scholarly journals Draft Genome Sequences of Five Paenibacillus Species of Dairy Origin

2020 ◽  
Vol 9 (37) ◽  
Author(s):  
Atinuke M. Olajide ◽  
Shu Chen ◽  
Gisèle LaPointe

ABSTRACT Paenibacillus species are important spoilage organisms in the dairy industry. The genomes of five Paenibacillus species which were isolated from dairy products in Canada were sequenced using the Illumina MiSeq platform. Draft genomes ranging from 5.1 to 7.1 Mb with GC contents of 49 to 53% were generated.

2018 ◽  
Vol 6 (13) ◽  
Author(s):  
Devon R. Radford ◽  
Carlos G. Leon-Velarde ◽  
Shu Chen ◽  
Amir M. Hamidi Oskouei ◽  
Sampathkumar Balamurugan

ABSTRACT The genomes of two strains of Salmonella enterica subsp. enterica serovar Cubana and serovar Muenchen, isolated from dry hazelnuts and chia seeds, respectively, were sequenced using the Illumina MiSeq platform, assembled de novo using the overlap-layout-consensus method, and aligned to their respective most identical sequence genome scaffolds using MUMMER and BLAST searches.


2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Kira Moon ◽  
Suhyun Kim ◽  
Ilnam Kang ◽  
Jang-Cheon Cho

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.


2017 ◽  
Vol 5 (30) ◽  
Author(s):  
Thamir H. Alkahem Albalawi ◽  
Douglas D. Rhoads ◽  
Ravi D. Barabote

ABSTRACT The draft genome of Anoxybacillus sp. strain UARK-01, a novel lignin-utilizing thermophilic soil bacterium, represents the first sequence of an Anoxybacillus isolate from the United States. The genome was sequenced using the Illumina MiSeq platform, de novo assembled using SeqMan NGen, and annotated at NCBI. The genome sequence revealed genes for laccase and lignocellulose degradation enzymes.


2020 ◽  
Author(s):  
Karamese Murat ◽  
Ozgur Didem ◽  
Tutuncu Emin Ediz

ABSTRACTIntroductionWe present the sequence analysis for 47 complete genomes for SARS-CoV-2 isolates on Turkish patients. To identify their genetic similarity, phylogenetic analysis was performed by comparing the worldwide SARS-CoV-2 sequences, selected from GISAID, to the complete genomes from Turkish isolates. In addition, we focused on the variation analysis to show the mutations on SARS-CoV-2 genomes.MethodsIllumina MiSeq platform was used for sequencing the libraries. The raw reads were aligned to the known SARS-CoV-2 genome (GenBank: MN908947.3) using the Burrows-Wheeler aligner (v.0.7.1). The phylogenetic tree was constructer using Phylip v.3.6 with Neighbor-Joining and composite likelihood method. The variants were detected by using Genome Analysis Toolkit-HaplotypeCaller v.3.8.0 and were inspected on GenomeBrowse v2.1.2.ResultsAll viral genome sequences of our isolates was located in lineage B under the different clusters such as B.1 (n=3), B.1.1 (n=28), and B.1.9 (n=16). According to the GISAID nomenclature, all our complete genomes were placed in G, GR and GH clades. Five hundred forty-nine total and 53 unique variants were detected. All 47 genomes exhibited different kinds of variants. The distinct variants consist of 274 missense, 225 synonymous, and 50 non-coding alleles.ConclusionThe results indicated that the SARS-CoV-2 sequences of our isolates have great similarity with all Turkish and European sequences. Further studies should be performed for better comparison of strains, after more complete genome sequences will be released. We also believe that collecting and sharing any data about SARS-CoV-2 virus and COVID-19 will be effective and may help the related studies.


2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Ji-Young Lee ◽  
Gyu-Sung Cho ◽  
Charles M. A. P. Franz ◽  
Dae-Ook Kang

ABSTRACT Bacillus subtilis subsp. subtilis MD 32 was isolated from kimchi. The strain was sequenced using an Illumina MiSeq platform, and the genome size was 4,238,856 bp with a GC content of 43.41 mol%. The genome encoded 4,396 proteins, with 45 tRNAs, 6 rRNAs, and 5 noncoding RNAs.


2021 ◽  
Vol 10 (20) ◽  
Author(s):  
Etinosa O. Igbinosa ◽  
Erik Brinks ◽  
Abeni Beshiru ◽  
Isoken H. Igbinosa ◽  
Maria Stein ◽  
...  

ABSTRACT Five Staphylococcus saprophyticus strains were isolated from the fermented milk product nono in Nigeria and were sequenced using an Illumina MiSeq platform. The genome sizes ranged from 2.53 to 2.60 Mbp, while the GC contents ranged from 32.99 to 33.07 mol%. The genomes possessed 2,505 to 2,687 protein-coding sequences.


2019 ◽  
Vol 8 (3) ◽  
Author(s):  
Ting Yu ◽  
Xi Yang ◽  
Zhilin Wang ◽  
Cui Zhu ◽  
Jinlong Bei ◽  
...  

Lactobacillus reuteri strain LR CGMCC 11154, which was isolated from the feces of healthy weaned piglets, was experimentally proven to be a probiotic bacterium. The whole genome was sequenced on the Illumina Miseq platform to obtain the draft genome, which consists of 120 contigs totaling 1.9 Mbp encoding 1,854 genes.


2018 ◽  
Vol 7 (6) ◽  
Author(s):  
Marcela Carina Audisio ◽  
Leonardo Albarracín ◽  
Maria Julia Torres ◽  
Lucila Saavedra ◽  
Elvira Maria Hebert ◽  
...  

This report describes the draft genome sequences of Lactobacillus salivarius A3iob and Lactobacillus johnsonii CRL1647, probiotic strains isolated from the gut of honeybee Apis mellifera workers. The reads were generated by a whole-genome sequencing (WGS) strategy on an Illumina MiSeq sequencer and were assembled into contigs with total sizes of 2,054,490 and 2,137,413 bp for the A3iob and CRL1647 strains, respectively.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10862
Author(s):  
Panyapon Pumkaeo ◽  
Junko Takahashi ◽  
Hitoshi Iwahashi

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.


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