scholarly journals Dental Biofilm and Saliva Microbiome and Its Interplay with Pediatric Allergies

2021 ◽  
Vol 9 (6) ◽  
pp. 1330
Author(s):  
Nicole B. Arweiler ◽  
Vivien Rahmel ◽  
Bilal Alashkar Alhamwe ◽  
Fahd Alhamdan ◽  
Michael Zemlin ◽  
...  
Keyword(s):  
Allergic Diseases ◽  
Rrna Gene ◽  
Healthy Controls ◽  
Asthmatic Children ◽  
Dental Biofilm ◽  
Β Diversity ◽  
Allergic Asthmatic ◽  
Single Center Study ◽  
Oral Microorganisms ◽  
Generation Sequencing

Little is known about the interplay and contribution of oral microorganisms to allergic diseases, especially in children. The aim of the clinical study was to associate saliva and dental biofilm microbiome with allergic disease, in particular with allergic asthma. In a single-center study, allergic/asthmatic children (n = 15; AA-Chd; age 10.7 ± 2.9), atopic/allergic children (n = 16; AT/AL-Chd; 11.3 ± 2.9), and healthy controls (n = 15; CON-Chd; age 9.9 ± 2.2) were recruited. After removing adhering biofilms from teeth and collecting saliva, microbiome was analyzed by using a 16s-rRNA gene-based next-generation sequencing in these two mediums. Microbiome structure differed significantly between saliva and dental biofilms (β-diversity). Within the groups, the dental biofilm microbiome of AA-Chd and AT/AL-Chd showed a similar microbial fingerprint characterized by only a small number of taxa that were enriched or depleted (4) compared to the CON-Chd, while both diseased groups showed a stronger microbial shift compared to CON-Chd, revealing 14 taxa in AA-Chd and 15 taxa in AT/AL-Chd that were different. This could be the first note to the contribution of dental biofilm and its metabolic activity to allergic health or disease.

scholarly journals Data analysis workflow for the detection of canine vector-borne pathogens using 16 S rRNA Next-Generation Sequencing

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Elton J. R. Vasconcelos ◽  
Chayan Roy ◽  
Joseph A. Geiger ◽  
Kristina M. Oney ◽  
Melody Koo ◽  
...  
Keyword(s):  
Veterinary Medicine ◽  
Next Generation Sequencing ◽  
Complete Analysis ◽  
Molecular Diagnostic ◽  
Rrna Gene ◽  
Spotted Fever Group ◽  
Next Generation ◽  
Vector Borne ◽  
16 S Rrna ◽  
Generation Sequencing

Abstract Background Vector-borne diseases (VBDs) impact both human and veterinary medicine and pose special public health challenges. The main bacterial vector-borne pathogens (VBPs) of importance in veterinary medicine include Anaplasma spp., Bartonella spp., Ehrlichia spp., and Spotted Fever Group Rickettsia. Taxon-targeted PCR assays are the current gold standard for VBP diagnostics but limitations on the detection of genetically diverse organisms support a novel approach for broader detection of VBPs. We present a methodology for genetic characterization of VBPs using Next-Generation Sequencing (NGS) and computational approaches. A major advantage of NGS is the ability to detect multiple organisms present in the same clinical sample in an unsupervised (i.e. non-targeted) and semi-quantitative way. The Standard Operating Procedure (SOP) presented here combines industry-standard microbiome analysis tools with our ad-hoc bioinformatic scripts to form a complete analysis pipeline accessible to veterinary scientists and freely available for download and use at https://github.com/eltonjrv/microbiome.westernu/tree/SOP. Results We tested and validated our SOP by mimicking single, double, and triple infections in genomic canine DNA using serial dilutions of plasmids containing the entire 16 S rRNA gene sequence of (A) phagocytophilum, (B) v. berkhoffii, and E. canis. NGS with broad-range 16 S rRNA primers followed by our bioinformatics SOP was capable of detecting these pathogens in biological replicates of different dilutions. These results illustrate the ability of NGS to detect and genetically characterize multi-infections with different amounts of pathogens in a single sample. Conclusions Bloodborne microbiomics & metagenomics approaches may help expand the molecular diagnostic toolbox in veterinary and human medicine. In this paper, we present both in vitro and in silico detailed protocols that can be combined into a single workflow that may provide a significant improvement in VBP diagnostics and also facilitate future applications of microbiome research in veterinary medicine.

scholarly journals Comparative analysis of bacterioplankton assemblages from two subtropical karst reservoirs of southwestern China with contrasting trophic status

