scholarly journals Sequencing SARS-CoV-2 in a Malaria Research Laboratory in Mali, West Africa: The Road to Sequencing the First SARS-CoV-2 Genome in Mali

Processes ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 2169
Author(s):  
Antoine Dara ◽  
Bourema Kouriba ◽  
Amadou Daou ◽  
Abdoul Karim Sangare ◽  
Djibril Kassogue ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
The Road ◽  
Genomic Epidemiology ◽  
Laboratory Setup ◽  
The United Kingdom ◽  
Illumina Miseq Platform ◽  
Miseq Platform ◽  
Next Generation Sequencing Ngs ◽  
High Quality Genome ◽  
Generation Sequencing

Next-generation sequencing (NGS) has become a necessary tool for genomic epidemiology. Even though the utility of genomics in human health has been proved, genomic surveillance has never been as important as during the COVID-19 pandemic. This has been demonstrated by the recent use of genomic surveillance to detect new variants of SARS-CoV-2 in the United Kingdom, South Africa, and Brazil. Until recently, Malian scientists did not have access to any local NGS platform, and samples had to be shipped abroad for sequencing. Here, we report on how we adapted a laboratory setup for Plasmodium research to generate the first complete SARS-CoV-2 genome locally. Total RNA underwent a library preparation using an Illumina TruSeq stranded RNA kit. A metagenomics sequencing was performed on an Illumina MiSeq platform, which was followed by bioinformatic analyses on a local server in Mali. We recovered a full genome of SARS-CoV-2 of 29 kb with an average depth coverage of 200×. We have demonstrated our capacity to generate a high-quality genome with limited resources and highlight the need to develop genomics capacity locally to solve health problems. We discuss challenges related to access to reagents during a pandemic period and propose some home-made solutions.

scholarly journals Detection and monitoring of insect traces in bioaerosols

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10862
Author(s):  
Panyapon Pumkaeo ◽  
Junko Takahashi ◽  
Hitoshi Iwahashi
Keyword(s):  
Aerosol Particles ◽  
Illumina Miseq ◽  
Identification Accuracy ◽  
Insect Community ◽  
Cytochrome C Oxidase I ◽  
True Bugs ◽  
Illumina Miseq Platform ◽  
Miseq Platform ◽  
Pm2.5 And Pm10 ◽  
First Time

Studies on bioaerosols have primarily focused on their chemical and biological compositions and their impact on public health and the ecosystem. However, most bioaerosol studies have only focused on viruses, bacteria, fungi, and pollen. To assess the diversity and composition of airborne insect material in particulate matter (PM) for the first time, we attempted to detect DNA traces of insect origin in dust samples collected over a two-year period. These samples were systematically collected at one-month intervals and categorized into two groups, PM2.5 and PM10, based on the aerodynamic diameter of the aerosol particles. Cytochrome-c oxidase I (COI) was the barcoding region used to identify the origins of the extracted DNA. The airborne insect community in these samples was analyzed using the Illumina MiSeq platform. The most abundant insect sequences belonged to the order Hemiptera (true bugs), whereas order Diptera were also detected in both PM2.5 and PM10 samples. Additionally, we inferred the presence of particulates of insect origin, such as brochosomes and integument particles, using scanning electron microscopy (SEM). This provided additional confirmation of the molecular results. In this study, we demonstrated the benefits of detection and monitoring of insect information in bioaerosols for understanding the source and composition. Our results suggest that the PM2.5 and PM10 groups are rich in insect diversity. Lastly, the development of databases can improve the identification accuracy of the analytical results.

scholarly journals Faecal Microbiota of Dogs Offered a Vegetarian Diet with or without the Supplementation of Feather Meal and either Cornmeal, Rye or Fermented Rye: A Preliminary Study

2020 ◽  
Vol 8 (9) ◽  
pp. 1363
Author(s):  
Julia Hankel ◽  
Amr Abd El-Wahab ◽  
Richard Grone ◽  
Birgit Keller ◽  
Eric Galvez ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Hypervariable Region ◽  
Illumina Miseq ◽  
Vegetarian Diet ◽  
Rrna Gene ◽  
Feather Meal ◽  
Illumina Miseq Platform ◽  
Faecal Samples ◽  
Miseq Platform ◽  
Preliminary Study

Anthropomorphism of dogs has affected feeding and the choice of components present in diets for dogs. Conflicting trends are present: raw or vegetarian appear more prevalent. Animal-derived proteins seem to have unfavourable impacts on intestinal microflora by decreasing the presence of Bacteroidetes. This preliminary study evaluates whether effects of diets with animal proteins on intestinal microbiota can be compensated by the addition of certain carbohydrates to dog diet. Eight female beagles were included in a cross-over study and fed a vegetarian diet or the same diet supplemented with feather meal (2.7%) and either 20% of cornmeal, fermented or non-fermented rye (moisture content of the diets about 42%). A 16S rRNA gene amplification was performed within the hypervariable region V4 on faecal samples and sequenced with the Illumina MiSeq platform. The Firmicutes/Bacteroidetes ratio tended to shift to the advantage of Firmicutes when feather meal and cornmeal were added (Firmicutes/Bacteroidetes ratio of 5.12 compared to 2.47 when offered the vegetarian diet) and tended to switch back to the advantage of Bacteroidetes if rye: fermented (2.17) or not (1.03) was added. The addition of rye might have the potential to compensate possible unfavourable effects of diets with animal proteins on intestinal microbiota of dogs.

