scholarly journals Biodeteriogens Characterization and Molecular Analyses of Diverse Funeral Accessories from XVII Century

2020 ◽  
Vol 10 (16) ◽  
pp. 5451 ◽  
Author(s):  
Zuzana Kisová ◽  
Matej Planý ◽  
Jelena Pavlović ◽  
Mária Bučková ◽  
Andrea Puškárová ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Phytopathogenic Fungi ◽  
Metal Corrosion ◽  
Animal Origin ◽  
Organic Substrates ◽  
Illumina Platform ◽  
Buried Objects ◽  
Independent Analysis ◽  
Culture Independent

A historical crypt offers us a particular view of the conditions of some buried materials (in this case textiles) and the various biogenic phenomena to which they were subjected over the centuries. In addition, significant knowledge can come by studying the DNA of buried objects which allows the recognition of materials, but also to reveal some practice of the funeral ceremony. In this study, the deteriorating microbial communities colonizing various funeral textile items were identified and characterized using microscopic observation, cultivation, polymerase chain reaction (PCR) and sequencing, hydrolytic tests; and culture-independent analysis (high-throughput sequencing, MinION platform). Different PCR assays and consequent sequencing of amplicons were employed to recognize the animal origin of bodice reinforcements and the type of plant used to embellish the young girl. The analysis of ancient DNA (aDNA from animal and plant) was also completed by the application of high-throughput sequencing through Illumina platform. The combination of all these techniques permitted the identification of a complex microbiota composed by dangerous degradative microorganisms able to hydrolyze various organic substrates such as fibroin, keratin, and cellulose. Bacteria responsible for metal corrosion and bio-mineralization, and entomopathogenic and phytopathogenic fungi. The analysis of aDNA identified the animal component used in bodice manufacturing, the plant utilized as ornament and probably the season of this fatal event.

scholarly journals Virome Characterization in Commercial Bovine Serum Batches—A Potentially Needed Testing Strategy for Biological Products

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2425
Author(s):  
Willian P. Paim ◽  
Mayara F. Maggioli ◽  
Shollie M. Falkenberg ◽  
Akhilesh Ramachandran ◽  
Matheus N. Weber ◽  
...  
Keyword(s):  
High Throughput ◽  
Bovine Serum ◽  
High Throughput Sequencing ◽  
Culture Media ◽  
The United States ◽  
Animal Origin ◽  
Emerging Viruses ◽  
Illumina Platform ◽  
Biological Products ◽  
Viral Contaminants

Bovine serum has been widely used as a universal supplement in culture media and other applications, including the manufacture of biological products and the production of synthetic meat. Currently, commercial bovine serum is tested for possible viral contaminants following regional guidelines. Regulatory agencies’ established tests focused on detecting selected animal origin viruses and are based on virus isolation, immunofluorescence, and hemadsorption assays. However, these tests may fail to detect new or emerging viruses in biological products. High-throughput sequencing is a powerful option since no prior knowledge of the viral targets is required. In the present study, we evaluate the virome of seven commercial batches of bovine serum from Mexico (one batch), New Zealand (two batches), and the United States (four batches) using a specific preparation and enrichment method for pooled samples and sequencing using an Illumina platform. A variety of circular replicase-encoding single-stranded (CRESS) DNA families (Genomoviridae, Circoviridae, and Smacoviridae) was identified. Additionally, CrAssphage, a recently discovered group of bacteriophage correlated with fecal contamination, was identified in 85% of the tested batches. Furthermore, sequences representing viral families with single-stranded DNA (Parvoviridae), double-stranded DNA (Polyomaviridae and Adenoviridae), single-stranded RNA (Flaviviridae, Picornaviridae, and Retroviridae), and double-stranded RNA (Reoviridae) were identified. These results support that high-throughput sequencing associated with viral enrichment is a robust tool and should be considered an additional layer of safety when testing pooled biologicals to detect viral contaminants overlooked by the current testing protocols.