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Qiang Li ◽  
Yadan Huang ◽  
Shenglin Xin ◽  
Zhongyi Li
Keyword(s):  
Trophic Status ◽  
Alpha Diversity ◽  
Decisive Role ◽  
Sensu Stricto ◽  
Karst Area ◽  
Southwestern China ◽  
Rrna Gene ◽  
Karst Water ◽  
Bacterioplankton Community ◽  
Generation Sequencing

AbstractAlthough bacterioplankton play an important role in aquatic ecosystems, less is known about bacterioplankton assemblages from subtropical karst reservoirs of southwestern China with contrasting trophic status. Here, 16S rRNA gene next-generation sequencing coupled with water chemistry analysis was applied to compare the bacterioplankton communities from a light eutrophic reservoir, DL Reservoir, and a mesotrophic reservoir, WL Reservoir, in subtropical karst area of southwestern China. Our findings indicated that Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Cyanobacteria and Verrucomicrobia dominated bacterioplankton community with contrasting relative frequency in the two subtropical karst reservoirs. Proteobacteria and Bacteroidetes were the core communities, which played important roles in karst biogeochemical cycles. Though WT, TN and DOC play the decisive role in assembling karst aquatic bacterioplankton, trophic status exerted significantly negative direct effects on bacterioplankton community composition and alpha diversity. Due to contrasting trophic status in the two reservoirs, the dominant taxa such as Enterobacter, Clostridium sensu stricto, Candidatus Methylacidiphilum and Flavobacteriia, that harbor potential functions as valuable and natural indicators of karst water health status, differed in DL Reservoir and WL Reservoir.

scholarly journals Targeted Next-Generation Sequencing and Informatics as an Effective Tool to Establish the Composition of Bovine Piroplasm Populations in Endemic Regions

2020 ◽  
Vol 9 (1) ◽  
pp. 21
Author(s):  
Abdul Ghafar ◽  
Anson V. Koehler ◽  
Ross S. Hall ◽  
Charles G. Gauci ◽  
Robin B. Gasser ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Water Buffalo ◽  
Hypervariable Region ◽  
Small Subunit ◽  
Rrna Gene ◽  
Next Generation ◽  
Small Subunit Rrna ◽  
Tropical Theileriosis ◽  
Ecological Zones ◽  
Generation Sequencing

Protists of the genera Babesia and Theileria (piroplasms) cause some of the most prevalent and debilitating diseases for bovines worldwide. In this study, we established and used a next-generation sequencing-informatic approach to explore the composition of Babesia and Theileria populations in cattle and water buffalo in a country (Pakistan) endemic for these pathogens. We collected individual blood samples from cattle (n = 212) and water buffalo (n = 154), extracted genomic DNAs, PCR-amplified the V4 hypervariable region of 18S small subunit rRNA gene from piroplasms, sequenced amplicons using Illumina technology, and then analysed data using bioinformatic platforms. The results revealed piroplasms in 68.9% (252/366) samples, with overall occurrence being markedly higher in cattle (85.8%) than in water buffaloes (45.5%). Babesia (B.) occultans and Theileria (T.) lestoquardi-like species were recorded for the first time in Pakistan, and, overall, T. annulata was most commonly detected (65.8%) followed by B. bovis (7.1%), B. bigemina (4.4%), and T. orientalis (0.5%), with the genetic variability within B. bovis being pronounced. The occurrence and composition of piroplasm species varied markedly across different agro-ecological zones. The high detection of T. annulata in asymptomatic animals suggested a relatively high level of endemic stability of tropical theileriosis in the bovine population.

scholarly journals Effect of hay type on cecal and fecal microbiome and fermentation parameters in horses

2020 ◽  
Author(s):  
Rachel J Sorensen ◽  
James S Drouillard ◽  
Teresa L Douthit ◽  
Qinghong Ran ◽  
Douglas G Marthaler ◽  
...  
Keyword(s):  
Fixed Effects ◽  
Volatile Fatty Acids ◽  
Random Effect ◽  
Alpha Diversity ◽  
Sampling Location ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Fecal Microbiome ◽  
Β Diversity ◽  
Fermentation Parameters