scholarly journals Viral metagenomes of Lake Soyang, the largest freshwater lake in South Korea

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Kira Moon ◽  
Suhyun Kim ◽  
Ilnam Kang ◽  
Jang-Cheon Cho
Keyword(s):  
South Korea ◽  
Illumina Miseq ◽  
Freshwater Lakes ◽  
Genome Sequences ◽  
Illumina Miseq Platform ◽  
Viral Community ◽  
Viral Communities ◽  
Miseq Platform ◽  
Metagenome Sequencing ◽  
Freshwater Reservoir

Abstract A high number of viral metagenomes have revealed countless genomes of putative bacteriophages that have not yet been identified due to limitations in bacteriophage cultures. However, most virome studies have been focused on marine or gut environments, thereby leaving the viral community structure of freshwater lakes unclear. Because the lakes located around the globe have independent ecosystems with unique characteristics, viral community structures are also distinctive but comparable. Here, we present data on viral metagenomes that were seasonally collected at a depth of 1 m from Lake Soyang, the largest freshwater reservoir in South Korea. Through shotgun metagenome sequencing using the Illumina MiSeq platform, 3.08 to 5.54-Gbps of reads per virome were obtained. To predict the viral genome sequences within Lake Soyang, contigs were constructed and 648 to 1,004 putative viral contigs were obtained per sample. We expect that both viral metagenome reads and viral contigs would contribute in comparing and understanding of viral communities among different freshwater lakes depending on seasonal changes.

scholarly journals Response of Fecal Bacterial Flora to the Exposure of Fumonisin B1 in BALB/c Mice

Toxins ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 612
Author(s):  
Fan Zhang ◽  
Zhiwei Chen ◽  
Lin Jiang ◽  
Zihan Chen ◽  
Hua Sun
Keyword(s):  
Animal Health ◽  
Bacterial Flora ◽  
Fumonisin B1 ◽  
Illumina Miseq ◽  
Fecal Microbiota ◽  
Control Group ◽  
Illumina Miseq Platform ◽  
Regulatory Limits ◽  
Miseq Platform ◽  
High Diversity

Fumonisins are a kind of mycotoxin that has harmful influence on the health of humans and animals. Although some research studies associated with fumonisins have been reported, the regulatory limits of fumonisins are imperfect, and the effects of fumonisins on fecal bacterial flora of mice have not been suggested. In this study, in order to investigate the effects of fumonisin B1 (FB1) on fecal bacterial flora, BALB/c mice were randomly divided into seven groups, which were fed intragastrically with 0 mg/kg, 0.018 mg/kg, 0.054 mg/kg, 0.162 mg/kg, 0.486 mg/kg, 1.458 mg/kg and 4.374 mg/kg of FB1 solutions, once a day for 8 weeks. Subsequently, feces were collected for analysis of microflora. The V3-V4 16S rRNA of fecal bacterial flora was sequenced using the Illumina MiSeq platform. The results revealed that fecal bacterial flora of mice treated with FB1 presented high diversity. Additionally, the composition of fecal bacterial flora of FB1 exposure groups showed marked differences from that of the control group, especially for the genus types including Alloprevotella, Prevotellaceae_NK3B31_group, Rikenellaceae_RC9_gut_group, Parabacteroides and phylum types including Cyanobacteria. In conclusion, our data indicate that FB1 alters the diversity and composition of fecal microbiota in mice. Moreover, the minimum dose of FB1 exposure also causes changes in fecal microbiota to some extent. This study is the first to focus on the dose-related effect of FB1 exposure on fecal microbiota in rodent animals and gives references to the regulatory doses of fumonisins for better protection of human and animal health.

scholarly journals Baseline Data of the Fungal Phytobiome of Three Sorghum (Sorghum bicolor) Cultivars in South Africa Using Targeted Environmental Sequencing

2021 ◽  
Vol 7 (11) ◽  
pp. 978
Author(s):  
Gilmore T. Pambuka ◽  
Tonjock Rosemary Kinge ◽  
Soumya Ghosh ◽  
Errol D. Cason ◽  
Martin M. Nyaga ◽  
...  
Keyword(s):  
Crop Production ◽  
Plant Pathogens ◽  
Illumina Miseq ◽  
Fungal Communities ◽  
Targeted Sequencing ◽  
Illumina Miseq Platform ◽  
Below Ground ◽  
Miseq Platform ◽  
Low Levels ◽  
Plant Surfaces

