scholarly journals Endometrial microbiota is more diverse in people with endometriosis than symptomatic controls

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jocelyn M. Wessels ◽  
Miguel A. Domínguez ◽  
Nicholas A. Leyland ◽  
Sanjay K. Agarwal ◽  
Warren G. Foster
Keyword(s):  
Diversity Index ◽  
16S Rrna Gene Sequencing ◽  
Endometrial Biopsy ◽  
Reproductive Age ◽  
Rrna Gene ◽  
Gram Positive ◽  
Gram Negative ◽  
Retrograde Menstruation ◽  
Reproductive Age Women ◽  
Rrna Gene Sequencing

AbstractEndometriosis is a chronic, estrogen-dependent gynecological condition affecting approximately 10% of reproductive age women. The most widely accepted theory of its etiology includes retrograde menstruation. Recent reports suggest the uterus is not sterile. Thus, the refluxed menstrual effluent may carry bacteria, and contribute to inflammation, the establishment and growth of endometriotic lesions. Here, we compared and contrasted uterine bacteria (endometrial microbiota) in people with surgically confirmed presence (N = 12) or absence of endometriosis (N = 9) using next-generation 16S rRNA gene sequencing. We obtained an average of > 9000 sequence reads per endometrial biopsy, and found the endometrial microbiota of people with endometriosis was more diverse (greater Shannon Diversity Index and proportion of ‘Other’ taxa) than symptomatic controls (with pelvic pain, surgically confirmed absence of endometriosis; diagnosed with other benign gynecological conditions). The relative abundance of bacterial taxa enriched in the endometrial microbiota of people with endometriosis belonged to the Actinobacteria phylum (Gram-positive), Oxalobacteraceae (Gram-negative) and Streptococcaceae (Gram-positive) families, and Tepidimonas (Gram-negative) genus, while those enriched in the symptomatic controls belonged to the Burkholderiaceae (Gram-negative) family, and Ralstonia (Gram-negative) genus. Taken together, results suggest the endometrial microbiota is perturbed in people with endometriosis.

scholarly journals Stool sampling and DNA isolation kits affect DNA quality and bacterial composition following 16S rRNA gene sequencing using MiSeq Illumina platform

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Petra Videnska ◽  
Kristyna Smerkova ◽  
Barbora Zwinsova ◽  
Vlad Popovici ◽  
Lenka Micenkova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Isolation ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Illumina Platform ◽  
Gram Positive ◽  
Bacterial Composition ◽  
Rrna Gene Sequencing

Abstract Many studies correlate changes in human gut microbiome with the onset of various diseases, mostly by 16S rRNA gene sequencing. Setting up the optimal sampling and DNA isolation procedures is crucial for robustness and reproducibility of the results. We performed a systematic comparison of several sampling and DNA isolation kits, quantified their effect on bacterial gDNA quality and the bacterial composition estimates at all taxonomic levels. Sixteen volunteers tested three sampling kits. All samples were consequently processed by two DNA isolation kits. We found that the choice of both stool sampling and DNA isolation kits have an effect on bacterial composition with respect to Gram-positivity, however the isolation kit had a stronger effect than the sampling kit. The proportion of bacteria affected by isolation and sampling kits was larger at higher taxa levels compared to lower taxa levels. The PowerLyzer PowerSoil DNA Isolation Kit outperformed the QIAamp DNA Stool Mini Kit mainly due to better lysis of Gram-positive bacteria while keeping the values of all the other assessed parameters within a reasonable range. The presented effects need to be taken into account when comparing results across multiple studies or computing ratios between Gram-positive and Gram-negative bacteria.

scholarly journals Detection of Cardiobacterium valvarum in a patient with aortic valve infective endocarditis by broad-range PCR

2010 ◽  
Vol 59 (2) ◽  
pp. 231-234 ◽  
Author(s):  
Martina Vaněrková ◽  
Barbora Žaloudíková ◽  
Eva Němcová ◽  
Jana Juránková ◽  
Jiří Pol ◽  
...  
Keyword(s):  
Infective Endocarditis ◽  
Aortic Valve ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Negative Bacterium ◽  
Review Of The Literature ◽  
Gram Negative ◽  
Prosthetic Aortic Valve ◽  
Rrna Gene Sequencing

Cardiobacterium valvarum, a fastidious Gram-negative bacterium, was detected in the aortic valve of a previously healthy 63-year-old man by broad-range PCR and 16S rRNA gene sequencing. In contrast to the patients in five previously published cases, our patient had neither a congenital bicuspid nor a prosthetic aortic valve. Here, we present a case of C. valvarum native tricuspid aortic valve infective endocarditis and a review of the literature.