Abstract The effect of hay type on the microbiome of the equine gastrointestinal tract is relatively unexplored. Our objective was to characterize the cecal and fecal microbiome of mature horses consuming alfalfa or Smooth Bromegrass (brome) hay. Six cecally cannulated horses were used in a split plot design run as a crossover in 2 periods. Whole plot treatment was ad libitum access to brome or alfalfa hay fed over two 21-d acclimation periods with subplots of sampling location (cecum and rectum) and sampling hour. Each acclimation period was followed by a 24-h collection period where cecal and fecal samples were collected every 3 h for analysis of pH and volatile fatty acids (VFA). Fecal and cecal samples were pooled and sent to a commercial lab (MR DNA, Shallowater, TX) for amplification of the V4 region of the 16S rRNA gene and sequenced using Illumina HiSeq. Main effects of hay on VFA, pH, and taxonomic abundances were analyzed using the MIXED procedure of SAS 9.4 with fixed effects of hay, hour, location, period, all possible interactions and random effect of horse. Alpha and β diversity were analyzed using the R Dame package. Horses fed alfalfa had greater fecal than cecal pH (P ≤ 0.05) whereas horses fed brome had greater cecal than fecal pH (P ≤ 0.05). Regardless of hay type, total volatile fatty acid (VFA) concentrations were greater (P ≤ 0.05) in the cecum than in feces, and alfalfa resulted in greater (P ≤ 0.05) VFA concentrations than brome in both sampling locations. Alpha diversity was greater (P ≤ 0.05) in fecal compared to cecal samples. Microbial community structure within each sampling location and hay type differed from one another (P ≤ 0.05). Bacteroidetes were greater (P ≤ 0.05) in the cecum compared to the rectum, regardless of hay type. Firmicutes and Firmicutes:Bacteroidetes were greater (P ≤ 0.05) in the feces compared to cecal samples of alfalfa-fed horses. In all, fermentation parameters and bacterial abundances were impacted by hay type and sampling location in the hindgut.

scholarly journals Structure of Microbial Communities When Complementary Effluents Are Anaerobically Digested

2021 ◽  
Vol 11 (3) ◽  
pp. 1293
Author(s):  
Ana Eusébio ◽  
André Neves ◽  
Isabel Paula Marques
Keyword(s):  
Anaerobic Digestion ◽  
Microbial Communities ◽  
Volatile Fatty Acids ◽  
Olive Mill Wastewater ◽  
Organic Load ◽  
Rrna Gene ◽  
Bacterial Populations ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Olive Mill

Olive oil and pig productions are important industries in Portugal that generate large volumes of wastewater with high organic load and toxicity, raising environmental concerns. The principal objective of this study is to energetically valorize these organic effluents—piggery effluent and olive mill wastewater—through the anaerobic digestion to the biogas/methane production, by means of the effluent complementarity concept. Several mixtures of piggery effluent were tested, with an increasing percentage of olive mill wastewater. The best performance was obtained for samples of piggery effluent alone and in admixture with 30% of OMW, which provided the same volume of biogas (0.8 L, 70% CH4), 63/75% COD removal, and 434/489 L CH4/kg SVin, respectively. The validation of the process was assessed by molecular evaluation through Next Generation Sequencing (NGS) of the 16S rRNA gene. The structure of the microbial communities for both samples, throughout the anaerobic process, was characterized by the predominance of bacterial populations belonging to the phylum Firmicutes, mainly Clostridiales, with Bacteroidetes being the subdominant populations. Archaea populations belonging to the genus Methanosarcina became predominant throughout anaerobic digestion, confirming the formation of methane mainly from acetate, in line with the greatest removal of volatile fatty acids (VFAs) in these samples.

scholarly journals Next-Generation Sequencing for Pathogen Identification in Infected Foot Ulcers

2020 ◽  
Vol 5 (4) ◽  
pp. 2473011420S0002
Author(s):  
Yoonjung Choi ◽  
Irvin Oh
Keyword(s):  
Next Generation Sequencing ◽  
False Positive ◽  
Bacterial Genome ◽  
Rrna Gene ◽  
Next Generation ◽  
Antibiotic Resistant ◽  
Streptococcus Species ◽  
Resistant Genes ◽  
Standard Culture ◽  
Generation Sequencing