scholarly journals High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

2013 ◽  
Vol 79 (10) ◽  
pp. 3148-3155 ◽  
Author(s):  
Danilo Ercolini
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Food Microbiology ◽  
Acid Extraction ◽  
Food Research ◽  
Independent Analysis ◽  
Culture Independent ◽  
Depth Study ◽  
Current Scenario ◽  
Recent Trends

ABSTRACTFollowing recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.

scholarly journals High-Throughput Sequencing to Investigate Phytopathogenic Fungal Propagules Caught in Baited Insect Traps

2019 ◽  
Vol 5 (1) ◽  
pp. 15 ◽  
Author(s):  
Émilie D. Tremblay ◽  
Troy Kimoto ◽  
Jean A. Bérubé ◽  
Guillaume J. Bilodeau
Keyword(s):  
High Throughput ◽  
Plant Pathogens ◽  
High Throughput Sequencing ◽  
Morphological Characteristics ◽  
Diagnostic Techniques ◽  
Phytopathogenic Fungi ◽  
Personal Genome ◽  
Annual Survey ◽  
Fungal Propagules ◽  
Wood Boring

Studying the means of dispersal of plant pathogens is crucial to better understand the dynamic interactions involved in plant infections. On one hand, entomologists rely mostly on both traditional molecular methods and morphological characteristics, to identify pests. On the other hand, high-throughput sequencing (HTS) is becoming the go-to avenue for scientists studying phytopathogens. These organisms sometimes infect plants, together with insects. Considering the growing number of exotic insect introductions in Canada, forest pest-management efforts would benefit from the development of a high-throughput strategy to investigate the phytopathogenic fungal and oomycete species interacting with wood-boring insects. We recycled formerly discarded preservative fluids from the Canadian Food Inspection Agency annual survey using insect traps and analysed more than one hundred samples originating from across Canada. Using the Ion Torrent Personal Genome Machine (PGM) HTS technology and fusion primers, we performed metabarcoding to screen unwanted fungi and oomycetes species, including Phytophthora spp. Community profiling was conducted on the four different wood-boring, insect-attracting semiochemicals; although the preservative (contained ethanol) also attracted other insects. Phytopathogenic fungi (e.g., Leptographium spp. and Meria laricis in the pine sawyer semiochemical) and oomycetes (mainly Peronospora spp. and Pythium aff. hypogynum in the General Longhorn semiochemical), solely associated with one of the four types of semiochemicals, were detected. This project demonstrated that the insect traps’ semiochemical microbiome represents a new and powerful matrix for screening phytopathogens. Compared to traditional diagnostic techniques, the fluids allowed for a faster and higher throughput assessment of the biodiversity contained within. Additionally, minimal modifications to this approach would allow it to be used in other phytopathology fields.

scholarly journals Exploring the Sources of Bacterial Spoilers in Beefsteaks by Culture-Independent High-Throughput Sequencing

PLoS ONE ◽  
2013 ◽  
Vol 8 (7) ◽  
pp. e70222 ◽  
Author(s):  
Francesca De Filippis ◽  
Antonietta La Storia ◽  
Francesco Villani ◽  
Danilo Ercolini
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Culture Independent

scholarly journals Antigenic and genetic characterization of Streptococcus pneumoniae strains isolated from patients with invasive and non-invasive pneumococcal infections by using high-throughput sequencing

2021 ◽  
Vol 98 (5) ◽  
pp. 512-518
Author(s):  
K. O. Mironov ◽  
I. I. Gaponova ◽  
V. I. Korchagin ◽  
Yu. V. Mikhailova ◽  
A. A. Shelenkov ◽  
...  
Keyword(s):  
Data Analysis ◽  
Streptococcus Pneumoniae ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Whole Genome ◽  
Pneumococcal Infections ◽  
Genome Sequences ◽  
Illumina Platform ◽  
Genetic Characteristics ◽  
Non Invasive

