scholarly journals Imbalanced Dermic Microbiome Aggravates Inflammation in Toenail Paronychia

2021 ◽  
Vol 11 ◽  
Author(s):  
Ying Li ◽  
Han Ma ◽  
Liang Xue ◽  
Huizhen Chen ◽  
Rui Pang ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Network Analysis ◽  
16S Rrna ◽  
Disease Progression ◽  
Antibiotic Treatment ◽  
Relative Abundance ◽  
Tissue Repair ◽  
Anaerobic Microorganisms ◽  
Skin Immunity ◽  
Key Microorganisms

The commensal microbiome influences skin immunity, but its function in toenail health remains unclear. Paronychia is one of the most common inflammatory toenail diseases, but antibiotic treatment is seldom effective in clinical cases. In this study, we performed 16S rRNA sequencing to investigate the characteristics of microbes associated with paronychia in order to identify the key microorganisms involved in inflammation. Seventy dermic samples were collected from patients with paronychia and the differences in dermic microbiota were analyzed in patients with different inflammation severities. Distinct clustering of dermal microbiota was observed in the dermis with different inflammation severities. A higher relative abundance of anaerobic microorganisms such as Parvimona, Prevotella, and Peptoniphilus was observed in severe paronychia, whereas Lactobacillus disappeared with disease progression. Co-occurring network analysis suggested that the disturbance of the dermic microbiome and attenuation of antagonism by Lactobacillus against anaerobic pathogens may aggravate inflammation in paronychia. Functional analysis showed that dermic microbiome disturbance may worsen microbial metabolism and tissue repair in the skin. In conclusion, we revealed that an increased abundance of anaerobic microorganisms and loss of Lactobacillus in the dermis may promote paronychia progression and microbiological imbalance may aggravate inflammation in patients with paronychia.

scholarly journals Microarray analysis reveals an inflammatory transcriptomic signature in peripheral blood for sciatica

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yi Wang ◽  
Guogang Dai ◽  
Ling Jiang ◽  
Shichuan Liao ◽  
Jiao Xia
Keyword(s):  
Functional Analysis ◽  
Network Analysis ◽  
Peripheral Blood ◽  
Differentially Expressed ◽  
Healthy Controls ◽  
Toll Like Receptor ◽  
Qrt Pcr ◽  
Transcriptomic Signature ◽  
Transcriptional Changes ◽  
Key Genes

Abstract Background Although the pathology of sciatica has been studied extensively, the transcriptional changes in the peripheral blood caused by sciatica have not been characterized. This study aimed to characterize the peripheral blood transcriptomic signature for sciatica. Methods We used a microarray to identify differentially expressed genes in the peripheral blood of patients with sciatica compared with that of healthy controls, performed a functional analysis to reveal the peripheral blood transcriptomic signature for sciatica, and conducted a network analysis to identify key genes that contribute to the observed transcriptional changes. The expression levels of these key genes were assessed by qRT-PCR. Results We found that 153 genes were differentially expressed in the peripheral blood of patients with sciatica compared with that of healthy controls, and 131 and 22 of these were upregulated and downregulated, respectively. A functional analysis revealed that these differentially expressed genes (DEGs) were strongly enriched for the inflammatory response or immunity. The network analysis revealed that a group of genes, most of which are related to the inflammatory response, played a key role in the dysregulation of these DEGs. These key genes are Toll-like receptor 4, matrix metallopeptidase 9, myeloperoxidase, cathelicidin antimicrobial peptide, resistin and Toll-like receptor 5, and a qRT-PCR analysis validated the higher transcript levels of these key genes in the peripheral blood of patients with sciatica than in that of healthy controls. Conclusion We revealed inflammatory characteristics that serve as a peripheral blood transcriptomic signature for sciatica and identified genes that are essential for mRNA dysregulation in the peripheral blood of patients with sciatica.

scholarly journals Effects of Supplement of Marichromatium gracile YL28 on Water Quality and Microbial Structures in Shrimp Mariculture Ecosystems

Genes ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 40
Author(s):  
Liang Cui ◽  
Bitong Zhu ◽  
Xiaobo Zhang ◽  
Zhuhua Chan ◽  
Chungui Zhao ◽  
...  
Keyword(s):  
Water Quality ◽  
16S Rrna ◽  
Relative Abundance ◽  
Animal Health ◽  
Denitrifying Bacteria ◽  
Nitrite Reduction ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Sequencing Analysis ◽  
Shrimp Culture