Plant-associated fungi, or the mycobiome, inhabit plant surfaces above ground, reside in plant tissues as endophytes, or are rhizosphere in the narrow zone of soil surrounding plant roots. Studies have characterized mycobiomes of various plant species, but little is known about the sorghum mycobiome, especially in Africa, despite sorghum being one of the most important indigenous and commercial cereals in Africa. In this study, the mycobiome associated with above- and below-ground tissues of three commercial sorghum cultivars, as well as from rhizosphere and surrounding bulk soil samples, were sequenced using targeted sequencing with the Illumina MiSeq platform. Relative abundance differences between fungal communities were found between above-ground and below-ground niches, with most differences mostly in the dominant MOTUs, such as Davidiellaceae sp. (Cladosporium), Didymellaceae sp. 1 (Phoma), Fusarium, Cryptococcus and Mucor. Above-ground communities also appeared to be more diverse than below-ground communities, and plants harboured the most diversity. A considerable number of MOTUs were shared between the cultivars although, especially for NS5511, their abundances often differed. Several of the detected fungal groups include species that are plant pathogens of sorghum, such as Fusarium, and, at low levels, Alternaria and the Ustilaginomycetes. Findings from this study illustrate the usefulness of targeted sequencing of the ITS rDNA gene region (ITS2) to survey and monitor sorghum fungal communities and those from associated soils. This knowledge may provide tools for disease management and crop production and improvement.

scholarly journals Comparison of microbiome and culture techniques for determination of gastrointestinal microbial communities in ceca of chickens

2018 ◽  
Author(s):  
Kimberly Wilson ◽  
Whitney Briggs ◽  
Audrey Duff ◽  
Chasser Kaylin ◽  
Xialoun Sun ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Illumina Miseq ◽  
Intestinal Microbiome ◽  
P Value ◽  
Culture Techniques ◽  
Operational Taxonomic Units ◽  
Colony Forming Units ◽  
Miseq Platform ◽  
Next Generation Sequencing Ngs

The use of 16S next generation sequencing (NGS) technology to identify the relative abundance of microbial communities have become the standard when studying the intestinal microbiome. The increased use is due to the ability to identify a proportion of bacteria that cannot be observed with culture-based methods. However, culture-based techniques are acceptable to identify key bacterial groups, yet may grossly underestimate the microbial community in question. Since there is limited research comparing NGS results to colony forming units (CFU), the objective of this study was to compare total Enterobacteriaceae and lactic acid bacteria (LAB) recovery with culture techniques (CFU/g ceca) to total number of reads from operational taxonomic units (OTU) categorized as Enterobacteriaceae or LAB from Illumina MiSeq platform from matched chick cecal samples at three and 10 days of age. Both CFU recovery (1.09x109 ± 2.42x108; 1.37x108 ± 5.57x107) and reads (5460 ± 1164 ; 282 ± 163) belonging to Enterobacteriaceae decreased by 10 days of age (p < 0.001). Similarly, LAB reads decreased over time (21,128 ± 2262; 6220 ± 817, respectively p < 0.0001). However, LAB CFU recovery increased by 10 days (1.18x108 ± 1.91x107; 1.62x109 ± 5.00x108, respectively p < 0.01). At three days the Pearson’s correlation was -0.082 between CFU of culturable Enterobacteriaceae to reads and culturable LAB CFU to reads at 0.097, showing no correlation (p = 0.606, 0.551; respectively). By 10 days, no correlation of reads and CFU occurred with Enterobacteriaceae (r=-0.049; p-value = 0.769) while with LAB the correlation was 0.290 (p = 0.066) at 10 days. The CFU may be appropriate to identify a few families that change due to treatment or product. Without identifying viable cells to DNA recovered from NGS, there will always be the question whether the reads within the binned OTU in the intestinal tract is accurate.

scholarly journals Current challenges in the implementation of precision oncology for the management of metastatic colorectal cancer

ESMO Open ◽  
2020 ◽  
Vol 5 (2) ◽  
pp. e000634 ◽  
Author(s):  
Sun Young Kim ◽  
Tae Won Kim
Keyword(s):  
Colorectal Cancer ◽  
Metastatic Colorectal Cancer ◽  
Precision Oncology ◽  
Controversial Issues ◽  
Considerable Uncertainty ◽  
The Road ◽  
Molecularly Targeted Agents ◽  
On The Road ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing

Over the last few decades, molecularly targeted agents have been used for the treatment of metastatic colorectal cancer. They have made remarkable contributions to prolonging the lives of patients. The emergence of several biomarkers and their introduction to the clinic have also aided in guiding such treatment. Recently, next-generation sequencing (NGS) has enabled clinicians to identify these biomarkers more easily and reliably. However, there is considerable uncertainty in interpreting and implementing the vast amount of information from NGS. The clinical relevance of biomarkers other than NGS are also subjects of debate. This review covers controversial issues and recent findings on such therapeutics and their molecular targets, including VEGF, EGFR, BRAF, HER2, RAS, actionable fusions, Wnt pathway and microsatellite instability for comprehensive understanding of obstacles on the road to precision oncology in metastatic colorectal cancer.

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