scholarly journals The profiling of microbiota in vaginal swab samples using 16S rRNA gene sequencing and IS-pro analysis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
M. Singer ◽  
R. Koedooder ◽  
M. P. Bos ◽  
L. Poort ◽  
S. Schoenmakers ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Diagnostic Techniques ◽  
Vaginal Swab ◽  
Reproductive Age ◽  
Rrna Gene ◽  
Rrna Gene Sequencing ◽  
High Level

Abstract Background 16S rRNA gene sequencing is currently the most common way of determining the composition of microbiota. This technique has enabled many new discoveries to be made regarding the relevance of microbiota to the health and disease of the host. However, compared to other diagnostic techniques, 16S rRNA gene sequencing is fairly costly and labor intensive, leaving room for other techniques to improve on these aspects. Results The current study aimed to compare the output of 16S rRNA gene sequencing to the output of the quick IS-pro analysis, using vaginal swab samples from 297 women of reproductive age. 16S rRNA gene sequencing and IS-pro analyses yielded very similar vaginal microbiome profiles, with a median Pearson’s R2 of 0.97, indicating a high level of similarity between both techniques. Conclusions We conclude that the results of 16S rRNA gene sequencing and IS-pro are highly comparable and that both can be used to accurately determine the vaginal microbiota composition, with the IS-pro analysis having the benefit of rapidity.

scholarly journals The Impact of Pre-Slaughter Fasting on the Ruminal Microbial Population of Commercial Angus Steers

2021 ◽  
Vol 9 (12) ◽  
pp. 2625
Author(s):  
Christina Breanne Welch ◽  
Jeferson M. Lourenco ◽  
Darren S. Seidel ◽  
Taylor Rae Krause ◽  
Michael J. Rothrock ◽  
...  
Keyword(s):  
Diversity Index ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Ecosystem Structure ◽  
Opportunistic Pathogens ◽  
Slaughter Cattle ◽  
Before And After ◽  
Ruminal Microbiota ◽  
Rrna Gene Sequencing ◽  
The Impact

Diet impacts the composition of the ruminal microbiota; however, prior to slaughter, cattle are fasted, which may change the ruminal microbial ecosystem structure and lead to dysbiosis. The objective of this study was to determine changes occurring in the rumen after pre-slaughter fasting, which can allow harmful pathogens an opportunity to establish in the rumen. Ruminal samples were collected before and after pre-slaughter fasting from seventeen commercial Angus steers. DNA extraction and 16S rRNA gene sequencing were performed to determine the ruminal microbiota, as well as volatile fatty acid (VFA) concentrations. Microbial richness (Chao 1 index), evenness, and Shannon diversity index all increased after fasting (p ≤ 0.040). During fasting, the two predominant families Prevotellaceae and Ruminococcaceae decreased (p ≤ 0.029), whereas the remaining minor families increased (p < 0.001). Fasting increased Blautia and Methanosphaera (p ≤ 0.003), while Campylobacter and Treponema tended to increase (p ≤ 0.086). Butyrate concentration tended to decrease (p = 0.068) after fasting. The present findings support that fasting causes ruminal nutrient depletion resulting in dysbiosis, allowing opportunistic pathogens to exploit the void in the ruminal ecological niche.

scholarly journals The Gut Microbiome and Diabetes Status in the Multiethnic Cohort

2020 ◽  
Vol 4 (Supplement_2) ◽  
pp. 1450-1450
Author(s):  
Gertraud Maskarinec ◽  
Phyllis Raquinio ◽  
Bruce Kristal ◽  
Lynne Wilkens ◽  
Adrian Franke ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiome ◽  
Diversity Index ◽  
16S Rrna Gene Sequencing ◽  
Sensu Stricto ◽  
Rrna Gene ◽  
Gram Negative ◽  
Bonferroni Adjustment ◽  
Multiethnic Cohort ◽  
Diabetes Status