The elevated NH3-N and NO2-N pollution problems in mariculture have raised concerns because they pose threats to animal health and coastal and offshore environments. Supplement of Marichromatium gracile YL28 (YL28) into polluted shrimp rearing water and sediment significantly decreased ammonia and nitrite concentrations, showing that YL28 functioned as a novel safe marine probiotic in the shrimp culture industry. The diversity of aquatic bacteria in the shrimp mariculture ecosystems was studied by sequencing the V4 region of 16S rRNA genes, with respect to additions of YL28 at the low and high concentrations. It was revealed by 16S rRNA sequencing analysis that Proteobacteria, Planctomycete and Bacteroidetes dominated the community (>80% of operational taxonomic units (OTUs)). Up to 41.6% of the predominant bacterial members were placed in the classes Gammaproteobacteria (14%), Deltaproteobacteria (14%), Planctomycetacia (8%) and Alphaproteobacteria (5.6%) while 40% of OTUs belonged to unclassified ones or others, indicating that the considerable bacterial populations were novel in our shrimp mariculture. Bacterial communities were similar between YL28 supplements and control groups (without addition of YL28) revealed by the β-diversity using PCoA, demonstrating that the additions of YL28 did not disturb the microbiota in shrimp mariculture ecosystems. Instead, the addition of YL28 increased the relative abundance of ammonia-oxidizing and denitrifying bacteria. The quantitative PCR analysis further showed that key genes including nifH and amoA involved in nitrification and nitrate or nitrite reduction significantly increased with YL28 supplementation (p < 0.05). The supplement of YL28 decreased the relative abundance of potential pathogen Vibrio. Together, our studies showed that supplement of YL28 improved the water quality by increasing the relative abundance of ammonia-oxidizing and denitrifying bacteria while the microbial community structure persisted in shrimp mariculture ecosystems.

O-143 Characterization of vaginal and endometrial microbiome in patients with chronic endometritis (CE)

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
P LOZANO ◽  
A Bernabeu ◽  
B Lledó ◽  
R Morales ◽  
F I Aranda ◽  
...  
Keyword(s):  
16S Rrna ◽  
Embryo Transfer ◽  
Relative Abundance ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Shannon Index ◽  
Small Sample ◽  
Diagnostic Methods ◽  
Vaginal Microbiome ◽  
Chronic Endometritis

Abstract Study question Could vaginal and endometrial microbiome by sequencing 16S rRNA be comparable to classic diagnostic methods or immunohistochemistry CD138 for diagnosis of chronic endometritis? Summary answer A characteristic endometrial and vaginal microbiome is present in patients with chronic endometritis. An abnormal vaginal microbiome correlates with the presence of chronic endometritis. What is known already Chronic endometritis is a disease characterized by persistent inflammation of the endometrial lining. Currently, histopathological evaluation by immunohistochemistry CD138 marker is most common diagnostic method for CE. Microbiome analysis based on subunit 16S rRNA sequencing is a fast tool that can enable the identification of pathogenic microorganisms associated with CE. The main bacteria at vaginal and endometrial level belong to genus Lactobacillus, producers of lactic acid that allows maintaining acidic pH of vagina and acts as barrier against pathogens. Investigations on the effect of an abnormal endometrial and vaginal microbiome could improve assisted reproductive technologies. Study design, size, duration This is a observational pilot study (60 patients and 120 samples). The study population consists of patients attending to our fertility clinic for frozen euploid embryo transfer (FET) from May 2017 to May 2019. Preimplantation Genetic Testing of aneuploidy (PGT-A) was performed at blastocyst stage using Veriseq (Illumina). The inclusion criteria to be meet by patients were: age between 18 and 50 years, own or donated oocytes and use of ICSI. Participants/materials, setting, methods Cohort study with sixty patients undergoing assisted reproductive treatment (TRA) with their own or donated gametes and PGT-A Vaginal and endometrial samples were taken in the cycle prior to embryo transfer. The vaginal and endometrial microbiome was analyzed by mass sequencing of the V3V4 region of 16S rRNA. Bioinformatics analysis was performed using QIIME2 and MicrobiomeAnalyst packages. Alpha, beta diversity and taxonomic characterization were compared with positive and negative CD138 groups for chronic endometritis (CE). Main results and the role of chance Different bacterial communities were detected when vaginal and endometrial samples were analyzed in patients with and without endometritis diagnosed with CD138 immunohistochemistry. In patients with endometritis, a higher alpha diversity index tendency was found in vaginal samples (p = 0.15 for the Shannon index) and significant differences in endometrial samples (p = 0.01 for the Shannon index). In the beta diversity analysis, no significant differences were observed between the groups established as per the diagnosis of endometritis. Vaginal and endometrial samples from women with endometritis showed a microbiome pattern not dominated by Lactobacillus spp. Relative abundance analysis identified the genera Ralstonia and Gardnerella in endometrial sample, and the genera Streptoccoccus and Ureaplasma in vaginal sample of patients diagnosed with CD138 for endometritis. Comparing endometrial and vaginal samples CD138 positive diagnosed for endometritis, alpha diversity (p = 0.06 for the Shannon index and p = 0.08 for the Simpson index) and beta diversity (p &lt; 0.001) showed significant differences. Relative abundance identified the genera Lactobacillus (p = 3.76E-4), Ralstonia (p = 8.19E-4), Delftia (p = 0.004) and Anaerobacillus (p = 0.004) in these sample groups. Limitations, reasons for caution The main limitation of this study is the small sample size. Larger studies including a higher number of samples are needed to confirm the different microbiome pattern observed at the vaginal and endometrial levels in correlation with chronic endometritis. The microbiome pattern has not been analyzed after treatment of CE. Wider implications of the findings Our findings suggest the existence of a characteristic vaginal and endometrial microbiota in patients with chronic endometritis. Different genera and species were identified in patients with and without endometritis depending on whether the sample was endometrial or vaginal. An abnormal vaginal microbiome appears to be strongly correlated with chronic endometritis. Trial registration number Not Applicable

