scholarly journals Bacterial diversity and composition of alfalfa silage as analyzed by Illumina MiSeq sequencing: Effects of Escherichia coli O157:H7 and silage additives

2018 ◽  
Vol 101 (3) ◽  
pp. 2048-2059 ◽  
Author(s):  
I.M. Ogunade ◽  
Y. Jiang ◽  
A.A. Pech Cervantes ◽  
D.H. Kim ◽  
A.S. Oliveira ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Bacterial Diversity ◽  
Illumina Miseq ◽  
Escherichia Coli O157 ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Alfalfa Silage ◽  
Silage Additives

Analysis of bacterial diversity of Chinese Luzhou-flavor liquor brewed in different seasons by Illumina Miseq sequencing

2016 ◽  
Vol 66 (3) ◽  
pp. 1293-1301 ◽  
Author(s):  
Weining Sun ◽  
Huazhi Xiao ◽  
Qian Peng ◽  
Qiaoge Zhang ◽  
Xingxing Li ◽  
...  
Keyword(s):  
Bacterial Diversity ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Different Seasons

scholarly journals Control of Escherichia coli O157:H7 in contaminated alfalfa silage: Effects of silage additives

2016 ◽  
Vol 99 (6) ◽  
pp. 4427-4436 ◽  
Author(s):  
I.M. Ogunade ◽  
D.H. Kim ◽  
Y. Jiang ◽  
Z.G. Weinberg ◽  
K.C. Jeong ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Escherichia Coli O157 ◽  
Alfalfa Silage ◽  
Silage Additives

scholarly journals Genome and Plasmid Sequences of Escherichia coli KV7, an Extended-Spectrum β-Lactamase Isolate Derived from Feces of a Healthy Pig

2017 ◽  
Vol 5 (38) ◽  
Author(s):  
Michael D. Bateman ◽  
Stefan P. W. de Vries ◽  
Srishti Gupta ◽  
Luca Guardabassi ◽  
Lina M. Cavaco ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Illumina Miseq ◽  
Phylogenetic Group ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Content Type ◽  
Pacbio Rs Ii ◽  
Protein Encoding ◽  
Encoding Genes ◽  
Group D

ABSTRACT We present single-contig assemblies for Escherichia coli strain KV7 (serotype O27, phylogenetic group D) and its six plasmids, isolated from a healthy pig, as determined by PacBio RS II and Illumina MiSeq sequencing. The chromosome of 4,997,475 bp and G+C content of 50.75% harbored 4,540 protein-encoding genes.

1525 Inhibiting the growth of Escherichia coli O157:H7 in alfalfa silage with silage additives

2016 ◽  
Vol 94 (suppl_5) ◽  
pp. 740-741
Author(s):  
I. M. Ogunade ◽  
D. Kim ◽  
Y. Jiang ◽  
K. G. Arriola ◽  
A. A. P. Cervantes ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Escherichia Coli O157 ◽  
Alfalfa Silage ◽  
Silage Additives

scholarly journals Pollutant-Removing Biofilter Strains Associated with High Ammonia and Hydrogen Sulfide Removal Rate in a Livestock Wastewater Treatment Facility

2021 ◽  
Vol 13 (13) ◽  
pp. 7358
Author(s):  
Dong-Hyun Kim ◽  
Hyun-Sik Yun ◽  
Young-Saeng Kim ◽  
Jong-Guk Kim
Keyword(s):  
Wastewater Treatment ◽  
Hydrogen Sulfide ◽  
Microbial Community ◽  
Microbial Communities ◽  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Treatment Facility ◽  
Livestock Wastewater ◽  
Wastewater Treatment Facility

This study analyzed the microbial community metagenomically to determine the cause of the functionality of a livestock wastewater treatment facility that can effectively remove pollutants, such as ammonia and hydrogen sulfide. Illumina MiSeq sequencing was used in analyzing the composition and structure of the microbial community, and the 16S rRNA gene was used. Through Illumina MiSeq sequencing, information such as diversity indicators as well as the composition and structure of microbial communities present in the livestock wastewater treatment facility were obtained, and differences between microbial communities present in the investigated samples were compared. The number of reads, operational taxonomic units, and species richness were lower in influent sample (NLF), where the wastewater enters, than in effluent sample (NL), in which treated wastewater is found. This difference was greater in June 2019 than in January 2020, and the removal rates of ammonia (86.93%) and hydrogen sulfide (99.72%) were also higher in June 2019. In both areas, the community composition was similar in January 2020, whereas the influent sample (NLF) and effluent sample (NL) areas in June 2019 were dominated by Proteobacteria (76.23%) and Firmicutes (67.13%), respectively. Oleiphilaceae (40.89%) and Thioalkalibacteraceae (12.91%), which are related to ammonia and hydrogen sulfide removal, respectively, were identified in influent sample (NLF) in June 2019. They were more abundant in June 2019 than in January 2020. Therefore, the functionality of the livestock wastewater treatment facility was affected by characteristics, including the composition of the microbial community. Compared to Illumina MiSeq sequencing, fewer species were isolated and identified in both areas using culture-based methods, suggesting Illumina MiSeq sequencing as a powerful tool to determine the relevance of microbial communities for pollutant removal.

scholarly journals Comparing dental plaque microbiome diversity of extrinsic black stain in the primary dentition using Illumina MiSeq sequencing technique

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Lulu Chen ◽  
Qiong Zhang ◽  
Yan Wang ◽  
Keke Zhang ◽  
Jing Zou
Keyword(s):  
Relative Abundance ◽  
Dental Plaque ◽  
Illumina Miseq ◽  
Primary Dentition ◽  
Tooth Surface ◽  
Oral Microbiota ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Cross Sectional ◽  
Sequencing Technique

Abstract Background Extrinsic black stain (EBS) is characterized by discrete dark dots or lines on the tooth surface. The relationship between EBS and oral microbiota in children remains elusive. The aim of this study was to compare dental plaque microbiome in EBS children with that in EBS-free children in the primary dentition. Methods The Illumina MiSeq sequencing technique was utilized in the cross-sectional pilot study to investigate the diversity and composition of the supragingival plaque microbiota from 10 EBS-positive and 10 EBS-free children. The results were analysed with nonparametric Mann-Whitney U test, Pearson Chi-Square test, Fisher’s Exact test and one-way ANOVA tests. Results We identified 13 different phyla, 22 classes, 33 orders, 54 families, 105 genera, and 227 species from a total of 52,646 high-quality sequences. Between two groups, no statistical differences were observed in the estimators of community richness and diversity at 97% similarity, as well as in the Unweighted Unifrac principal co-ordinates analysis (PCoA). At the species level, higher level of relative abundance of Actinomyces naeslundii and lower level of relative abundance of a species belonging to Candidate_division_TM7 was observed in dental plaque of EBS-positive subjects, compared to dental plaque of EBS-free subjects (P < 0.05). This indicated that some species might be involved in the EBS process. Conclusion Changes in dental plaque microbiota is possibly relevant to the process of EBS in the primary dentition.

Developmental validation of a Nextera XT mitogenome Illumina MiSeq sequencing method for high-quality samples

2018 ◽  
Vol 34 ◽  
pp. 25-36 ◽  
Author(s):  
Michelle A. Peck ◽  
Kimberly Sturk-Andreaggi ◽  
Jacqueline T. Thomas ◽  
Robert S. Oliver ◽  
Suzanne Barritt-Ross ◽  
...  
Keyword(s):  
Illumina Miseq ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
High Quality ◽  
Sequencing Method ◽  
Developmental Validation
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