Category: Other Introduction/Purpose: Foot infections are often polymicrobial with diverse microbiomes. Accurate identification of the main pathogen in diabetic foot ulcer (DFU) remain challenging due to contamination or negative cultures often leading to ineffective post-surgical antibiotic treatment. Application of molecular diagnostics, such as next generation sequencing (NGS) has been explored as an alternative to standard culture in orthopaedic infections. NGS is highly sensitive and detects an entire bacterial genome along with pharmacologic resistant genes in a given sample. We sought to investigate the potential use of NGS for accurate diagnosis and quantification of various species in infected DFU. We hypothesize that NGS will provide a more accurate means of diagnosing and profiling microorganisms in infected DFU compared to the standard culture method. Methods: We investigated 30 infected DFU patients who underwent surgical treatment by a single academic orthopaedic surgeon from October 2018 to September 2019. The average age of the patient was 60.4 (range 33-82) years-old. Surgical procedures performed were irrigation and debridement (12), toe or ray amputation (13), calcanectomies (4), and below-knee amputation (1). Infected bone specimens were obtained intraoperatively and processed for standard culture and NGS. Quantitative PCR was performed to determine the bacterial burden present in the sample. DNA was amplified by PCR from a highly conserved region of the rRNA gene in the bacteria (16S rRNA). Once a high level of DNA was generated and determined, it was compared against NIH GenBank database. Concordance between the standard culture and NGS was assessed. Results: In 28 of 29 patients, pathogens were identified by both NGS and culture, with complete consistency of organisms in 13 cases (concordance rate: 43.3%). NGS provided relative quantitative measures and the presence of antibiotic resistant genes for each pathogen. In NGS, Anaerococcus species (79.3%) was the most common organism, followed by Streptococcus species (44.8%), Prevotella species (44.8%), Finegoldia magna (44.8%). In culture, S. aureus (58.6%) was the most common, followed by Streptococcus species (34.5%), coagulase-negative Staphylococci (24.1%), Corynebacterium species (20.7%). On average, NGS revealed 5.1 (1-11) number of pathogens, whereas standard culture revealed 2.6 (1-6) pathogens in a given sample. NGS identified 2 cases with false positive standard culture and detected antibiotic resistant organisms in 15 specimens. Conclusion: NGS is an emerging method of microbial identification in orthopedic infection. It is particularly helpful in profiling diverse microbes in polymicrobial infected DFU. It can identify major pathogens and may correct false positive or false negative culture. NGS may allow a faster invitation of postoperative targeted antibiotic therapy. [Table: see text]

Gut microbiome of the emerald ash borer, Agrilus planipennis Fairmaire, and its relationship with insect population density

2020 ◽  
Vol 96 (8) ◽  
Author(s):  
Judith Mogouong ◽  
Philippe Constant ◽  
Robert Lavallée ◽  
Claude Guertin
Keyword(s):  
Population Density ◽  
Gut Microbiome ◽  
Emerald Ash Borer ◽  
Agrilus Planipennis ◽  
Economic Damage ◽  
Taxonomic Structure ◽  
Rrna Gene ◽  
Local Conditions ◽  
Β Diversity ◽  
Α Diversity

ABSTRACT The gut microbial communities of beetles play crucial roles in their adaptive capacities. Environmental factors such as temperature or nutrition naturally affect the insect microbiome, but a shift in local conditions like the population density on a host tree could also lead to changes in the microbiota. The emerald ash borer (EAB), Agrilus planipennis Fairmaire, is an exotic wood borer that causes environmental and economic damage to ash trees in North America. This study aimed to describe the taxonomic structure of the EAB gut microbiome and explore its potential relationship with borer population size. The number of EAB adults collected per tree through a 75 km transect from an epicenter allowed the creation of distinct classes of population density. The Gammaproteobacteria and Ascomycota predominated in bacterial and fungal communities respectively, as determined by sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer ITS2. Species richness and diversity of the bacterial community showed significant dependence on population density. Moreover, α-diversity and β-diversity analysis revealed some indicator amplicon sequence variants suggesting that the plasticity of the gut microbiome could be related to the EAB population density in host trees.

scholarly journals Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

2009 ◽  
Vol 75 (23) ◽  
pp. 7537-7541 ◽  
Author(s):  
Patrick D. Schloss ◽  
Sarah L. Westcott ◽  
Thomas Ryabin ◽  
Justine R. Hall ◽  
Martin Hartmann ◽  
...  
Keyword(s):  
16S Rrna ◽  
Software Package ◽  
Sequence Data ◽  
Rrna Gene ◽  
Sequencing Data ◽  
Laptop Computer ◽  
Operational Taxonomic Units ◽  
Β Diversity ◽  
Single Piece

ABSTRACT mothur aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. It builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. As a case study, we used mothur to trim, screen, and align sequences; calculate distances; assign sequences to operational taxonomic units; and describe the α and β diversity of eight marine samples previously characterized by pyrosequencing of 16S rRNA gene fragments. This analysis of more than 222,000 sequences was completed in less than 2 h with a laptop computer.

Sign in / Sign up

Export Citation Format

Share Document