scholarly journals 126. Robust and Persistent Vaginal Colonization with LACTIN-V Vaginal Lactobacillus crispatus Probiotic in a Double-Blind, Placebo-Controlled (DBPC) Phase 2b Trial to Prevent Recurrent UTI (rUTI)

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S8-S8
Author(s):  
Ann Stapleton ◽  
Aurelio Silvestroni ◽  
Pacita Roberts ◽  
Marsha Cox ◽  
Hillary Hayden ◽  
...  
Keyword(s):  
16S Rrna ◽  
Relative Abundance ◽  
Premenopausal Women ◽  
Probiotic Strain ◽  
Lactobacillus Strain ◽  
Post Intervention ◽  
Double Blind ◽  
Active Intervention ◽  
Vaginal Colonization ◽  
Probiotic Lactobacillus

Abstract Background We investigated vaginal colonization using repetitive sequence PCR (repPCR) and 16S rRNA sequencing in a Phase 2b DBPC trial of a L. crispatus intravaginal suppository probiotic for prevention of rUTI in premenopausal women. Methods Twenty-four young women with a history of rUTI and current culture-confirmed symptomatic UTI were enrolled and treated (Visit 0), then randomized (Visit 1) to receive an intravaginal suppository containing L. crispatus CTV-05 (LACTIN-V®, Osel, Inc.) or placebo daily for 5 days, then once weekly for 2 months. Participants were followed up during the 2-month probiotic/placebo intervention (Visits 2 to 4; active intervention) and during 2 months following the intervention (Visits 5 and 6; post-intervention). At each visit, vaginal swabs were collected for repPCR to determine the presence or absence of the probiotic strain and the duration of its presence in the vagina and for 16S rRNA-based sequence analysis to determine relative abundance of any L. crispatus. Results LACTIN-V vaginal suppository induced selective and sustained colonization in the probiotic but not the placebo recipients, as follows. Pre-intervention: Probiotic lactobacillus strain, not found in vaginal specimens obtained from participants in either arm of study. Active intervention: (1) Probiotic lactobacillus strain, (a) Probiotic arm: 100% of participants positive at one or more visits and (b) Placebo arm: 0% of participants positive at any time. (2) L. crispatus relative abundance, (a) Probiotic arm: above 90%, all specimens, all visits and (b) Placebo arm: below 15%, all specimens, all visits. Post-intervention: (1) Probiotic lactobacillus strain, (a) Probiotic arm: 75% of participants positive at Visit 5, 58% at Visit 6 and (b) Placebo arm: 0% of participants positive at Visits 5 and 6. (2) L. crispatus relative abundance, (a) Probiotic arm: 70% to 100% and (b) Placebo arm: below 15%. Conclusion LACTIN-V L. crispatus vaginal probiotic achieved robust and persistent colonization throughout 2 months of weekly dosing and for 2 months after the last dose in most participants. Disclosures All authors: No reported disclosures.