Abstract Objectives As features of the gut microbiome may promote the development of type 2 diabetes (T2D), we examined the hypothesis that gut microbiome composition differs by glycemic/diabetes status within a subset of the Multiethnic Cohort. We also estimated the association of lipopolysaccharide-binding protein (LBP) as a measure of circulating bacterial endotoxin with T2D. This outer membrane component of gram-negative bacteria may affect glucose metabolism. Methods In 2013–16, cohort members from 5 ethnic groups completed clinic visits, questionnaires, and stool collections. Participants with self-reported T2D and/or taking medication were considered T2D cases. Those with fasting glucose &gt;125 and 100–125 mg/dL were classified as undiagnosed (UT2D) and prediabetes (PT2D). We characterized the gut microbiome through 16S rRNA gene sequencing (V1-V3). Plasma LBP was measured by ELISA. Linear regression was applied to estimate associations of gut microbiome community structure and LBP with T2D status adjusting for relevant confounders. Results Among 1756 participants (59.9–77.4 years), 315 (18%) were T2D, 158 (9%) UT2D, 518 (29%) PT2D, and 765 (44%) normoglycemic (NG). The Shannon diversity index was lower (6.30, 6.25, 6.28, 6.18; P = 0.02) and LBP was higher (26.0, 26.6, 28.6, 28.2 µg/mL; P = 0.0009) in T2D than NG participants. Of 10 phyla, Actinobacteria and Firmicutes were inversely associated with T2D status (P = 0.004). Six of 161 genera were significantly related to T2D status after Bonferroni adjustment: the abundance of Clostridium sensu stricto 1, Lachnospira, Lachnospiraceae NC2004, and Peptostreptococcaceae was lower, while Lachnospiraceae uncultured and Escherichia-Shigella were more abundant among T2D than NG participants. In general, those with PT2D and UT2D had values closer to NG than T2D individuals. Conclusions Participants with T2D showed a lower abundance of bacteria capable of fermenting plant polysaccharides and higher levels of gram-negative endotoxin-producing bacteria indicating that a less favorable pattern of gut microbiome community structure may contribute to T2D through endotoxin binding to toll-like receptors via LBP and activation of the NFkB pathway associated with chronic systemic inflammation. Funding Sources NIH grants P01CA169530, U01CA164973, P30CA071789, #UL1TR000130, R01HL140335.

scholarly journals IN-VITRO ANTIMICROBIAL ACTIVITY OF BIOLOGICAL SYNTHESIZED SILVER NANOPARTICLES USING STENOTROPHOMONAS MALTOPHILIA STRAIN NS-24 FROM NON-RHIZOSPHERE SOIL

2020 ◽  
pp. 73-79
Author(s):  
SREENIVASA NAYAKA ◽  
BIDHAYAK CHAKRABORTY ◽  
DATTATREYA AIRODGI ◽  
MEGHASHYAMA P. BHAT ◽  
SHASHIRAJ K. NAGARAJA ◽  
...  
Keyword(s):  
Antimicrobial Activity ◽  
Silver Nanoparticles ◽  
Stenotrophomonas Maltophilia ◽  
Gene Sequencing ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Gram Negative ◽  
Uv Visible ◽  
Rrna Gene Sequencing ◽  
And Staphylococcus Aureus

Objective: The present goals of our study were biological synthesis, characterizations of silver nanoparticles, and evaluation of its antimicrobial activity against microbial pathogens like Escherichia coli, Enterococcus faecalis, Streptococcus pneumoniae and Staphylococcus aureus. Methods: The bacterial Strain NS-24 was isolated on nutrient agar medium and was selected for the synthesis of silver nanoparticles based on its gram-negative characteristics. The characterizations of silver nanoparticles were done by UV-Visible spectroscopy, Atomic Force Microscopy (AFM), High Resolution-Transmission Electron Microscopy (HR-TEM), Scanning Electron Microscopy (SEM) with Energy Dispersive Spectroscopy (EDX), X-ray Diffraction (XRD) and Fourier Transform Infrared Spectroscopy (FTIR). Later, the molecular characterization of the Strain NS-24 was done by DNA extraction and 16S rRNA gene sequencing. Results: The UV-visible spectrophotometric observation of the Strain NS-24 supernatant and AgNO3 solution showed maximum absorbance at 423 nm. The AFM data confirmed that the particles were polydispersed and spherical in shape. Additionally, the FTIR analysis revealed the IR spectral band patterning and TEM analyzes showed the size of biological AgNPs was in the range of 12.56 nm to 27.32 nm, with an average of 18.06 nm in size. Further, the 16S rRNA gene sequencing revealed the identity of Strain NS-24 as Stenotrophomonas maltophilia. The antimicrobial activity of AgNPs was studied on different gram-negative and gram-positive bacterial strains like Escherichia coli (MTCC 40), Enterococcus faecalis (MTCC 6845), Streptococcus pneumoniae (MTCC 8874) and Staphylococcus aureus (MTCC 2825), which showed good inhibition of their growth at varying concentrations of AgNPs against all the pathogens. Conclusion: Our findings showed that the synthesized AgNPs from the isolated bacterium was small in size and had profound antibacterial activity against pathogenic micro-organisms.

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