections. This retrospective cohort study investigated clinical and microbiological...
Delftia acidovorans () is a Gram-negative bacteria and an uncommon cause of human infections. This retrospective cohort study investigated clinical and microbiological characteristics and outcomes of patients with infections. We included patients with culture-confirmed infections attending Rigshospitalet, during 2002-2020. Fifty-nine patients with a median interquartile ranges (IQR) age of 47 (15-67) years were included. Thirty-five (59%) were males, and 57 (97%) had at least one comorbidity, including 25 (42%) with solid or hematologic malignancies. Eight (14%) were admitted to ICU, and 15 (25%) died within 365 days after infection. Persistent infection was found in 4 (6.8%) patients, and 41 (70%) had polymicrobial cultures, mainly with Pseudomonas spp. and Stenotrophomonas maltophilia. More than 85% of the isolates were susceptible to meropenem or ceftazidime. Although, 88% and 62% of the isolates were resistant to gentamicin and colistin, respectively. infections mainly affect patients with preexisting comorbidities, including malignancies. In the first year, all-cause mortality is considerable, polymicrobial cultures are common, and meropenem or cephalosporins with antipseudomonal activity could be the antibiotics of choice. Delftia acidovorans () is a Gram-negative bacteria that can cause infection in immunocompetent and immunocompromised individuals. The current knowledge comes mainly from case reports and case series. In this retrospective cohort study, we found that infections mainly affect male patients with preexisting comorbidities, including malignancies. Persistent infections were not common, and most of the patients had polymicrobial cultures, mainly with Pseudomonas spp. and Stenotrophomonas maltophilia. More than 85% of the isolates were susceptible to meropenem or ceftazidime. In contrast, 88% and 62% of the isolates were resistant to gentamicin and colistin, respectively.
Topics: Adolescent; Adult; Aged; Anti-Bacterial Agents; Ceftazidime; Colistin; Delftia acidovorans; Female; Gentamicins; Gram-Negative Bacteria; Gram-Negative Bacterial Infections; Humans; Male; Meropenem; Microbial Sensitivity Tests; Middle Aged; Retrospective Studies; Stenotrophomonas maltophilia; Young Adult
PubMed: 35862984
DOI: 10.1128/spectrum.00326-22 -
Journal of Reproductive Immunology Jun 2023There have been few studies concerning an association between unexplained recurrent pregnancy loss (RPL) and the microbiome. A recent study including 67 patients...
There have been few studies concerning an association between unexplained recurrent pregnancy loss (RPL) and the microbiome. A recent study including 67 patients demonstrated that an increase in Ureaplasma species in the endometrium raised the risk of miscarriage with an euploid karyotype. While endometrial sampling is invasive, cervicovaginal sampling is not. We compared vaginal and cervical microbiomes with a 16 S ribosomal RNA sequence between 88 patients with unexplained RPL and 17 healthy women with no history of miscarriage. We prospectively assessed risk factors for maternal colonization at a subsequent miscarriage without an aneuploid karyotype in patients. Cervicovaginal bacteria were dominated by Lactobacillus iners, Gardnerella vaginalis, Atopobium vaginae and Bifidobacterium breve in Japanese population. The proportions of Delftia and unknown bacteria in the cervix were significantly higher in patients with RPL than in controls. Streptococcus, Microbacterium, Delftia, Anaerobacillus and Chloroplast in the cervix were significantly higher in patients with a history of chorioamnionitis compared to the controls. The abundance of Cutibacterium and Anaerobacillus in the cervix was significantly higher in patients who had subsequently miscarried compared to those who gave birth. The miscarriage rate in patients with higher proportions of both Cutibacterium and Anaerobacillus (66.7%, 2/3) was significantly greater than that of patients who lacked these bacteria (9.2%, 6/65, adjusted odds ratio 16.90, 95% confidence interval 1.27-225.47, p = 0.032). The presence of certain bacteria could be a predictor of subsequent miscarriage without an aneuploid karyotype. The cervicovaginal microbiome might be useful for investigating a possible cause of RPL.
Topics: Pregnancy; Humans; Female; Vagina; Cervix Uteri; Abortion, Habitual; Aneuploidy; Microbiota
PubMed: 37060795
DOI: 10.1016/j.jri.2023.103944 -
International Journal of Molecular... Jun 2022in recent years, many studies were carried out to explore the role of vaginal microbiota in HPV infections and cervical intraepithelial neoplasia (CIN) progression. The... (Review)
Review
BACKGROUND
in recent years, many studies were carried out to explore the role of vaginal microbiota in HPV infections and cervical intraepithelial neoplasia (CIN) progression. The aim of this study was to conduct a review of the literature to analyze the interaction between the vaginal microbiota, the CIN, and the immunological response.
METHODS
we performed a literature search, considering papers published between November 2015 and September 2021.
RESULTS
despite significant evidence suggesting a role of vaginal microbiota in the pathogenesis of HPV-related lesions, some studies still struggle to demonstrate this correlation. However, the vaginal microbiota of HPV-positive women shows an increased diversity, combined with a reduced relative abundance of spp. and a higher pH. In cervical dysplasia progression, a strong association is found with new bacteria, and with the deregulation of pathways and hyperexpression of cytokines leading to chronic inflammation.