scholarly journals Changes of Soil Microbes Related with Carbon and Nitrogen Cycling after Long-Term CO2 Enrichment in a Typical Chinese Maize Field

2020 ◽  
Vol 12 (3) ◽  
pp. 1250 ◽  
Author(s):  
Tiantian Diao ◽  
Zhengping Peng ◽  
Xiaoguang Niu ◽  
Rongquan Yang ◽  
Fen Ma ◽  
...  
Keyword(s):  
16S Rrna ◽  
Nitrogen Cycling ◽  
Relative Abundance ◽  
Soil Microbes ◽  
Inorganic Nitrogen ◽  
Ammonia Oxidizing Bacteria ◽  
Rhizospheric Soil ◽  
Carbon And Nitrogen ◽  
Carbon And Nitrogen Cycling ◽  
Maize Field

Elevated atmospheric CO2 concentration (eCO2) has been the most important driving factor and characteristic of climate change. To clarify the effects of eCO2 on the soil microbes and on the concurrent status of soil carbon and nitrogen, an experiment was conducted in a typical summer maize field based on a 10-year mini FACE (Free Air Carbon Dioxide Enrichment) system in North China. Both rhizospheric and bulk soils were collected for measurement. The soil microbial carbon (MBC), nitrogen (MBN), and soil mineral N were measured at two stages. Characteristics of microbes were assayed for both rhizospheric soil and bulk soils at the key stage. We examined the plasmid copy numbers, diversities, and community structures of bacteria (in terms of 16s rRNA), fungi (in terms of ITS-internal transcribed spacer), ammonia oxidizing bacteria (AOB) and denitrifiers including nirK, nirS, and nosZ using the Miseq sequencing technique. Results showed that under eCO2 conditions, both MBC and MBN in rhizospheric soil were increased significantly. The quantity of ITS was increased in the eCO2 treatment compared with that in the ambient CO2 (aCO2) treatment, while the quantity of 16s rRNA in rhizospheric soil showed decrease in the rhizospheric soil in the eCO2 treatment. ECO2 changed the relative abundance of microbes in terms of compositional proportion of some orders or genera particularly in the rhizospheric soil-n particular, Chaetomium increased for ITS, Subgroups 4 and 6 increased for 16s rRNA, Nitrosospira decreased for AOB, and some genera showed increase for nirS, nirK, and nosZ. Nitrate N was the main inorganic nitrogen form at the tasseling stage and both quantities of AOB and denitrifiers, as well as the nosZ/(nirS+nirK) showed an increase under eCO2 conditions particularly in the rhizospheric soil. The Nitrosospira decreased in abundance under eCO2 conditions in the rhizospheric soil and some genera of denitrifiers also showed differences in abundance. ECO2 did not change the diversities of microbes significantly. In general, results suggested that 10 years of eCO2 did affect the active component of C and N pools (such as MBC and MBN) and both the quantities and relative abundance of microbes which are involved in carbon and nitrogen cycling, possibly due to the differences in both the quantities and component of substrate for relevant microbes in the rhizospheric soils.

scholarly journals Soil Depth Determines the Composition and Diversity of Bacterial and Archaeal Communities in a Poplar Plantation

Forests ◽  
2019 ◽  
Vol 10 (7) ◽  
pp. 550 ◽  
Author(s):  
Huili Feng ◽  
Jiahuan Guo ◽  
Weifeng Wang ◽  
Xinzhang Song ◽  
Shuiqiang Yu
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Relative Abundance ◽  
Rrna Gene ◽  
Poplar Plantation ◽  
Plantation Forest ◽  
Bacterial And Archaeal Communities ◽  
Different Depths ◽  
Archaeal Communities