The objective of this study was to characterize and compare antigenic and genetic characteristics of Streptococcus pneumoniae strains isolated from patients with invasive and non-invasive pneumococcal infections (PIs) by using the data of high-throughput sequencing.Materials and methods. A total of 158 S. pneumoniae strains were studied. All of them were isolated during different stages of the PEHASus multicenter study performed in 2015-2020. The data analysis was based on the information about whole-genome sequences of 46 strains isolated during the above study. Real-time PCR methods and high-throughput sequencing (the Illumina platform) were used for identification of serotypes. The SeroBA, PneumoCaT software and PubMLST.org website resources were used in the data processing.Results and discussion. The serotypes of all the studied strains were identified. A number of discrepancies among serotypes in serogroup 6 and one discordant result were revealed by the analysis of whole-genome sequences using 2 programs. The PCR methods were effectively used to characterize serotypes in 87% and 69% of the pathogens of invasive and non-invasive PIs, respectively. The serotypes contained in PCV13 accounted for 59% and 37%, while PPV23 serotypes accounted for 78% and 53% of the strains isolated from patients with invasive and non-invasive PIs, respectively. The data analysis was unable to identify either the dominant sequence type (a total of 81 sequence types have been identified) or clonal complexes, except for serotype 3 strains, thus demonstrating consistency with the data from previous studies suggesting the absence of a well-represented clonal structure of S. pneumoniae associated with pneumococcal meningitis in Russia.Conclusion. The obtained data made it possible to identify the distribution of the circulating serotypes and genetic characteristics of the strains isolated from PI patients, thus being instrumental for assessment of the effectiveness of the existing polyvalent vaccines and providing information for improvement of the PCR-based methods of serotyping.

scholarly journals Community Structures and Antifungal Activity of Root-Associated Endophytic Actinobacteria of Healthy and Diseased Soybean

2019 ◽  
Vol 7 (8) ◽  
pp. 243 ◽  
Author(s):  
Chongxi Liu ◽  
Xiaoxin Zhuang ◽  
Zhiyin Yu ◽  
Zhiyan Wang ◽  
Yongjiang Wang ◽  
...  
Keyword(s):  
Antifungal Activity ◽  
High Throughput Sequencing ◽  
Antagonistic Activity ◽  
Diseased Plant ◽  
Natural Defense ◽  
Independent Analysis ◽  
Culture Independent ◽  
Potential Reservoir ◽  
Endophytic Actinobacteria

The present study was conducted to examine the influence of a pathogen Sclerotinia sclerotiorum (Lib.) de Bary on the actinobacterial community associated with the soybean roots. A total of 70 endophytic actinobacteria were isolated from the surface-sterilized roots of either healthy or diseased soybeans, and they were distributed under 14 genera. Some rare genera, including Rhodococcus, Kribbella, Glycomyces, Saccharothrix, Streptosporangium and Cellulosimicrobium, were endemic to the diseased samples, and the actinobacterial community was more diverse in the diseased samples compared with that in the heathy samples. Culture-independent analysis of root-associated actinobacterial community using the high-throughput sequencing approach also showed similar results. Four Streptomyces strains that were significantly abundant in the diseased samples exhibited strong antagonistic activity with the inhibition percentage of 54.1–87.6%. A bioactivity-guided approach was then employed to isolate and determine the chemical identity of antifungal constituents derived from the four strains. One new maremycin analogue, together with eight known compounds, were detected. All compounds showed significantly antifungal activity against S. sclerotiorum with the 50% inhibition (EC50) values of 49.14–0.21 mg/L. The higher actinobacterial diversity and more antifungal strains associated with roots of diseased plants indicate a possible role of the root-associated actinobacteria in natural defense against phytopathogens. Furthermore, these results also suggest that the root of diseased plant may be a potential reservoir of actinobacteria producing new agroactive compounds.