CONCLUSIONS
in HPV progression, there is a strong correlation between potential biomarkers, such as found in community state types IV and II, and chronic inflammation with cytokine overexpression. Better analysis of these factors could be of use in the prevention of the progression of the disease and, eventually, in new therapeutic strategies.
Topics: Female; Humans; Inflammation; Microbiota; Papillomaviridae; Papillomavirus Infections; Tumor Microenvironment; Uterine Cervical Neoplasms; Uterine Cervical Dysplasia
PubMed: 35806188
DOI: 10.3390/ijms23137174 -
Pancreas Apr 2022Most previous studies have analyzed bacteria in tumors using resected pancreatic cancer (PC) tissues, because it is difficult to obtain tissue samples from unresectable...
OBJECTIVES
Most previous studies have analyzed bacteria in tumors using resected pancreatic cancer (PC) tissues, because it is difficult to obtain tissue samples from unresectable advanced PC. We aimed to determine whether minimal tissue obtained by endoscopic ultrasound-guided fine-needle aspiration is useful for microbiome analysis.
METHODS
Thirty PC and matched duodenal and stomach tissues (N = 90) were prospectively collected from 30 patients who underwent endoscopic ultrasound-guided fine-needle aspiration. Bacterial DNA was extracted, and 16S rRNA sequencing was performed. The primary outcome was the success rate of bacterial detection in tumors. Bacterial diversity and structure were investigated.
RESULTS
The bacterial detection rates were 80%, 100%, and 97% in PC, gastric, and duodenal samples, respectively. Pancreatic cancer tissues showed a lower α-diversity and a significantly different microbial structure than stomach and duodenal tissues. Proteobacteria were more abundant, whereas Firmicutes, Bacteroidetes, and Fusobacteria were less abundant in PC tissues than in stomach and duodenal tissues. Acinetobacter was more abundant in PC tissues than in stomach and duodenal tissues, and Delftia was more frequently detected in resectable PC.
CONCLUSIONS
Endoscopic ultrasound-guided fine-needle aspiration samples were valuable for PC microbiome analysis, revealing that the bacterial composition of PC is different from that of the stomach and duodenum.
Topics: Endoscopic Ultrasound-Guided Fine Needle Aspiration; Humans; Microbiota; Pancreatic Neoplasms; RNA, Ribosomal, 16S
PubMed: 35695806
DOI: 10.1097/MPA.0000000000002028 -
Improvement of growth, yield and associated bacteriome of rice by the application of probiotic and .Frontiers in Microbiology 2023Plant probiotic bacteria enhance growth and yield of crop plants when applied at the appropriate time and dose. Two rice probiotic bacteria, strain BRRh-4 and sp....
Plant probiotic bacteria enhance growth and yield of crop plants when applied at the appropriate time and dose. Two rice probiotic bacteria, strain BRRh-4 and sp. strain BTL-M2 promote growth and yield of plants. However, no information is available on application of these two bacteria on growth, yield, and diversity and population of bacteriome in roots and rhizosphere soils of the treated rice plants. This study aimed to assess the effect of BRRh-4 and BTL-M2 application on growth, yield and bacteriome in roots and rhizosphere soil of rice under varying doses of N, P and K fertilizers. Application of BRRh-4 and BTL-M2 strains significantly ( < 0.05) increased seed germination, growth and yield of rice compared to an untreated control. Interestingly, the grain yield of rice by these bacteria with 50% less of the recommended doses of N, P, and K fertilizers were statistically similar to or better than the rice plants treated with 100% doses of these fertilizers. Targeted amplicon (16S rRNA) sequence-based analysis revealed significant differences (PERMANOVA, = 0.00035) in alpha-diversity between the root (R) and rhizosphere soil (S) samples, showing higher diversity in the microbial ecosystem of root samples. Additionally, the bacteriome diversity in the root of rice plants that received both probiotic bacteria and chemical fertilizers were significantly higher (PERMANOVA, = 0.0312) compared to the rice plants treated with fertilizers only. Out of 185 bacterial genera detected, , an anaerobic and Gram-negative bacterium, was found to be the predominant genus in both rhizosphere soil and root metagenomes. However, the relative abundance of remained two-fold higher in the rhizosphere soil metagenome (52.02%) than in the root metagenome (25.04%). The other predominant bacterial genera detected in the rice root metagenome were (11.07%), (4.06%), (3.91%), (2.97%), (2.61%), and (2.30%). On the other hand, rhizosphere soil metagenome had (12.38%), (9.50%), (5.94%), (3.40%), and (3.02%). Interestingly, we found the presence and/or abundance of specific genera of bacteria in rice associated with the application of a specific probiotic bacterium. Taken together, our results indicate that improvement of growth and yield of rice by strain BRRh-4 and sp. strain BTL-M2 is likely linked with modulation of diversity, structures, and signature of bacteriome in roots and rhizosphere soils. This study for the first time demonstrated that application of plant growth promoting bacteria significantly improve growth, yield and increase the diversity of bacterial community in rice.
PubMed: 37520368
DOI: 10.3389/fmicb.2023.1212505