Understanding the composition and diversity of soil microorganisms that typically mediate the soil biogeochemical cycle is crucial for estimating greenhouse gas flux and mitigating global changes in plantation forests. Therefore, the objectives of this study were to investigate changes in diversity and relative abundance of bacteria and archaea with soil profiles and the potential factors influencing the vertical differentiation of microbial communities in a poplar plantation. We investigated soil bacterial and archaeal community compositions and diversities by 16S rRNA gene Illumina MiSeq sequencing at different depths of a poplar plantation forest in Chenwei forest farm, Sihong County, Jiangsu, China. More than 882,422 quality-filtered 16S rRNA gene sequences were obtained from 15 samples, corresponding to 34 classified phyla and 68 known classes. Ten major bacterial phyla and two archaeal phyla were found. The diversity of bacterial and archaeal communities decreased with depth of the plantation soil. Analysis of variance (ANOVA) of relative abundance of microbial communities exhibited that Nitrospirae, Verrucomicrobia, Latescibacteria, GAL15, SBR1093, and Euryarchaeota had significant differences at different depths. The transition zone of the community composition between the surface and subsurface occurred at 10–20 cm. Overall, our findings highlighted the importance of depth with regard to the complexity and diversity of microbial community composition in plantation forest soils.

scholarly journals First Case of Disseminated Infection with Nocardia cerradoensis in a Human

2015 ◽  
Vol 53 (3) ◽  
pp. 1034-1037 ◽  
Author(s):  
Caroline Piau ◽  
Mallorie Kerjouan ◽  
Marc Le Mouel ◽  
Solene Patrat-Delon ◽  
Pierre-Louis Henaux ◽  
...  
Keyword(s):  
Renal Transplant ◽  
16S Rrna ◽  
Species Identification ◽  
Antibiotic Treatment ◽  
Renal Transplant Patient ◽  
Transplant Patient ◽  
Brain Biopsy ◽  
Content Type ◽  
Disseminated Infection ◽  
First Case

Here we report in a human, a renal transplant patient, the first disseminated infection withNocardia cerradoensis, isolated after a brain biopsy. Species identification was based on 16S rRNA,gyrB, andhsp65gene analyses. Antibiotic treatment was successful by combining carbapenems and aminoglycosides and then switching to oral trimethoprim-sulfamethoxazole.

The use of functional analysis of the ribosome as a tool to determine archaebacterial phylogeny

1989 ◽  
Vol 35 (1) ◽  
pp. 141-147 ◽  
Author(s):  
R. Amils ◽  
L. Ramírez ◽  
J. L. Sanz ◽  
I. Marín ◽  
A. G. Pisabarro ◽  
...  
Keyword(s):  
Functional Analysis ◽  
16S Rrna ◽  
Phylogenetic Tree ◽  
Functional Information ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Sequence Comparisons ◽  
Free System ◽  
Translation Apparatus ◽  
Evolutionary Clock

Forty different antibiotics with diverse kingdom and functional specificities were used to measure the functional characteristics of the archaebacterial translation apparatus. The resulting inhibitory curves, which are characteristic of the cell-free system analyzed, were transformed into quantitative values that were used to cluster the different archaebacteria analyzed. This cluster resembles the phylogenetic tree generated by 16S rRNA sequence comparisons. These results strongly suggest that functional analysis of an appropriate evolutionary clock, such as the ribosome, is of intrinsic phylogenetic value. More importantly, they indicate that the study of the nexus between genotypic and phenotypic (functional) information may shed considerable light on the evolution of the protein synthetic machinery.Key words: antibiotics, ribosomes, archaebacteria, phylogeny, functional analysis.

scholarly journals Importance of Micromonospora spp. as Colonizers of Cellulose in Freshwater Lakes as Demonstrated by Quantitative Reverse Transcriptase PCR of 16S rRNA

2012 ◽  
Vol 78 (9) ◽  
pp. 3495-3499 ◽  
Author(s):  
Alexandre B. de Menezes ◽  
James E. McDonald ◽  
Heather E. Allison ◽  
Alan J. McCarthy
Keyword(s):  
16S Rrna ◽  
Reverse Transcriptase ◽  
Quantitative Pcr ◽  
Lake Sediment ◽  
Relative Abundance ◽  
Bacterial Communities ◽  
Bacterial Population ◽  
Freshwater Lakes ◽  
Content Type ◽  
Water Columns

ABSTRACTThe relative abundance of micromonosporas in the bacterial communities inhabiting cellulose baits, water columns, and sediments of two freshwater lakes was determined by quantitative PCR (qPCR) of reverse-transcribed 16S rRNA.Micromonosporaspp. were shown to be significant members of the active bacterial population colonizing cellulosic substrates in the lake sediment, and their increased prevalence with greater depth was confirmed by enumeration of CFU.

Sign in / Sign up

Export Citation Format

Share Document