scholarly journals Transcriptome-seq provides insights into sex-preference pattern of gene expression between testis and ovary of the crucifix crab (Charybdis feriatus)

2018 ◽  
Vol 50 (5) ◽  
pp. 393-405 ◽  
Author(s):  
Yin Zhang ◽  
Guidong Miao ◽  
Hanafiah Fazhan ◽  
Khor Waiho ◽  
Huaiping Zheng ◽  
...  
Keyword(s):  
Sex Determination ◽  
Candidate Genes ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Transcriptome Profiling ◽  
Nucleotide Polymorphisms ◽  
Illumina Platform ◽  
Single Nucleotide ◽  
Good Consistency ◽  
Simple Sequence

The crucifix crab, Charybdis feriatus, which mainly inhabits Indo-Pacific region, is regarded as one of the most high-potential species for domestication and incorporation into the aquaculture sector. However, the regulatory mechanisms of sex determination and differentiation of this species remain unclear. To identify candidate genes involved in sex determination and differentiation, high throughput sequencing of transcriptome from the testis and ovary of C. feriatus was performed by the Illumina platform. After removing adaptor primers, low-quality sequences and very short (<50 nt) reads, we obtained 80.9 million and 66.2 million clean reads from testis and ovary, respectively. A total of 86,433 unigenes were assembled, and ~43% (37,500 unigenes) were successfully annotated to the NR, NT, Swiss-Prot, KEGG, COG, GO databases. By comparing the testis and ovary libraries, we obtained 27,636 differentially expressed genes. Some candidate genes involved in the sex determination and differentiation of C. feriatus were identified, such as vasa, pgds, vgr, hsp90, dsx-f, fem-1, and gpr. In addition, 88,608 simple sequence repeats were obtained, and 61,929 and 77,473 single nucleotide polymorphisms from testis and ovary were detected, respectively. The transcriptome profiling was validated by quantitative real-time PCR in 30 selected genes, which showed a good consistency. The present study is the first high-throughput transcriptome sequencing of C. feriatus. These findings will be useful for future functional analysis of sex-associated genes and molecular marker-assisted selections in C. feriatus.

scholarly journals gndDb, a Database of Partial gnd Sequences To Assist with Analysis of Escherichia coli Communities Using High-Throughput Sequencing

2019 ◽  
Vol 8 (33) ◽  
Author(s):  
Adrian L. Cookson ◽  
David W. Lacher ◽  
Flemming Scheutz ◽  
David A. Wilkinson ◽  
Patrick J. Biggs ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Community Analysis ◽  
Culture Methods ◽  
Content Type ◽  
E Coli ◽  
Content Diversity ◽  
Culture Independent ◽  
Low Levels

The use of culture methods to detect Escherichia coli diversity does not provide sufficient resolution to identify strains present at low levels. Here, we target the hypervariable gnd gene and describe a database containing 534 distinct partial gnd sequences and associated O groups for use with culture-independent E. coli community analysis.

scholarly journals “Remake” by High-Throughput Sequencing of the Microbiota Involved in the Production of Water Buffalo Mozzarella Cheese

2012 ◽  
Vol 78 (22) ◽  
pp. 8142-8145 ◽  
Author(s):  
Danilo Ercolini ◽  
Francesca De Filippis ◽  
Antonietta La Storia ◽  
Michele Iacono
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Water Buffalo ◽  
Raw Milk ◽  
Mozzarella Cheese ◽  
Quantitative Distribution ◽  
Culture Independent ◽  
Thermophilic Lactic Acid Bacteria

ABSTRACTIntermediates of production of two batches of traditional mozzarella cheese were analyzed by culture-independent pyrosequencing. The quantitative distribution of taxa within the samples suggested that thermophilic lactic acid bacteria from the natural starter were mainly responsible for the fermentation, while microorganisms found in raw milk did not develop during fermentation.

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